6,659 Matching Annotations
  1. Feb 2026
    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript by Hao Jiang et al described a systematic approach to identify proline hydroxylation proteins. The authors implemented a proteomic strategy with HILIC-chromatographic separation and reported an identification of 4993 sites from HEK293 cells (4 replicates) and 3247 sites from RCC4 sites (3 replicates) with 1412 sites overlapping between the two cell lines. From the analysis, the authors identified 225 sites and 184 sites respectively from 293 and RCC4 cells with HyPro diagnostic ion. The identifications were validated by analyzing a few synthetic peptides, with a specific focus on Repo-man (CDCA2) through comparing MS/MS spectra, retention time, and diagnostic ions. With SILAC analysis and recombinant enzyme assay, the study showed that Repo-man HyPro604 is a target of the PHD1 enzyme.

      Strengths:

      The study involved extensive LC-MS analysis and was carefully implemented. The identification of over 4000 confident proline hydroxylation sites would be a valuable resource for the community. The characterization of Repo-man proline hydroxylation is a novel finding.

      Weaknesses:

      However, as a study mainly focused on methodology, the findings from the experimental data did not convincingly demonstrate the sensitivity and specificity of the workflow for site-specific identification of proline hydroxylation in global studies.

      Proline hydroxylation is an enzymatic post translational protein modification, catalysed by prolyl Hydroxylases (PHDs), which can have profound biological significance, e.g. altering protein half-life and/or the stability of protein-protein interactions. Furthermore, there has been controversy in the field as to the true number of protein targets for PHDs in cells. Thus, there is a clear need for methods to enable the robust identification of genuine PHD targets and to reliably map sites of PHD-catalysed proline hydroxylation in proteins. We believe, therefore, that our methodology, as reported here in Jiang et al., is an important contribution towards this goal. We note that our methodology has already been used successfully by others

      (https://doi.org/10.1016/j.mcpro.2025.100969). While further improvements in this methodology may of course be developed in future, we are not currently aware of any superior methods that have been reported previously in the literature. The criticism made by the reviewer notably does not include reference to any such alternative published methodology that interested researchers can use which would offer superior results to the approach we document in this study.

      Major concerns:

      (1) The study applied HILIC-based chromatographic separation with a goal of enriching and separating hydroxyproline-containing peptides. However, as the authors mentioned, such an approach is not specific to proline hydroxylation. In addition, many other chromatography techniques can achieve deep proteome fractionation such as high pH reverse phase fractionation, strong-cation exchange etc. There was no data in this study to demonstrate that the strategy offered improved coverage of proline hydroxylation proteins, as the identifications of the HyPro sites could be achieved through deep fractionation and a highly sensitive LCMS setup. The data of Figure 2A and S1A were somewhat confusing without a clear explanation of the heat map representations. 

      The data we present in this study demonstrate clearly that peptides with hydroxylated prolines are enriched in specific HILIC fractions (F10-F18), in comparison with total unfractionated peptides derived from cell extracts. We also refer the reviewer to our previously published study by Bensaddek et al (International Journal of Mass Spectrometry: doi:10.1016/j.ijms.2015.07.029), which was reference 41 in this study, in which we compared directly the performance of both HILIC and strong anionic exchange chromatography, (hSAX). This showed that HILIC provided superior enrichment to hSAX for enrichment of peptides containing hydroxylated proline residues. To clarify this point for readers, we have now included a specific reference to our previous study at the start of the Results section in our current revision. Currently, we use HILIC to provide a degree of enrichment for proline hydroxylated peptides because we are not aware of alternative chromatographic methods that in our hands provide better results.

      We have included descriptions of the information shown in the heatmaps in the associated figure legends and captions.

      (2) The study reported that the HyPro immonium ion is a diagnostic ion for HyPro identification. However, the data showed that only around 5% of the identifications had such a diagnostic ion. In comparison, acetyl-lysine immonium ion was previously reported to be a useful marker for acetyllysine peptides (PMID: 18338905), and the strategy offered a sensitivity of 70% with a specificity of 98%. In this study, the sensitivity of HyPro immonium ion was quite low. The authors also clearly demonstrated that the presence of immonium ion varied significantly due to MS settings, peptide sequence, and abundance. With further complications from L/I immonium ions, it became very challenging to implement this strategy in a global LC-MS analysis to either validate or invalidate HyPro identifications.

      The reviewer appears to have misunderstood the point we make with regard to the identification of the immonium ion and its use as a diagnostic marker for proline hydroxylation in MS analyses. We do not claim that this immonium ion is an essential diagnostic marker for proline hydroxylation. As the reviewer notes, with respect to the acetyl-lysine modification, the corresponding immonium ion is often used in MS studies as a diagnostic for identification of specific post translational modifications. Previous studies have reported that the immonium ion for hydroxylated proline is detected when the transcription factor HIF is analysed, but is often absent with other putative PHD targets, which has been used as an argument that these targets are not genuine proline hydroxylation sites. We are not, therefore, introducing the idea in this study that the hydroxy-proline immonium ion is a required diagnostic marker for proline hydroxylation, but instead demonstrating that detection of this ion, at least in some peptide sequences, may require the use of higher MS collision energies than are typically required for routine peptide identification. We believe that this is an interesting observation that can help to clear up discussions in the literature regarding the true prevalence of PHD-catalysed proline hydroxylation in different target proteins. Our data suggest that, in future MS studies analysing suspected PHD target proteins, two different collision energy might need to be used, i.e., normal collision energy for the routine identification of a peptide, combined with use of a higher collision energy if the hydroxy-proline immonium ion was not already detected.

      (3) The study aimed to apply the HILIC-based proteomics workflow to identify HyPro proteins regulated by the PHD enzyme. However, the quantification strategy was not rigorous. The study just considered the HyPro proteins not identified by FG-4592 treatment as potential PHD targeted proteins. There are a few issues. First, such an analysis was not quantitative without reproducibility or statistical analysis. Second, it did not take into consideration that data-dependent LC-MS analysis was not comprehensive and some peptide ions may not be identified due to background interferences. Lastly, FG-4592 treatment for 24 hrs could lead to wide changes in gene expressions and protein abundances. Therefore, it is not informative to draw conclusions based on the data for bioinformatic analysis.

      We refer the reviewer to the data we present in this study using SILAC analysis, combined with our MS workflow. to achieve a more accurate quantitative picture of proline hydroxylation levels. While we agree that the point the reviewer makes is valid, regarding our data dependent LC-MS/MS analysis potentially not being comprehensive, this means, however, that we are potentially underestimating the true prevalence of proline hydroxylated peptides, not overestimating the level of these modified peptides. We also refer the reviewer to the accompanying study by Druker et al., (eLife 2025; doi.org/10.7554/eLife.108131.1)  in which we present a detailed follow-on study demonstrating the functional significance of the novel proline hydroxylation site we detected in the protein RepoMan (CDCA2). Therefore, even if we have not achieved a fully comprehensive analysis of all proline hydroxylated peptides catalysed by PHD enzymes, we believe that we have advanced the field by documenting a workflow that is able to identify and validate novel PHD targets.

      (4) The authors performed an in vitro PHD1 enzyme assay to validate that Repo-man can be hydroxylated by PHD1. However, Figure 9 did not show quantitatively PHD1-induced increase in Repo-man HyPro abundance and it is difficult to assess its reaction efficiency to compare with HIF1a HyPro.

      The analysis shown in Figure 9 was not intended to quantify the efficiency of in vitro hydroxylation of RepoMan by PHD1, but rather to answer the question, ‘Can recombinant PHD1 alone hydroxylate P604 on RepoMan in vitro, yes or no?’. The data show that the answer here is ‘yes’. Clearly, the HIF peptide is a more efficient substrate in vitro for recombinant PHD1 than the RepoMan peptide and we have now included a statement in the Discussion that addresses the significance of this observation more directly.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Jiang et al. developed a robust workflow for identifying proline hydroxylation sites in proteins. They identified proline hydroxylation sites in HEK293 and RCC4 cells, respectively. The authors found that the more hydrophilic HILIC fractions were enriched in peptides containing hydroxylated proline residues. These peptides showed differences in charge and mass distribution compared to unmodified or oxidized peptides. The intensity of the diagnostic hydroxyproline iminium ion depended on parameters including MS collision energy, parent peptide concentration, and the sequence of amino acids adjacent to the modified proline residue. Additionally, they demonstrate that a combination of retention time in LC and optimized MS parameter settings reliably identifies proline hydroxylation sites in peptides, even when multiple proline residues are present.

      Strengths:

      Overall, the manuscript presents an advanced, standardized protocol for identifying proline hydroxylation. The experiments were well designed, and the developed protocol is straightforward, which may help resolve confusion in the field.

      Weaknesses:

      (1) The authors should provide a summary of the standard protocol for identifying proline hydroxylation sites in proteins that can easily be followed by others.

      This is a good suggestion and we have now included a figure (Figure 10) with a summary of our workflow in the current revision.

      (2) Cockman et al. proposed that HIF-α is the only physiologically relevant target for PHDs. Their approach is considered the gold standard for identifying PHD targets. Therefore, the authors should discuss the major progress they made in this manuscript that challenges Cockman's conclusion.

      While we had mentioned the Cockman et al., paper in the Introduction, we had not focussed on this somewhat controversial issue. However, in response to the Reviewer’s request, we have now added a comment in the Discussion section in the current revision of how our new data address the proposal discussed previously by Cockman et al. In brief, we believe that our findings are not consistent with a model in which PHDs have no protein targets other than HIFs.

      Reviewer #3 (Public review): 

      Summary:

      The authors present a new method for detecting and identifying proline hydroxylation sites within the proteome. This tool utilizes traditional LC-MS technology with optimized parameters, combined with HILIC-based separation techniques. The authors show that they pick up known hydroxy-proline sites and also validate a new site discovered through their pipeline.

      Strengths:

      The manuscript utilizes state-of-the-art mass spectrometric techniques with optimized collision parameters to ensure proper detection of the immonium ions, which is an advance compared to other similar approaches before. The use of synthetic control peptides on the HILIC separation step clearly demonstrates the ability of the method to reliably distinguish hydroxy-proline from oxidized methionine - containing peptides. Using this method, they identify a site on CDCA2, which they go on to validate in vitro and also study its role in regulation of mitotic progression in an associated manuscript.

      Weaknesses:

      Despite the authors' claim about the specificity of this method in picking up the intended peptides, there is a good amount of potential false positives that also happen to get picked (owing to the limitations of MS-based readout), and the authors' criteria for downstream filtering of such peptides require further clarification. In the same vein, greater and more diverse cell-based validation approach will be helpful to substantiate the claims regarding enrichment of peptides in the described pathway analyses.

      We of course agree that false positives may arise, as is true for essentially all PTM studies. There are two issues here; first, are identified sites technically correct? (i.e. not misidentifications from the MS data) and second, are the identified modifications of biological significance? We have addressed this using the popular MaxQuant software suite to evaluate the modifications identified and to control the false discovery rate (FDR) at both the precursor and protein level, as described in the manuscript. We are aware that false positives could arise from confusing oxidation of methionine with hydroxylation of proline. Therefore, to address the issue as to whether we could identify bona fide PHD protein targets outside of the HIF family, we adopted a conservative approach by simply filtering out peptides where there was a methionine residue within three amino acids of the predicted proline hydroxylation site. This was a pragmatic decision made to reduce the likelihood of false positives in our dataset and we recognise that this likely results in us overlooking some genuine proline hydroxylation sites that occur nearby methionine residues. To address the potential biological relevance of the proline hydroxylation sites identified, we analysed extracts from cells treated with FG inhibitors. Of course a detailed understanding of biological significance relies upon follow-on experimental analyses for each site, which we have performed for P604 on RepoMan in accompanying study by Druker et al., (eLife 2025; doi.org/10.7554/eLife.108131.1).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The finding that the immonium ion intensities of L/I did not increase with increasing collision energy was surprising. Was this specific to this synthetic peptide?

      We agree this is an interesting and unexpected finding. We have no reason to believe that it is specific to synthetic peptides per se, but rather think this reflects an effect of amino acid composition in the peptides analysed. It will be interesting to explore this phenomenon in more detail in future.

      (2) The sequence logos in Figure 4 seemed to lack any amino acid enrichment in most positions except for collagen peptides. Have these findings been tested with statistical analysis?

      The results we show for sequence logo analysis were generated using WebLogo (10.1101/gr.849004) and correspond to an analysis of all proline hydroxylated peptides we detected across all cell lines and replicates analysed. The fact that collagens are highly abundant proteins with very high levels of proline hydroxylation likely explains why collagen peptides dominated the outcome of the sequence logo analysis. There is clearly scope for more detailed follow up analysis in future of the sequence specificity of proline hydroxylation sites in no- collagen proteins that are validated PHD targets.

      (3) Overall figure quality was not ideal. The resolution and font sizes of figures should be carefully evaluated and adjusted. The figure legend should contain a title for the figure. Annotations of the figures were somewhat confusing. 

      We agree with the criticism of the figure resolution in the review copies - the lower resolution appears to have been generated after we had uploaded higher resolution original images. We are providing again higher resolution versions of all figures for the current revision.

      Reviewer #3 (Recommendations for the authors):

      Certain concerns regarding portions of the manuscript that need addressing:

      (1) " These data show that two different cell lines show unique profiles of proteins with hydroxylated peptides." - It is difficult to conclusively say this statement after profiling the prolyl hydroxy proteome from just two cell lines, especially since the amino acids with the highest frequency in the most enriched peptides are similar in both cell lines.

      We agree with this point and have changed the current revision to state instead, “This shows that each of the two cell lines analysed have distinct profiles.”

      (2) "We noted that there was a high frequency of a methionine residues appearing either at the first, second, or even third positions after the HyPro site.." - according to the authors, claim, the advantage of their method was that they were able to overcome the limitation of older methods that couldn't separate methionine oxidation from proline hydroxylation. However, in this statement, they say that the high frequency of methionine residues may be because of the similar mass shift. These statements are contradictory. The authors should either tone down the claim or prove that those are indeed hydroxyproline sites. Is it possible that in the filtering step of excluding these high-frequency of methionine - containing peptides, we are losing potential positive hits for hydroxy-proline sites? What is the authors' take on this?

      We respectfully do not agree that our, “statements are contradictory”, with respect to the potential confusion between identification of methionine oxidation and proline hydroxylation, but acknowledge that we have not explained this issue clearly enough. It is a fact that the similar mass shift resulting from proline hydroxylation and methionine oxidation is a technical challenge that can potentially lead to misidentifications in MS studies and that is what we state clearly in the manuscript. We have addressed this issue head on experimentally in this study and show using synthetic peptides how detailed analysis of specific proline hydroxylation sites in target proteins can be distinguished from methionine oxidation, based upon differential chromatographic behaviour of peptides with either hydroxylated proline or oxidised methionine, as well as by detailed analysis of fragmentation spectra. However, in the case of our global analysis, as we were not able to perform synthetic peptide comparisons for every putative site identified, we took the pragmatic approach of filtering out examples of peptides where a methionine residue was present within three residues of a potential proline hydroxylation site. This was done simply to reduce the possibility of misidentification in the set of novel proline hydroxylated peptides identified and we accept that as a consequence we are likely filtering out peptides that include bona fide proline hydroxylation sites. We have clarified this point in the current revision and hope to be able to address this issue more comprehensively in future studies.

      (3) "Accordingly, a score cut-off of 40 for hydroxylated peptides and a localisation probability cut-off of more than 0.5 for hydroxylated peptides was performed." Could the authors shed more light and clarify what was the basis for this value of cut-off to be used in this filtering step? Is this sample dependent? What should be the criteria to determine this value?

      We used MaxQuant software (10.1016/j.cell.2006.09.026), for PTM analysis, in which a localization probability score of 0.75 and score cut-off of 40 is a commonly used threshold to define high confidence. The reason that we used 0.5 at the first step was to investigate how likely it might be that the misassignment of delta m/z +16 Da (oxidation) on Methionine would affect the identification of hydroxylation on Proline. However, we note that in the final results set used for analysis, all putative proline hydroxylated peptides that had a Methionine residue near to the hydroxylated proline were disregarded as a pragmatic step to reduce the probability of false identifications.

      (4) The authors are requested to kindly make the HPLC and MS traces more legible and use highresolution images, with clearly labeled values on the peaks. Kindly extract coordinates from the underlying data files to plot the curves if needed to make it clearer.

      We have reviewed the clarity of all images and figures in the current revision.

      (5) There seems to be no error bars in Figure 3, Figure 7E, and panels of Figure 8 with bar graphs. Are those single replicate data?

      These specific figures are from single replicate data.

      (6) For Figure 9C, the control with only PHD1 (no peptide) is missing. 

      The ‘no peptide control’ was not included in the figure because it is simply a blank lane and there is nothing to see.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study aimed to determine whether bacterial translation inhibitors affect mitochondria through the same mechanisms. Using mitoribosome profiling, the authors found that most antibiotics, except telithromycin, act similarly in both systems. These insights could help in the development of antibiotics with reduced mitochondrial toxicity.

      They also identified potential novel mitochondrial translation events, proposing new initiation sites for MT-ND1 and MT-ND5. These insights not only challenge existing annotations but also open new avenues for research on mitochondrial function.

      Strengths:

      Ribosome profiling is a state-of-the-art method for monitoring the translatome at very high resolution. Using mitoribosome profiling, the authors convincingly demonstrate that most of the analyzed antibiotics act in the same way on both bacterial and mitochondrial ribosomes, except for telithromycin. Additionally, the authors report possible alternative translation events, raising new questions about the mechanisms behind mitochondrial initiation and start codon recognition in mammals.

      Weaknesses:

      The main weaknesses of this study are:

      While the authors highlight an interesting difference in the inhibitory mechanism of telithromycin on bacterial and mitochondrial ribosomes, mechanistic explanations or hypotheses are lacking.

      We acknowledge that we were not able to present a clear explanation for potential mechanistic differences of telithromycin inhibition between mitochondrial and bacterial ribosomes. In future work, structural analyses in collaboration with experts will provide these insights.

      The assignment of alternative start codons in MT-ND1 and MT-ND5 is very interesting but does not seem to fully align with structural data.

      We appreciate the reviewer’s comment and consulted a cryo-EM expert to review our findings in the context of the available structural data. We downloaded the density map and reviewed the N-termini of MT-ND1 and MT-ND5. We only observed the density of the N-terminus of MT-ND1 at low confidence. At an RMSD of 2, we could not observe density for the side chains of Met and Pro, and there are gaps in the density for what is modeled as the main chain. The assignment of these residues may have been overlooked due to the expectation that they should be present in the peptide.

      For MT-ND5, we did observe some density that could be part of the main chain; however, it did not fill out until we reduced the stringency, and we did not observe density mapping to side chain residues. To summarize, we do not confidently see density for either the side chain or the main chain for either peptide.

      The newly proposed translation events in the ncRNAs are preliminary and should be further substantiated with additional evidence or interpreted with more caution.

      We agree with the reviewer that we did not provide conclusive evidence that our phased ribosome footprinting data on mitochondrial non-coding RNAs are proof of novel translation events. We do acknowledge this in the main text:” Due to both the short ORFs, minimal read coverage, and lack of a detectable peptide we could not determine if translation elongation occurred on the mitochondrial tRNAs. These sites may be unproductive mitoribosome binding events or simply from tRNAs partially digesting during MNase treatment.”

      Reviewer #2 (Public review):

      In this study, the authors set out to explore how antibiotics known to inhibit bacterial protein synthesis also affect mitoribosomes in HEK cells. They achieved this through mitoribosome profiling, where RNase I and Mnase were used to generate mitoribosome-protected fragments, followed by sequencing to map the regions where translation arrest occurs. This profiling identified the codon-specific impact of antibiotics on mitochondrial translation.

      The study finds that most antibiotics tested inhibit mitochondrial translation similarly to their bacterial counterparts, except telithromycin, which exhibited distinct stalling patterns. Specifically, chloramphenicol and linezolid selectively inhibited translation when certain amino acids were in the penultimate position of the nascent peptide, which aligns with their known bacterial mechanism. Telithromycin stalls translation at an R/K-X-R/K motif in bacteria, and the study demonstrated a preference for arresting at an R/K/A-X-K motif in mitochondria. Additionally, alternative translation initiation sites were identified in MT-ND1 and MT-ND5, with non-canonical start codons. Overall, the paper presents a comprehensive analysis of antibiotics in the context of mitochondrial translation toxicity, and the identification of alternative translation initiation sites will provide valuable insights for researchers in the mitochondrial translation field.

      From my perspective as a structural biologist working on the human mitoribosome, I appreciate the use of mitoribosome profiling to explore off-target antibiotic effects and the discovery of alternative mitochondrial translation initiation sites. However, the description is somewhat limited by a focus on this single methodology. The authors could strengthen their discussion by incorporating structural approaches, which have contributed significantly to the field. For example, antibiotics such as paromomycin and linezolid have been modeled in the human mitoribosome (PMID: 25838379), while streptomycin has been resolved (10.7554/eLife.77460), and erythromycin was previously discussed (PMID: 24675956). The reason we can now describe off-target effects more meaningfully is due to the availability of fully modified human mitoribosome structures, including mitochondria-specific modifications and their roles in stabilizing the decoding center and binding ligands, mRNA, and tRNAs (10.1038/s41467-024-48163-x).

      These and other relevant studies should be acknowledged throughout the paper to provide additional context.

      We appreciate the work that has previously revealed how different antibiotics bind the mitochondrial ribosome. We have included these references in the manuscript to provide background and context for this work in relationship to the field.

      Reviewer #3 (Public review):

      Summary:

      Recently, the off-target activity of antibiotics on human mitoribosome has been paid more attention in the mitochondrial field. Hafner et al applied mitoribosome profilling to study the effect of antibiotics on protein translation in mitochondria as there are similarities between bacterial ribosome and mitoribosome. The authors conclude that some antibiotics act on mitochondrial translation initiation by the same mechanism as in bacteria. On the other hand, the authors showed that chloramphenicol, linezolid and telithromycin trap mitochondrial translation in a context-dependent manner. More interesting, during deep analysis of 5' end of ORF, the authors reported the alternative start codon for ND1 and ND5 proteins instead of previously known one. This is a novel finding in the field and it also provides another application of the technique to further study on mitochondrial translation.

      Strengths:

      This is the first study which applied mitoribosome profiling method to analyze mutiple antibiotics treatment cells.

      The mitoribosome profiling method had been optimized carefully and has been suggested to be a novel method to study translation events in mitochondria. The manuscript is constructive and written well.

      Weaknesses:

      This is a novel and interesting study, however, most of the conclusion comes from mitoribosome profiling analysis, as a result, the manuscript lacks the cellular biochemical data to provide more evidence and support the findings.

      We thank the reviewer for the positive assessment of our work. We agree that future biochemical and structural experiments will strengthen the conclusions we derive from the ribosome profiling.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In Fig. 1A, the quality of the Western blot for the sucrose gradient is suboptimal. I recommend enhancing the quality of the Western blot image and providing the sucrose gradient sedimentation patterns for both the mtSSU and mtLSU to confirm the accurate selection of the monosome fraction. Additionally, to correctly assign the A260 peaks to mitochondrial and cytosolic ribosomes, it would be helpful to include markers for both the cytoribosomal LSU and SSU, too. Furthermore, do the authors observe mitochondrial polysomes in their sucrose gradient? If so, were those fractions fully excluded from the analysis?

      We repeated our sucrose gradient and Western blotting with antibodies for the large and small subunits of the mitoribosome. We did not repeat western blotting for the cytoribosomes as the 40S, 60S, and 80S peaks are present in their canonical heights and locations on a sucrose gradient. Western blotting indicates that the large and small subunits of the mitoribosome are located in the fraction taken for mitoribo-seq. We do see trace amounts of mitoribosome in fractions past the 55S site. Those fractions were excluded from library preparation.

      The MNase footprints exhibited a bimodal distribution, which the authors suggest may indicate that "MNase-treatment may have captured two distinct conformations of the ribosome." It would be relevant to clarify whether an enzyme titration was performed, as excessive MNase could lead to ribosomal RNA degradation, potentially influencing the footprints.

      We did not perform a titration and instead based our concentration on the protocol from Rooijers et al, 2013. We included a statement of this and a reference to the concentration in the methods.

      Is there an explanation for why RNase I footprinting reveals a very high peak at the 5'-end of the MT-CYB transcript, whereas this is not observed with MNase footprinting?

      It is not clear. The intensity of peaks at the 5’ end of the transcripts varies. We do observe that the relative intensity of the 5’ peak is greater for RNase I footprinted samples than MNase-treated samples.

      I understand that throughout the manuscript, the authors use MT-CYB as an example to illustrate the effects of the antibiotics on mitochondrial translation. However, to strengthen the generality of the conclusions, it would be beneficial to provide the read distribution across the entire mitochondrial transcriptome, possibly in the supplementary material. Additionally, I suggest including the read distribution for MT-CYB in untreated cells to improve data interpretation and enhance the clarity of figures (e.g., Figs. 1B, 2B, 3B).

      As these experiments were generated across multiple mitoribo-seq experiments, each was done with its own control experiment. It would be inaccurate to show a single trace as representative of all experiments. Instead, we include Supplementary Figure 1, which shows the untreated MT-CYB trace for all control samples and indicates which treatment they pair with.

      It would be very valuable to label each individual data point in the read phasing shown in Fig. 1D with the corresponding transcripts. For improved data visualization, I suggest assigning distinct colors to each transcript.

      We are concerned that including the name of each gene in the main figure would be too difficult for the reader to accurately interpret. Instead, we have added a Supplementary Table with those values.

      How do the authors explain the significant peak (approx. 10,000 reads) at the 5' end of the transcript in the presence of tiamulin (Fig. 2B)? Does this peak correspond to the start codon, and how does it relate to the quantification reported in Fig. 2C?

      Yes, this represents the start codon. These reads are likely derived from the start codon as they are mapping to the 5’ end of the transcript. There are differences in sequencing depth depending on the experiment, so what is critical is the relative distribution of reads on the transcript rather than comparing absolute reads between experiments. MT-CYB has 54% of the reads at the start site, which is representative of what we see across all genes.

      Throughout the manuscript, I found the usage of the terms "5' end" and "start codon" somewhat confusing, as they appear to be used synonymously in some instances. For example, in Fig. 2C, the y-axis label states "ribosomes at start codon," while the figure caption mentions "...percentage of reads that map to the 5' end of mitochondrial transcripts." Given the size of the graphs, it is also challenging for the reader to determine whether the peaks correspond specifically to the start codon or if multiple peaks accumulate at the initial codons.

      We were selected for this language because two different types of analysis are being carried out. Ribosome profiling carried out in Figures 2 and 3 is carried out with RNase I, which poorly maps the ribosomes at the start codon when we do the read length analysis in Figure 4. Ribosome footprint at the 5’ end may include ribosomes that are on the 2-4 codons following the start codon, so it would not be accurate to label those as “ribosomes at a start codon.” We have renamed the axis to “Ribosomes at 5’ end”. Wig files are available online for all mitoribosome profiling experiments. In this case, the assigned “P-site” is several codons after the start codon due to the offset applied and the minimal 5’ UTR. Thus, it is less important to see which codon density is assigned to, but rather the general distribution of the reads.

      The authors state, "Cells treated with telithromycin did show a slight increase in MRPF abundance at the 5' end of MT-CYB" and "the cumulative distribution of MRPFs suggested that ribosome density was biased towards the 5' end of the gene for chloramphenicol and telithromycin, but not significantly for linezolid." Could this observation be linked to the presence of specific stalling motifs in that region? If so, it would be beneficial to display such motifs on the graphs of the read distribution across the transcriptome to substantiate the context-dependent inhibition.

      Thank you for this suggestion. For chloramphenicol and linezolid, alanine, serine, and threonine make up nearly 25% of the mitochondrial proteome. As such, there are numerous stall sites across the transcript. Given their identical stalling motifs, the difference between chloramphenicol and linezolid is due to sequence-specific differences. Potentially, this could be due to conditions such as the final concentration of antibiotic inside the mitochondria and the on/off rate of an inhibitor with the translating mitoribosome. Both may affect the kinetics of stalling and allow mitoribosomes to evade early stall sites.

      We have also included the sites of all A/K/R-X-K motifs located in the genome and the calculated fold change for each position. As a note, this includes sites that do not pass the minimum filter set by our analysis and we note this in the text.

      The comment raises an additional question: Does the increased density at the 5’ end derive from stalled mitoribosomes or queued mitoribosomes behind a stalling event? Recent work by Iwasaki’s group shows that mitoribosomes can form disomes and queue behind each other. However, we could not observe 30 aa periodicities behind stalling events that would be indicative of collided mitoribosomes.

      In Fig. 3E, the authors report an additional and very interesting observation that is not discussed. Linezolid treatment causes reduced ribosome occupancy when proline or glycine codons occupy the P-site, or when the amino acids have been incorporated into the polypeptide chain and occupy the -1 position. It is known that the translation of proline and glycine frequently leads to ribosome stalling due to the physicochemical properties of these amino acids. Has this effect of linezolid been reported in the bacterial translation system? Additionally, can the authors propose hypotheses for the mechanism behind this observation? A similar observation is noted for telithromycin when glycine occupies the same positions, as well as when aspartate occupies the P- and A-sites.

      In bacteria, Linezolid does have an “anti-stalling” motif when glycine is present in the A-site. However, this is due to the size of the residue being compatible with antibiotic binding.

      The most likely cause of this effect is a redistribution of ribosome footprints. As the antibiotics introduce new arrest sites, ribosome density at other sites relatively decreases. This is likely an artifact from mitoribosomes redistributing from endogenously slow codons to new arrest sites. When looking at carrying out our disome profiling in the presence of anisomycin, we see a similar effect. Cytoribosomes are redistributed from endogenous stalling sites, such as proline, and are redistributed throughout the gene. As a result, translation at proline appears “more efficient” upon treatment with an inhibitor but is instead an artifact of analysis.

      Figure 3F could benefit from indicating which mtDNA-encoded protein corresponds to each of the strongest stalling motifs.

      We have included a supplementary figure to highlight which mitochondrially-encoded genes containing the R/K/A-X-K motif and noted in the text that mitochondrial translation may be unevenly inhibited.

      The legend "increasing mRPF abundance" in Fig. 4C may be missing the corresponding colors.

      The legend applies to all sections of the figure. We double-checked the range of the colors in the tables, and they do match the legend.

      The observation that the start codons in MT-ND1 and MT-ND5 might differ from the annotated canonical ones is intriguing. While the ribosome profiling data appear clear, mass spectrometry (MS) analysis may be misleading. The absence of evidence does not necessarily imply evidence of absence. How does this proposed conclusion correlate with the structural data obtained from HEK cells? For instance, the cryo-EM structural model of a complex I-containing human supercomplex (PDB: 5XTD, PMID: 28844695) shows the presence of Pro2 in MT-ND1 and the full-length MT-ND5 protein. The authors should carefully examine structural data to ascertain whether alternative forms of MT-ND1 and MT-ND5 are actually observed in the assembled complex I.

      We really appreciate this comment. We sat down with an expert in cryo-EM and reviewed the figure. We downloaded the density map and reviewed the N-termini of MT-ND1 and MT-ND5. We only observed the density of the N-terminus of MT-ND1 at low confidence. At an RMSD of 2, we could not observe density for the side chains of Met and Pro, and there are gaps in the density for what is modeled as the main chain. The assignment of these residues may have been overlooked due to the expectation that they should be present in the peptide.

      For MT-ND5, we did observe some density that could be part of the main chain; however, it did not fill out until we reduced the stringency, and we did not observe density mapping to side chain residues. To summarize, we do not confidently see density for either the side chain or the main chain for either peptide.

      Given that ribosome profiling is based on the assumption that ribosomes protect mRNA fragments from RNase digestion, interpreting the data related to Fig. 5 and the proposed existence of translation events involving ncRNAs is challenging. Most importantly, tRNAs and rRNAs are highly folded RNA molecules and, by definition, are protected by ribosomal proteins. Simultaneously, as the authors point out, "These reads could either be products of random digestion of the abundant background of ncRNAs or be genuine MRPFs." RNase I preferentially digests single-stranded RNA (ssRNA), but excess enzyme can still lead to degradation. Consequently, many random tRNA/rRNA fragments may be generated by RNase digestion, potentially resulting in artifacts. I suggest that the authors examine what happens to these reads when mitochondrial translation is inhibited.

      We have low-quality mitoribo-seq with initiation inhibitors and Mnase showing footprints of the same size. We do not have a small-molecule inhibitor that is able to completely ablate translation, as they instead stabilize mitoribosomes at different steps in translation. We have considered alternative ways of capturing a background rRNA and tRNA digestion pattern; however, these have their own drawbacks. Dissociation with EDTA prior to digestion or carrying out library prep on the small and large subunits may capture mitoribosomes no longer in the process of translation; however, dissociated subunits would have different surfaces now available for digestion and may not capture tRNAs.

      Regarding the statement, "While the ORF on MT-TS1 is longer, MRPF density was low and we did not observe read phasing and thus it is likely not translated (not shown)," the data should not be excluded unless a clear explanation is provided for why translation would not occur from this specific RNA.

      We have included this value in the graph as well as in Supplementary Figure 1.

      The graph in Fig. 5B shows the periodicity of only the putative RNR1 ORF, but not that of the other proposed ORFs. What is the reason for this?

      We have included the MT-TS1 putative ORF in Figure 5 and Figure S1. Other ORFs did not have density in the ORF. If these are real mitoribosome footprints at these start codons, it may be due to them being transient binding events that never result in elongation. Alternatively, they may be due to tRNA degradation during library preparation.

      The assumption that the UUG codon can serve as a start site for mitochondrial translation has not been substantiated. Recent data have identified translation initiation events from non-ATG/ATA codons (near-cognate and sub-cognate) using retapamulin, but UUG was not among them. Can the authors detect such events in their ribosome profiling data collected in the presence of retapamulin, tiamulin, or josamycin?

      The report of translation initiation at non-ATG/ATA codons strongly disagrees with our findings. We report that sites of translation initiation observed within annotated coding regions in mitochondria occur at the annotated start sites, while the other report finds frequent alternative initiation events. We have looked for those arrest sites and did not observe them.

      In the section "Mitoribosome profiling reveals novel translation events," the title may be misleading given the preliminary nature of the results. To support such a claim, the authors should provide experimental evidence demonstrating that the proposed translation events genuinely exist and result in the synthesis of previously unidentified polypeptides. Alternatively, the interpretation should be approached with greater caution and more clearly indicated as preliminary.

      We agree with the reviewers that a distinction should be made between reporting truly novel translation events, like the recently reported MT-ND5-dORF, and sites we suspect mitoribosomes may be binding and that require detailed follow-up. We altered the section title to suggest that this may be showing novel translation events. Additionally, we included a statement in the discussion that these MRPFs may be simply tRNA digestion by RNase I.

      Although located at the 5' end of RNR1, the newly identified ORF is situated 79 nt downstream. According to current knowledge, this appears to be a lengthened 5' UTR that may hinder mitoribosome loading. The authors should speculate on potential initiation mechanisms.

      The start of the putative ORF is not located 79 nts down, but at the 8<sup>th</sup> nucleotide. The reviewer may be including the tRNA-Phe in their calculation, which is cleaved from MT-RNR1. This start site is closer to the 5’ end than our findings with MT-ND5.

      To enhance the interpretation of the mitoribosome profiling data, the authors could complement their findings with classical metabolic labeling using (35)S-methionine. This approach would allow for a different assessment of the stringency of the inhibition under the tested experimental conditions.

      We are currently working on these experiments using mito-funcats. A future direction we are taking this work is to understand how the cell responds to different mechanisms of translation inhibition. For example, we are trying to understand if telithromycin, which appears highly selective, only partially inhibits translation of the mtDNA-encoded proteome.

      Reviewer #2 (Recommendations for the authors):

      Other small editorial comments:

      Line 24: "translate proteins"?

      Revised for clarity

      Line 24: The sentence describing mitochondrial translation as "closely resembling the one in prokaryotes" could be reformulated. While the core of the mitoribosome is conserved, the entire apparatus has many mitochondria-specific features.

      Since this is the abstract, we simplified the point by saying that mitoribosomes are more similar to prokaryotic than cytosolic ribosomes.

      Clarified to highlight that the mitochondrial system is more similar to the bacterial system than the eukaryotic system.

      Line 33: "novel" or "previously unrecognized" ?

      Rewritten for clarity.

      Lines 33-35: The claim made here is not shown in the paper.

      We removed the more aspirational goal of this paper and focused on the main findings of the paper.

      Lines 44, 47, 89 (and elsewhere): "cytoplasmic" or "cytosolic" ?

      Both terms are used in the literature. We opted for cytoplasmic as it can also include ribosomes not free in the cytosol, such as those bound to the ER.

      Reviewer #3 (Recommendations for the authors):

      (1) The authors should state why they chose these antibiotics for mitoribosome profiling analysis over other antibiotics from same group. Did they screen multiple antibiotics to determine the candidates for next step?

      We selected antibiotics that had a known stalling motif in bacteria (initiation or context-dependent elongation inhibitors). In addition, we carried out mitoribosome profiling with erythromycin, azithromycin, thiostrepton, and kanamycin in this work. However, we did not see any effect from these drugs in mitoribosome profiling. We are currently testing other inhibitors, such as doxycycline and tigecycline, and looking at optimizing treatment conditions to identify stalling motifs in samples that previously showed no difference.

      (2) What is the reason for choosing the concentration of antibiotics retapamulin, tiamulin and josamycin, this is IC50 value or above this value? On the other hand, none of this information has been provided for the antibiotics in the next part. The authors should provide biochemical study for the effect of these antibiotics on cell survival and/or protein translation such as S35 assay or steady state level of mtDNA-encoded proteins upon cell treatment with these antibiotics.

      Prior to mitoribo-seq, we carried out time and concentration assays with all antibiotics. 100 µg/ml and a 30-minute treatment was tolerable for all antibiotics except retapamulin. We aimed to treat cells with a relatively high concentration of inhibitor in order to capture actively translating mitoribosomes. We were concerned that longer treatments may lead to decreased translation initiation, leading to the capture of fewer mitoribosomes. These concentrations were nearly identical to contemporary conditions carried out in Bibel et al, RNA 2025.

      (3) Why did the authors choose MT-CYB as the representative for further analysis in the second and third parts of the manuscript?

      We chose MT-CYB because its length allowed for easy visualization. Some mitochondrial genes, such as MT-ND6, had a propensity for stronger stalling at initiation. While coverage was throughout the genes, it was difficult to visualize the changes within the ORF. Also, MT-CYB was less visually complex than polycistronic transcripts. All wigs were uploaded to GEO.

      (4) Page 11, line 233-234: the authors state that telithromycin induces stalling at R/K/A-X-K motif. The authors should do further analysis on mitochondrial genome which proteins contain this motif. Furthermore, same as comment 2: the authors should confirm by 35S assay or WB to know which mtDNA-encoded proteins are affected.

      We have included a supplementary figure showing which mitochondrial genes contain these motifs.

      (5) The results and conclusion from the fourth paragraph are very interesting. The authors suggest alternative start codon for two mtDNA encoded proteins: ND1 and ND5 based on ribosome profiling analysis. Again, I have several comments on this part: <br /> (a) For the accumulation of the alternative start codon of ND1 and ND5 as suggested in the manuscript, do the authors observe this trend with the initiation inhibitors used in the second paragraphs of the manuscript?

      We did not observe similar read lengths with retapamulin, tiamulin, or josamycin, which produced read lengths that were consistent with other RNase I footprinted samples.

      (b) This observation was further confirmed by MS with a peptide form ND1 protein, the authors should show MS peak indicating MW of the peptide and MS/MS data for the peptide which supports this hypothesis.

      We are including the MS/MS report for this peptide.

      (c) Interestingly, several high-resolution structures of mammalian complex I have been reported so far (PMID: 7614227, 10396290, 38870289), ND1 and ND5 protein express full sequences with fMet at the distal N-terminal. This is different to the suggestion from the manuscript. Could the author discuss or comment on that?

      This point was brought up by another reviewer. We have carefully analyzed the density map of PMID: 28844695. We sat down with an expert in cryo-EM and reviewed the figure. We downloaded the density map and reviewed the N-termini of MT-ND1 and MT-ND5. We only observed the density of the N-terminus of MT-ND1 at low confidence. At an RMSD of 2, we could not observe density for the sidechains of Met and Pro, and there is a gap in density for what is modeled as the main chain. The assignment of these residues may have been overlooked due to the expectation that they should be present in the peptide.

      For MT-ND5, we did observe some density that could be part of the main chain; however, it did not fill out until we reduced the stringency, and we did not observe density mapping to side chain residues. To summarize, we do not confidently see density for either the side chain or the main chain for either peptide.

      Minor comments:

      The method should be written more accurately for easily repeating experiments by other groups. For example:

      (1) The authors should indicate what was exact HEK293 cell line used in this study.

      We have indicated the exact cell line.

      (2) Page 22, line 471: which (number) fractions had been collected. The Western Blot analysis shown in Figure 1A should be repeated with both proteins from small and large subunits.

      We have repeated the Western blot with antibodies for large and small subunits. We took fractions 8 and 9, which are now indicated in the text and figure.

      (3) Page 23, line 502: is this number of cells used for MS experiment is correct? Or is this number of cells per mL?

      This is correct and is based on the kit protocol. It is not cells per mL. We have clarified the kit being used in the methods.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This work provides an important resource identifying 72 proteins as novel candidates for plasma membrane and/or cell wall damage repair in budding yeast, and describes the temporal coordination of exocytosis and endocytosis during the repair process. The data are convincing; however, additional experimental validation will better support the claim that repair proteins shuttle between the bud tip and the damage site.

      We thank the editors and reviewers for their positive assessment of our work and the constructive feedback to improve our manuscript. We agree with the assessment that additional validation of repair protein shuttling between the bud tip and the damage site is required to further support the model.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Yamazaki et al. conducted multiple microscopy-based GFP localization screens, from which they identified proteins that are associated with PM/cell wall damage stress response. Specifically, the authors identified that budlocalized TMD-containing proteins and endocytotic proteins are associated with PM damage stress. The authors further demonstrated that polarized exocytosis and CME are temporally coupled in response to PM damage, and CME is required for polarized exocytosis and the targeting of TMD-containing proteins to the damage site. From these results, the authors proposed a model that CME delivers TMD-containing repair proteins between the bud tip and the damage site.

      Strengths:

      Overall, this is a well-written manuscript, and the experiments are well-conducted. The authors identified many repair proteins and revealed the temporal coordination of different categories of repair proteins. Furthermore, the authors demonstrated that CME is required for targeting of repair proteins to the damage site, as well as cellular survival in response to stress related to PM/cell wall damage. Although the roles of CME and bud-localized proteins in damage repair are not completely new to the field, this work does have conceptual advances by identifying novel repair proteins and proposing the intriguing model that the repairing cargoes are shuttled between the bud tip and the damaged site through coupled exocytosis and endocytosis.

      Weaknesses:

      While the results presented in this manuscript are convincing, they might not be sufficient to support some of the authors' claims. Especially in the last two result sessions, the authors claimed CME delivers TMD-containing repair proteins from the bud tip to the damage site. The model is no doubt highly possible based on the data, but caveats still exist. For example, the repair proteins might not be transported from one localization to another localization, but are degraded and resynthesized. Although the Gal-induced expression system can further support the model to some extent, I think more direct verification (such as FLIP or photo-convertible fluorescence tags to distinguish between pre-existing and newly synthesized proteins) would significantly improve the strength of evidence.

      Major experiment suggestions:

      (1) The authors may want to provide more direct evidence for "protein shuttling" and for excluding the possibility that proteins at the bud are degraded and synthesized de novo near the damage site. For example, if the authors could use FLIP to bleach budlocalized fluorescent proteins, and the damaged site does not show fluorescent proteins upon laser damage, this will strongly support the authors' model. Alternatively, the authors could use photo-convertible tags (e.g., Dendra) to differentiate between preexisting repair proteins and newly synthesized proteins.

      We thank the reviewer for evaluating our work and giving us important feedback. We agree that the FLIP and photo-convertible experiments will further confirm our model. Here, due to time and resource constraints, we decided not to perform this experiment. Instead, we have discussed this limitation in 363-366. Our proposed model of repair protein shuttling should be further tested in our future work.

      (2) In line with point 1, the authors used Gal-inducible expression, which supported their model. However, the author may need to show protein abundance in galactose, glucose, and upon PM damage. Western blot would be ideal to show the level of fulllength proteins, or whole-cell fluorescence quantification can also roughly indicate the protein abundance. Otherwise, we cannot assume that the tagged proteins are only expressed when they are growing in galactose-containing media.

      Thank you very much for raising the concern and suggesting the important experiments.We agree that the Western blot experiment to confirm the mNG-Snc1 expression in each medium will further strengthen our conclusion. Along with point (1), further investigation of repair protein shuttling between the bud tip and the damage site and the mechanisms underlying it will be an important future direction. As described above, we have discussed this limitation in 363-366.

      (3) Similarly, for Myo2 and Exo70 localization in CME mutants (Figure 4), it might be worth doing a western or whole-cell fluorescence quantification to exclude the caveat that CME deficiency might affect protein abundance or synthesis.

      We thank the reviewer for suggesting the point. Following the reviewer’s suggestion, we quantified the whole-cell fluorescence of WT and CME mutants and verified that the effect of the CME deletion on the expression levels of Myo2-sfGFP and Exo70-mNG is minimal ( Figure S6). We added the description in lines 211-212.

      (4) From the authors' model in Figure 7, it looks like the repair proteins contribute to bud growth. Does laser damage to the mother cell prevent bud growth due to the reduction of TMD-containing repair proteins at the bud? If the authors could provide evidence for that, it would further support the model.

      Thank you very much for raising the important point. We speculate that the reduction of TMD-containing proteins at the bud by CME is one of the causes of cell growth arrest after PM damage (1). This is because TMD-containing repair proteins at the bud tip, including phospholipid flippases (Dnf1/Dnf2), Snc1, and Dfg5, are involved in polarized cell growth (2-4). This will be an important future direction as well.

      (5) Is the PM repair cell-cycle-dependent? For example, would the recruitment of repair proteins to the damage site be impaired when the cells are under alpha-factor arrest?

      Thank you for raising this interesting point. Indeed, the senior author Kono previously performed this experiment when she was in David Pellman’s lab. The preliminary results suggest that Pkc1 can be targeted to the damage site, without any impairment, under alpha-factor arrest. A more comprehensive analysis in the future will contribute to concluding the relation between PM repair and the cell cycle.

      Reviewer #2 (Public review):

      This paper remarkably reveals the identification of plasma membrane repair proteins, revealing spatiotemporal cellular responses to plasma membrane damage. The study highlights a combination of sodium dodecyl sulfate (SDS) and lase for identifying and characterizing proteins involved in plasma membrane (PM) repair in Saccharomyces cerevisiae. From 80 PM, repair proteins that were identified, 72 of them were novel proteins. The use of both proteomic and microscopy approaches provided a spatiotemporal coordination of exocytosis and clathrin-mediated endocytosis (CME) during repair. Interestingly, the authors were able to demonstrate that exocytosis dominates early and CME later, with CME also playing an essential role in trafficking transmembrane-domain (TMD)containing repair proteins between the bud tip and the damage site.

      Weaknesses/limitations:

      (1) Why are the authors saying that Pkc1 is the best characterized repair protein? What is the evidence?

      We would like to thank the reviewer for taking his/her time to evaluate our work and for valuable suggestions. We described Pkc1 as “best characterized” because it was the first protein reported to accumulate at the laser damage site in budding yeast (5). However, as the reviewer suggested, we do not have enough evidence to describe Pkc1 as “best characterized”. We therefore used “one of the known repair proteins” to mention Pkc1 in the manuscript (lines 90-91).

      (2) It is unclear why the authors decided on the C-terminal GFP-tagged library to continue with the laser damage assay, exclusively the C-terminal GFP-tagged library. Potentially, this could have missed N-terminal tag-dependent localizations and functions and may have excluded functionally important repair proteins

      Thank you very much for the comments. We decided to use the C-terminal GFP-tagged library for the laser damage assay because we intended to evaluate the proteins of endogenous expression levels. The N-terminal sfGFP-tagged library is expressed by the NOP1 promoter, while the C-terminal GFP-tagged library is expressed by the endogenous promoters. We clarified these points in lines 114-118. We agree with the reviewer on that we may have missed some portion of repair proteins in the N-terminaldependent localization and functions by this approach. Therefore, in our manuscript, we discussed these limitations in lines 281-289.

      (3) The use of SDS and laser damage may bias toward proteins responsive to these specific stresses, potentially missing proteins involved in other forms of plasma membrane injuries, such as mechanical, osmotic, etc.). SDS stress is known to indirectly induce oxidative stress and heat-shock responses.

      Thank you very much for raising this point. We agree that the combination of SDS and laser may be biased to identify PM repair proteins. Therefore, in the manuscript, we discussed this point as a limitation of this work in lines 292-298.

      (4) It is unclear what the scale bars of Figures 3, 5, and 6 are. These should be included in the figure legend.

      We apologize for the missing scale bars. We added them to the legends of the figures in the manuscript.

      (5) Figure 4 should be organized to compare WT vs. mutant, which would emphasize the magnitude of impairment.

      Thank you for raising this point. Following the suggestion, we updated Figure 4. In the Figure 4, we compared WT vs mutant in the manuscript. We clarified it in the legends in the manuscript. 

      (6) It would be interesting to expand on possible mechanisms for CME-mediated sorting and retargeting of TMD proteins, including a speculative model.

      Thank you very much for this important suggestion. We think it will be very important to characterize the mechanism of CME-mediated TMD protein trafficking between the bud tip and the damage site. In the manuscript, we discussed the possible mechanism for CME activation at the damage site in lines 328-333. We speculate that the activation of the CME may facilitate the retargeting of the TMD proteins from the damage site to the bud tip.

      We do not have a model of how CMEs activate at the bud tip to sort and target the TMD proteins to the damage site. One possibility is that the cell cycle arrest after PM damage (1) may affect the localization of CME proteins because the cell cycle affects the localization of some of the CME proteins (6). We will work on the mechanism of repair protein sorting from the bud tip to the damage site in our future work.

      Reviewer #3 (Public review):

      Summary:

      This work aims to understand how cells repair damage to the plasma membrane (PM). This is important, as failure to do so will result in cell lysis and death. Therefore, this is an important fundamental question with broad implications for all eukaryotic cells. Despite this importance, there are relatively few proteins known to contribute to this repair process. This study expands the number of experimentally validated PM from 8 to 80. Further, they use precise laser-induced damage of the PM/cell wall and use livecell imaging to track the recruitment of repair proteins to these damage sites. They focus on repair proteins that are involved in either exocytosis or clathrin-mediated endocytosis (CME) to understand how these membrane remodeling processes contribute to PM repair. Through these experiments, they find that while exocytosis and CME both occur at the sites of PM damage, exocytosis predominates in the early stages of repairs, while CME predominates in the later stages of repairs. Lastly, they propose that CME is responsible for diverting repair proteins localized to the growing bud cell to the site of PM damage.

      Strengths:

      The manuscript is very well written, and the experiments presented flow logically. The use of laser-induced damage and live-cell imaging to validate the proteome-wide screen using SDS-induced damage strengthens the role of the identified candidates in PM/cell wall repair.

      Weaknesses:

      (1) Could the authors estimate the fraction of their candidates that are associated with cell wall repair versus plasma membrane repair? Understanding how many of these proteins may be associated with the repair of the cell wall or PM may be useful for thinking about how these results are relevant to systems that do or do not have a cell wall. Perhaps this is already in their GO analysis, but I don't see it mentioned in the manuscript.

      We would like to thank the reviewer for taking his/her time to evaluate our work and valuable suggestions. We agree that this is important information to include. Although it may be difficult to completely distinguish the PM repair and cell wall repair proteins, we have identified at least six proteins involved in cell wall synthesis (Flc1, Dfg5, Smi1, Skg1, Tos7, and Chs3). We included this information in lines 142-146 in the manuscript.

      (2) Do the authors identify actin cable-associated proteins or formin regulators associated with sites of PM damage? Prior work from the senior author (reference 26) shows that the formin Bnr1 relocalizes to sites of PM damage, so it would be interesting if Bnr1 and its regulators (e.g., Bud14, Smy1, etc) are recruited to these sites as well. These may play a role in directing PM repair proteins (see more below).

      Thank you for the suggestion. We identified several Bnr1-interacting proteins, including Bud6, Bil1, and Smy1 (Table S2), although Bnr1 itself was not identified in our screening. This could be attributed to the fact that (1) C-terminal GFP fusion impaired the function of Bnr1, and (2) a single GFP fusion is not sufficient to visualize the weak signal at the damage site. Indeed, in reference 26, 3GFP-Bnr1 (N-terminal 3xGFP fusion) was used.

      (3) Do the authors suspect that actin cables play a role in the relocalization of material from the bud tip to PM damage sites? They mention that TMD proteins are secretory vesicle cargo (lines 134-143) and that Myo2 localizes to damage sites. Together, this suggests a possible role for cable-based transport of repair proteins. While this may be the focus of future work, some additional discussion of the role of cables would strengthen their proposed mechanism (steps 3 and 4 in Figure 7).

      Thank you very much for the suggestion. We agree that actin cables may play a role in the targeting of vesicles and repair proteins to the damage site. Following the reviewer’s suggestion, we discussed the roles of Bnr1 and actin cables for repair protein trafficking in lines 309-313 in the manuscript.

      (4) Lines 248-249: I find the rationale for using an inducible Gal promoter here unclear. Some clarification is needed.

      Thank you for raising this point. We clarified this as possible as we could in lines 249255 in the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The N-terminal GFP collection screen is interesting but seems irrelevant to the rest of the results. The authors discussed that in the discussion part, but it might be worth showing how many hits from the laser damage screen (in Figure 2) overlap with the Nterminal GFP screen hits.

      Thank you for the suggestion. We found that 48 out of 80 repair proteins are hits in the N-terminal GFP library (Table S1 and S2). This result suggested that the N-terminal library is also a useful resource for identifying repair proteins. In the manuscript, we discussed it in lines 288-289.

      (2) SDS treatment seems a harsh stressor. As the authors mentioned, the overlapped hits from the N- and C-terminal GFP screen might be more general stress factors. Thus, I think Line 84 (the subtitle) might be overclaiming, and the authors might need to tone down the sentence.

      Thank you for the suggestion. Following the reviewer’s suggestion, we changed the sentence to “Proteome-scale identification of SDS-responsive proteins” in the manuscript. We believe that the new sentence describes our findings more precisely.

      (3) Line 103-106, it does not seem obvious to me that the protein puncta in the cytoplasm are due to endocytosis. The authors might need to provide more experimental evidence for the conclusion, or at least provide more reasoning/references on that aspect (e.g.,several specific protein hits belonging to that group have been shown to be endocytosed).

      Thank you very much for raising this point. We agree with the reviewer and deleted the description that these puncta are due to endocytosis in the manuscript.

      (4) For Figure 1D and S1C, the authors annotated some of the localization changes clearly, but some are confusing to me. For example," from bud tip/neck" to where? And from where to "Puncta/foci"? A clearer annotation might help the readers to understand the categorization.

      Thank you very much for the suggestion. These annotations were defined because it is difficult to conclusively describe the protein localization after SDS treatment. To convincingly identify the destination of the GFP fusion proteins, the dual color imaging of proteins with organelle markers or deep learning-based localization estimation is required. We feel that this might be out of the scope of this work. Therefore, as criteria, we used the localization of protein localization in normal/non-stressed conditions reported in (7) and the Saccharomyces Genome Database (SGD). We clarified this annotation definition in the manuscript (lines 413-436).

      (5) For localization in Figure 2C, as I understand, does it refer to6 the "before damage/normal" localization? If so, I think it would be helpful to state that these localizations are based on the untreated/normal conditions in the text.

      Yes, it refers to the “before damage/normal localization”. Following the reviewer’s suggestion, we stated that these localizations are based on these conditions in the manuscript (line 130).

      (6) The authors mentioned "four classes" in Line 120, but did not mention the "PM to cytoplasm" class in the text. It would be helpful to discuss/speculate why these transporters might contribute to PM damage repair.

      Thank you very much for this suggestion. We speculated that these transporters are endocytosed after PM damage because endocytosis of PM proteins contributes to cell adaptation to environmental stress (8). We mentioned it in the manuscript (lines 120-122).

      (7) Line 175-180 My understanding of the text is that the signals of Exo70-mNG/Dnf1mNG peak before the Ede1-mSc-I peaks. They occur simultaneously, but their dominating phase are different. It is clearer when looking at the data, but I think the conclusion sentences themselves are confusing to me. The authors might consider rewriting the sentences to make them more straightforward.

      Thank you very much for pointing this out. Following the reviewer’s suggestion, we revised the sentence (lines 177-182 in the manuscript).

      Reviewer #2 (Recommendations for the authors):

      It would be interesting to expand on the functional characterization of the 72 novel candidates and explore possible mechanisms for CME-mediated sorting and retargeting of TMD proteins by including a speculative model.

      Thank you very much for the comment. We agree that the further characterization of novel repair proteins and exploration of the possible mechanisms for CME-mediated TMD protein sorting and retargeting are truly important. This should be our important future direction.

      Reviewer #3 (Recommendations for the authors):

      The x-axis in Figure 1C is labeled 'Ratio' - what is this a ratio of?

      Thank you for raising this point. It is the ratio of the number of proteins associated with a GO term to the total number of proteins in the background. We clarified it in the legend of Figure 1C in the manuscript.

      References

      (1) K. Kono, A. Al-Zain, L. Schroeder, M. Nakanishi, A. E. Ikui, Plasma membrane/cell wall perturbation activates a novel cell cycle checkpoint during G1 in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 113, 6910-6915 (2016).

      (2) A. Das et al., Flippase-mediated phospholipid asymmetry promotes fast Cdc42 recycling in dynamic maintenance of cell polarity. Nat Cell Biol 14, 304-310 (2012).

      (3) M. Adnan et al., SNARE Protein Snc1 Is Essential for Vesicle Trafficking, Membrane Fusion and Protein Secretion in Fungi. Cells 12 (2023).

      (4) H.-U. Mösch, G. R. Fink, Dissection of Filamentous Growth by Transposon Mutagenesis in Saccharomyces cerevisiae. Genetics 145, 671-684 (1997).

      (5) K. Kono, Y. Saeki, S. Yoshida, K. Tanaka, D. Pellman, Proteasomal degradation resolves competition between cell polarization and cellular wound healing. Cell 150, 151-164 (2012).

      (6) A. Litsios et al., Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle. Cell 187, 1490-1507.e1421 (2024).

      (7) W.-K. Huh et al., Global analysis of protein localization in budding yeast.Nature 425, 686-691 (2003).

      (8) T. López-Hernández, V. Haucke, T. Maritzen, Endocytosis in the adaptation to cellular stress. Cell Stress 4, 230-247 (2020).

    1. Author response:

      Public Reviews: 

      Reviewer #1 (Public review):

      Summary:

      Morgan et al. studied how paternal dietary alteration influenced testicular phenotype, placental and fetal growth using a mouse model of paternal low protein diet (LPD) or Western Diet (WD) feeding, with or without supplementation of methyl-donors and carriers (MD). They found diet- and sex-specific effects of paternal diet alteration. All experimental diets decreased paternal body weight and the number of spermatogonial stem cells, while fertility was unaffected. WD males (irrespective of MD) showed signs of adiposity and metabolic dysfunction, abnormal seminiferous tubules, and dysregulation of testicular genes related to chromatin homeostasis. Conversely, LPD induced abnormalities in the early placental cone, fetal growth restriction, and placental insufficiency, which were partly ameliorated by MD. The paternal diets changed the placental transcriptome in a sex-specific manner and led to a loss of sexual dimorphism in the placental transcriptome. These data provide a novel insight into how paternal health can affect the outcome of pregnancies, which is often overlooked in prenatal care.

      Strengths:

      The authors have performed a well-designed study using commonly used mouse models of paternal underfeeding (low protein) and overfeeding (Western diet). They performed comprehensive phenotyping at multiple timepoints, including the fathers, the early placenta, and the late gestation feto-placental unit. The inclusion of both testicular and placental morphological and transcriptomic analysis is a powerful, non-biased tool for such exploratory observational studies. The authors describe changes in testicular gene expression revolving around histone (methylation) pathways that are linked to altered offspring development (H3.3 and H3K4), which is in line with hypothesised paternal contributions to offspring health. The authors report sex differences in control placentas that mimic those in humans, providing potential for translatability of the findings. The exploration of sexual dimorphism (often overlooked) and its absence in response to dietary modification is novel and contributes to the evidence-base for the inclusion of both sexes in developmental studies.

      Weaknesses:

      The data are overall consistent with the conclusions of the authors. The paternal and pregnancy data are discussed separately, instead of linking the paternal phenotype to offspring outcomes. Some clarifications regarding the methods and the model would improve the interpretation of the findings.

      (1) The authors insufficiently discuss their rationale for studying methyl-donors and carriers as micronutrient supplementation in their mouse model. The impact of the findings would be better disseminated if their role were explained in more detail.

      We acknowledge the Reviewer’s comments regarding the amount of detail in support of the inclusion of methyl carriers and donors within our diet. Therefore, we will revise the manuscript to include more justification, especially within the Introduction section, for their inclusion.

      (2) It is unclear from the methods exactly how long the male mice were kept on their respective diets at the time of mating and culling. Male mice were kept on the diet between 8 and 24 weeks before mating, which is a large window in which the males undergo a considerable change in body weight (Figure 1A). If males were mated at 8 weeks but phenotyped at 24 weeks, or if there were differences between groups, this complicates the interpretation of the findings and the extrapolation of the paternal phenotype to changes seen in the fetoplacental unit. The same applies to paternal age, which is an important known factor affecting male fertility and offspring outcomes.

      We thank the Reviewer for their comments regarding the ages of the males analysed. We will provide more detailed descriptions of the males in our manuscript. However, all male ages were balanced across all groups.

      (3) The male mice exhibited lower body weights when fed experimental diets compared to the control diet, even when placed on the hypercaloric Western Diet. As paternal body weight is an important contributor to offspring health, this is an important confounder that needs to be addressed. This may also have translational implications; in humans, consumption of a Western-style diet is often associated with weight gain. The cause of the weight discrepancy is also unaddressed. It is mentioned that the isocaloric LPD was fed ad libitum, while it is unclear whether the WD was also fed ad libitum, or whether males under- or over-ate on each experimental diet.

      We agree with the Reviewer that the general trend towards a lighter body weight for our experimental animals is unexpected. We can confirm that all diets were fed ad libitum. However, as males were group housed, we were unable to measure food consumption for individual males. We also observed that for males fed the high fat diets, they often shredded significant quantities of their diet, rather than eating it, so preventing accurate measurement of food intake.

      We also agree with the Reviewer that body weight can be a significant confounder for many paternal and offspring parameters. However, while the experimental males did become lighter, there were no statistical differences between groups in mean body weight. As such, body weight was not included as a variable within our statistical analysis.

      (4) The description and presentation of certain statistical analyses could be improved.

      (i) It is unclear what statistical analysis has been performed on the time-course data in Figure 1A (if any). If one-way ANOVA was performed at each timepoint (as the methods and legend suggest), this is an inaccurate method to analyse time-course data.

      (ii) It is unclear what methods were used to test the relative abundance of microbiome species at the family level (Figure 2L), whether correction was applied for multiple testing, and what the stars represent in the figure. 3) Mentioning whether siblings were used in any analyses would improve transparency, and if so, whether statistical correction needed to be applied to control for confounding by the father.

      We apologize for the lack of clarity regarding the statistical analyses. Going forward, we will revise the manuscript and include a more detailed description of the different analyses, the inclusion of siblings, and the correction for multiple testing.

      Reviewer #2 (Public review):

      Summary:

      The authors investigated the effects of a low-protein diet (LPD) and a high sugar- and fat-rich diet (Western diet, WD) on paternal metabolic and reproductive parameters and fetoplacental development and gene expression. They did not observe significant effects on fertility; however, they reported gut microbiota dysbiosis, alterations in testicular morphology, and severe detrimental effects on spermatogenesis. In addition, they examined whether the adverse effects of these diets could be prevented by supplementation with methyl donors. Although LPD and WD showed limited negative effects on paternal reproductive health (with no impairment of reproductive success), the consequences on fetal and placental development were evident and, as reported in many previous studies, were sex-dependent.

      Strengths:

      This study is of high quality and addresses a research question of great global relevance, particularly in light of the growing concern regarding the exponential increase in metabolic disorders, such as obesity and diabetes, worldwide. The work highlights the importance of a balanced paternal diet in regulating the expression of metabolic genes in the offspring at both fetal and placental levels. The identification of genes involved in metabolic pathways that may influence offspring health after birth is highly valuable, strengthening the manuscript and emphasizing the need to further investigate long-term outcomes in adult offspring.

      The histological analyses performed on paternal testes clearly demonstrate diet-induced damage. Moreover, although placental morphometric analyses and detailed histological assessments of the different placental zones did not reveal significant differences between groups, their inclusion is important. These results indicate that even in the absence of overt placental phenotypic changes, placental function may still be altered, with potential consequences for fetal programming.

      Weaknesses:

      Overall, this manuscript presents a rich and comprehensive dataset; however, this has resulted in the analysis of paternal gut dysbiosis remaining largely descriptive. While still valuable, this raises questions regarding why supplementation with methyl donors was unable to restore gut microbial balance in animals receiving the modified diets.

      We thank the Reviewer for their considered thoughts on the gut dysbiosis induced in our models the minimal impact of the methyl donors and carriers. We will include additional text within the Discussion to acknowledge this. However, at this point in time, we are unsure as to why the methyl donors had minimal impact. It could be that the macronutrients (i.e. protein, fat, carbohydrates) have more of an influence on gut bacterial profiles than micronutrients. Alternatively, due to the prolonged nature of our feeding regimens, any initial influences of the methyl donors may become diluted out over time. We will amend the text to reflect these potential factors.

    1. Author response:

      Weaknesses:

      (1) Several conclusions are insufficiently supported at this point. For example, evidence that the Hiw foci represent bona fide liquid-liquid phase (LLP) separated condensates is limited. Sensitivity to 1,6-hexanediol is not definitive proof of their liquid condensate nature, and their recovery kinetics after 1,6-hexanediol wash-out and their morphology are inconsistent with a pure liquid behaviour. Furthermore, the claim that the Hiw foci are non-vesicular is not strongly supported, as it is only based on the lack of colocalization with a handful of endosomal proteins.

      We agree that, at the current stage of the manuscript, we have presented data only on Hiw foci in the VNC and shown that they are sensitive to 1,6-HD but not to 2,5-HD. To further provide definitive proof that these are bona fide condensates, we will now perform in vitro analysis of different domains of Hiw and the Hiw IDR region. In addition, we will also investigate the Hiw-GFP behavior in non-neuronal and transiently transfected cell lines using FRAP and other protocols previously applied to condensate-forming proteins.

      Finally, we will perform an in-depth analysis of the Hiw condensates for their colocalization with endocytic proteins and cellular compartments and determine whether they are part of any known vesicular structures.

      (2) Importantly, the appearance of the putative condensates is correlative rather than causative for synaptic overgrowth, and in the absence of a mechanistic link between endocytosis and Hiw condensation, the causality is difficult to address. Of note is that the putative condensates are already present (albeit to a lesser extent) in the absence of endocytic defects and that the conclusions rely heavily on overexpressed GFP-Hiw, which may perturb normal protein behaviour and artificially induce condensation or aggregation.

      To investigate the formation of condensates and their relation to synaptic growth, we will perform a time-course analysis of changes at the NMJ and correlate with the Hiw condensate appearance in the VNC of shi<sup>ts</sup> expressing GFP-Hiw, along with appropriate controls. The GFP transgene used is a functional transgene and well established for studying Hiw behaviour. The Hiw condensates do not form when expressed on an otherwise wild-type background. We will further assess the formation of Hiw condensates in other endocytic mutants with appropriate controls.

      (3) The use of hypomorphic mutants in genetic experiments also introduces some ambiguity in their interpretation, as the results may reflect dosage effects from multiple pathways rather than pathway order. Finally, the manuscript would benefit from a more comprehensive reference to relevant literature on JNKKKs and BMP signalling, as well as on the recycling endosome function in synaptic growth and the regulation of the aforementioned pathways.

      We will perform genetic analysis using homozygous mutants of the wit and saxophone genes to further support epistatic interactions between the BMP signaling pathway and synaptic growth. We will strengthen the discussion part.

    1. Author response:

      eLife Assessment

      The authors use sequencing of nascent DNA (DNA linked to an RNA primer, "SNS-Seq") to localise DNA replication origins in Trypanosoma brucei, so this work will be of interest to those studying either Kinetoplastids or DNA replication. The paper presents the SNS-seq results for only part of the genome, and there are significant discrepancies between the SNS-Seq results and those from other, previously-published results obtained using other origin mapping methods. The reasons for the differences are unknown and from the data available, it is not possible to assess which origin-mapping method is most suitable for origin mapping in T. brucei. Thus at present, the evidence that origins are distributed as the authors claim - and not where previously mapped - is inadequate.

      We would like to clarify a few points regarding our study. Our primary objective was to characterise the topology and genome-wide distribution of short nascent-strand (SNS) enrichments. The stranded SNS-seq approach provides the high strand-specific resolution required to analyse origins. The observation that SNS-seq peaks (potential origins) are most frequently found in intergenic regions is not an artefact of analysing only part of the genome; rather, it is a result of analysing the entire genome.

      We agree that orthogonal validation is necessary. However, neither MFA-seq nor TbORC1/CDC6 ChIP-on-chip has yet been experimentally validated as definitive markers of origin activity in T. brucei, nor do they validate each other. 

      Public Reviews:

      Reviewer #1 (Public review):

      In this paper, Stanojcic and colleagues attempt to map sites of DNA replication initiation in the genome of the African trypanosome, Trypanosoma brucei. Their approach to this mapping is to isolate 'short-nascent strands' (SNSs), a strategy adopted previously in other eukaryotes (including in the related parasite Leishmania major), which involves isolation of DNA molecules whose termini contain replication-priming RNA. By mapping the isolated and sequenced SNSs to the genome (SNS-seq), the authors suggest that they have identified origins, which they localise to intergenic (strictly, inter-CDS) regions within polycistronic transcription units and suggest display very extensive overlap with previously mapped R-loops in the same loci. Finally, having defined locations of SNS-seq mapping, they suggest they have identified G4 and nucleosome features of origins, again using previously generated data.

      Though there is merit in applying a new approach to understand DNA replication initiation in T. brucei, where previous work has used MFA-seq and ChIP of a subunit of the Origin Replication Complex (ORC), there are two significant deficiencies in the study that must be addressed to ensure rigour and accuracy.

      (1) The suggestion that the SNS-seq data is mapping DNA replication origins that are present in inter-CDS regions of the polycistronic transcription units of T. brucei is novel and does not agree with existing data on the localisation of ORC1/CDC6, and it is very unclear if it agrees with previous mapping of DNA replication by MFA-seq due to the way the authors have presented this correlation. For these reasons, the findings essentially rely on a single experimental approach, which must be further tested to ensure SNS-seq is truly detecting origins. Indeed, in this regard, the very extensive overlap of SNS-seq signal with RNA-DNA hybrids should be tested further to rule out the possibility that the approach is mapping these structures and not origins.

      (2) The authors' presentation of their SNS-seq data is too limited and therefore potentially provides a misleading view of DNA replication in the genome of T. brucei. The work is presented through a narrow focus on SNS-seq signal in the inter-CDS regions within polycistronic transcription units, which constitute only part of the genome, ignoring both the transcription start and stop sites at the ends of the units and the large subtelomeres, which are mainly transcriptionally silent. The authors must present a fuller and more balanced view of SNS-seq mapping across the whole genome to ensure full understanding and clarity.

      Regarding comparisons with previous work:

      Two other attempts to identify origins in T. brucei —ORC1/CDC6 binding sites (ChIP-on-chip, PMID: 22840408) and MFA-seq (PMID: 22840408, 27228154)—were both produced by the McCulloch group. These methods do not validate each other; in fact, MFA-seq origins overlap with only 4.4% of the 953 ORC1/CDC6 sites (PMID: 29491738). Therefore, low overlap between SNS-seq peaks and ORC1/CDC6 sites cannot disqualify our findings. Similar low overlaps are observed in other parasites (PMID: 38441981, PMID: 38038269, PMID: 36808528) and in human cells (PMID: 38567819).

      We also would like to emphasize that the ORC1/CDC6 dataset originally published (PMID: 22840408) is no longer available; only a re-analysis by TritrypDB exists, which differs significantly from the published version (personal communication from Richard McCulloch). While the McCulloch group reported a predominant localization of ORC1/CDC6 sites within SSRs at transcription start and termination regions, our re-analysis indicates that only 10.3% of TbORC1/CDC6-12Myc sites overlapped with 41.8% of SSRs.

      MFA-seq does not map individual origins, it rather detects replicated genomic regions by comparing DNA copy number between S- and G1-phases of the cell cycle (PMID: 36640769; PMID: 37469113; PMID: 36455525). The broad replicated regions (0.1–0.5 Mbp) identified by MFA-seq in T. brucei are likely to contain multiple origins, rather than just one. In that sense we disagree with the McCulloch's group who claimed that there is a single origin per broad peak. Our analysis shows that up to 50% of the origins detected by stranded SNS-seq locate within broad MFA-seq regions. The methodology used by McCulloch’s group to infer single origins from MFA-seq regions has not been published or made available, as well as the precise position of these regions, making direct comparison difficult.

      Finally, the genomic features we describe—poly(dA/dT) stretches, G4 structures and nucleosome occupancy patterns—are consistent with origin topology described in other organisms.

      On the concern that SNS-seq may map RNA-DNA hybrids rather than replication origins: Isolation and sequencing of short nascent strands (SNS) is a well-established and widely used technique for high-resolution origin mapping. This technique has been employed for decades in various laboratories, with numerous publications documenting its use. We followed the published protocol for SNS isolation (Cayrou et al., Methods, 2012, PMID: 22796403). RNA-DNA hybrids cannot persist through the multiple denaturation steps in our workflow, as they melt at 95°C (Roberts and Crothers, Science, 1992; PMID: 1279808). Even in the unlikely event that some hybrids remained, they would not be incorporated into libraries prepared using a single-stranded DNA protocol and therefore would not be sequenced (see Figure 1B and Methods).

      Furthermore, our analysis shows that only a small proportion (1.7%) of previously reported RNA-DNA hybrids overlap with SNS-seq origins. It is important to note that RNA-primed nascent strands naturally form RNA-DNA hybrids during replication initiation, meaning the enrichment of RNA-DNA hybrids near origins is both expected and biologically relevant.

      On the claim that our analysis focuses narrowly on inter-CDS regions and ignores other genomic compartments: this is incorrect. We mapped and analyzed stranded SNS-seq data across the entire genome of T. brucei 427 wild-type strain (Müller et al., Nature, 2018; PMID: 30333624), including both core and subtelomeric regions. Our findings indicate that most origins are located in intergenic regions, but all analyses were performed using the full set of detected origins, regardless of location.

      We did not ignore transcription start and stop sites (TSS/TTS). The manuscript already includes origin distribution across genomic compartments as defined by TriTrypDB (Fig. 2C) and addresses overlap with TSS, TTS and HT in the section “Spatial coordination between the activity of the origin and transcription”. While this overlap is minimal, we have included metaplots in the revised manuscript for clarity.

      Reviewer #2 (Public review):

      Summary: 

      Stanojcic et al. investigate the origins of DNA replication in the unicellular parasite Trypanosoma brucei. They perform two experiments, stranded SNS-seq and DNA molecular combing. Further, they integrate various publicly available datasets, such as G4-seq and DRIP-seq, into their extensive analysis. Using this data, they elucidate the structure of the origins of replication. In particular, they find various properties located at or around origins, such as polynucleotide stretches, G-quadruplex structures, regions of low and high nucleosome occupancy, R-loops, and that origins are mostly present in intergenic regions. Combining their population-level SNS-seq and their single-molecule DNA molecular combing data, they elucidate the total number of origins as well as the number of origins active in a single cell.

      Strengths:

      (1) A very strong part of this manuscript is that the authors integrate several other datasets and investigate a large number of properties around origins of replication. Data analysis clearly shows the enrichment of various properties at the origins, and the manuscript concludes with a very well-presented model that clearly explains the authors' understanding and interpretation of the data.

      We sincerely thank you for this positive feedback.

      (2) The DNA combing experiment is an excellent orthogonal approach to the SNS-seq data. The authors used the different properties of the two experiments (one giving location information, one giving single-molecule information) well to extract information and contrast the experiments.

      Thank you very much for this remark.

      (3) The discussion is exemplary, as the authors openly discuss the strengths and weaknesses of the approaches used. Further, the discussion serves its purpose of putting the results in both an evolutionary and a trypanosome-focused context.

      Thank you for appreciating our discussion.

      Weaknesses:

      I have major concerns about the origin of replication sites determined from the SNS-seq data. As a caveat, I want to state that, before reading this manuscript, SNS-seq was unknown to me; hence, some of my concerns might be misplaced.

      (1) I do not understand why SNS-seq would create peaks. Replication should originate in one locus, then move outward in both directions until the replication fork moving outward from another origin is encountered. Hence, in an asynchronous population average measurement, I would expect SNS data to be broad regions of + and -, which, taken together, cover the whole genome. Why are there so many regions not covered at all by reads, and why are there such narrow peaks?

      Thank you for asking these questions. As you correctly point out, replication forks progress in both directions from their origins and ultimately converge at termination sites. However, the SNS-seq method specifically isolates short nascent strands (SNSs) of 0.5–2.5 kb using a sucrose gradient. These short fragments are generated immediately after origin firing and mark the sites of replication initiation, rather than the entire replicated regions. Consequently: (i) SNS-seq does not capture long replication forks or termination regions, only the immediate vicinity of origins. (ii) The narrow peaks indicate the size of selected SNSs (0.5–2.5 kb) and the fact that many cells initiate replication at the same genomic sites, leading to localized enrichment. (iii) Regions without coverage refer to genomic areas that do not serve as efficient origins in the analyzed cell population. Thus, SNS-seq is designed to map origin positions, but not the entire replicated regions.

      (2) I am concerned that up to 96% percent of all peaks are filtered away. If there is so much noise in the data, how can one be sure that the peaks that remain are real? Specifically, if the authors placed the same number of peaks as was measured randomly in intergenic regions, would 4% of these peaks pass the filtering process by chance?

      Maintaining the strandness of the sequenced DNA fibres enabled us to filter the peaks, thereby increasing the probability that the filtered peak pairs corresponded to origins. Two SNS peaks must be oriented in a way that reflects the topology of the SNS strands within an active origin: the upstream peak must be on the minus strand and followed by the downstream peak on the plus strand.

      As suggested by the reviewer, we tested whether randomly placed plus and minus peaks could reproduce the number of filter-passing peaks using the same bioinformatics workflow. Only 1–6% of random peaks passed the filters, compared with 4–12% in our experimental data, resulting in about 50% fewer selected regions (origins). Moreover, the “origins” from random peaks showed 0% reproducibility across replicates, whereas the experimental data showed 7–64% reproducibility. These results indicate that the retainee peaks are highly unlikely to arise by chance and support the specificity of our approach. Thank you for this suggestion.

      (3) There are 3 previous studies that map origins of replication in T. brucei. Devlin et al. 2016, Tiengwe et al. 2012, and Krasiļņikova et al. 2025 (https://doi.org/10.1038/s41467-025-56087-3), all with a different technique: MFA-seq. All three previous studies mostly agree on the locations and number of origins. The authors compared their results to the first two, but not the last study; they found that their results are vastly different from the previous studies (see Supplementary Figure 8A). In their discussion, the authors defend this discrepancy mostly by stating that the discrepancy between these methods has been observed in other organisms. I believe that, given the situation that the other studies precede this manuscript, it is the authors' duty to investigate the differences more than by merely pointing to other organisms. A conclusion should be reached on why the results are different, e.g., by orthogonally validating origins absent in the previous studies.

      The MFA-seq data for T. brucei were published in two studies by McCulloch’s group: Tiengwe et al. (2012) using TREU927 PCF cells, and Devlin et al. (2016) using PCF and BSF Lister427 cells. In Krasilnikova et al. (2025), previously published MFA-seq data from Devlin et al. were remapped to a new genome assembly without generating new MFA-seq data, which explains why we did not include that comparison.

      Clarifying the differences between MFA-seq and our stranded SNS-seq data is essential. MFA-seq and SNS-seq interrogate different aspects of replication. SNS-seq is a widely used, high-resolution method for mapping individual replication origins, whereas MFA-seq detects replicated regions by comparing DNA copy number between S and G1 phases. MFA-seq identified broad replicated regions (0.1–0.5 Mb) that were interpreted by McCulloch’s group as containing a single origin. We disagree with this interpretation and consider that there are multiple origins in each broad peaks; theoretical considerations of replication timing indicate that far more origins are required for complete genome duplication during the short S-phase. Once this assumption is reconsidered, MFA-seq and SNS-seq results become complementary: MFA-seq identifies replicated regions, while SNS-seq pinpoints individual origins within those regions. Our analysis revealed that up to 50% of the origins detected by stranded SNS-seq were located within the broad MFA peaks. This pattern—broad MFA-seq regions containing multiple initiation sites—has also recently been found in Leishmania by McCulloch’s team using nanopore sequencing (PMID: 26481451). Nanopore sequencing showed numerous initiation sites within MFA-seq regions and additional numerous sites outside these regions in asynchronous cells, consistent with what we observed using stranded SNS-seq in T. brucei. We will expand our discussion and conclude that the discrepancy arises from methodological differences and interpretation. The two approaches provide complementary insights into replication dynamics, rather than ‘vastly different’ results.

      We recognize the importance of validating our results in future using an alternative mapping method and functional assays. However, it is important to emphasize that stranded SNS-seq is an origin mapping technique with a very high level of resolution. This technique can detect regions between two divergent SNS peaks, which should represent regions of DNA replication initiation. At present, no alternative technique has been developed that can match this level of resolution.

      (4) Some patterns that were identified to be associated with origins of replication, such as G-quadruplexes and nucleosomes phasing, are known to be biases of SNS-seq (see Foulk et al. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res. 2015;25(5):725-735. doi:10.1101/gr.183848.114).

      It is important to note that the conditions used in our study differ significantly from those applied in the Foulk et al. Genome Res. 2015. We used SNS isolation and enzymatic treatments as described in previous reports (Cayrou, C. et al. Genome Res, 2015 and Cayrou, C et al. Methods, 2012). Here, we enriched the SNS by size on a sucrose gradient and then treated this SNS-enriched fraction with high amounts of repeated λ-exonuclease treatments (100u for 16h at 37oC - see Methods). In contrast, Foulk et al. used sonicated total genomic DNA for origin mapping, without enrichment of SNS on a sucrose gradient as we did, and then they performed a λ-exonuclease treatment. A previous study (Cayrou, C. et al. Genome Res, 2015, Figure S2, which can be found at https://genome.cshlp.org/content/25/12/1873/suppl/DC1) has shown that complete digestion of G4-rich DNA sequences is achieved under the conditions we used.

      Furthermore, the SNS depleted control (without RNA) was included in our experimental approach. This control represents all molecules that are difficult to digest with lambda exonuclease, including G4 structures. Peak calling was performed against this background control, with the aim of removing false positive peaks resulting from undigested DNA structures. We explained better this step in the revised manuscript.

      The key benefit of our study is that the orientation of the enrichments (peaks) remains consistent throughout the sequencing process. We identified an enrichment of two divergent strands synthesised on complementary strands containing G4s. These two divergent strands themselves do not, however, contain G4s (see Fig. 8 for the model). Therefore, the enriched molecules detected in our study do not contain G4s. They are complementary to the strands enriched with G4s. This means that the observed enrichment of

      G4s cannot be an artefact of the enzymatic treatments used in this study. We added this part in the discussion of the revised manuscript.

      We also performed an additional control which is not mentioned in the manuscript. In parallel with replicating cells, we isolated the DNA from the stationary phase of growth, which primarily contains non-replicating cells. Following the three λ-exonuclease treatments, there was insufficient DNA remaining from the stationary phase cells to prepare the libraries for sequencing. This control strongly indicated that there was little to no contaminating DNA present with the SNS molecules after λ-exonuclease enrichment.

    1. Author response:

      The following is the authors’ response to the current reviews

      eLife Assessment

      This study offers valuable insights into how humans detect and adapt to regime shifts, highlighting dissociable contributions of the frontoparietal network and ventromedial prefrontal cortex to sensitivity to signal diagnosticity and transition probabilities. The combination of an innovative instructed-probability task, Bayesian behavioural modeling, and model-based fMRI analyses provides a solid foundation for the main claims; however, major interpretational limitations remain, particularly a potential confound between posterior switch probability and time in the neuroimaging results. At the behavioural level, reliance on explicitly instructed conditional probabilities leaves open alternative explanations that complicate attribution to a single computational mechanism, such that clearer disambiguation between competing accounts and stronger control of temporal and representational confounds would further strengthen the evidence.

      Thank you. In this revision, we will focus on addressing Reviewer 3’s concern on the potential confound between posterior probability and time in neuroimaging results. First, we will present whole-brain results of subjects’ probability estimates (their subjective posterior probability of switch) after controlling for the effect of time on probability of switch (the intertemporal prior). Second, we will compare the effect of probability estimates (Pt) on vmPFC and ventral striatum activity—which we found to correlate with Pt—with and without including intertemporal prior in the GLM. Third, to address Reviewer 3’s comment that from the Tables of activation in the supplement vmPFC and ventral striatum cannot be located, we will add slice-by-slice image of the whole-brain results on Pt in the Supplemental Information in addition to the Tables of Activation.

      Public Reviews:

      Reviewer #1 (Public review):<br /> Summary:

      The study examines human biases in a regime-change task, in which participants have to report the probability of a regime change in the face of noisy data. The behavioral results indicate that humans display systematic biases, in particular, overreaction in stable but noisy environments and underreaction in volatile settings with more certain signals. fMRI results suggest that a frontoparietal brain network is selectively involved in representing subjective sensitivity to noise, while the vmPFC selectively represents sensitivity to the rate of change.

      Strengths:

      The study relies on a task that measures regime-change detection primarily based on descriptive information about the noisiness and rate of change. This distinguishes the study from prior work using reversal-learning or change-point tasks in which participants are required to learn these parameters from experiences. The authors discuss these differences comprehensively.

      The study uses a simple Bayes-optimal model combined with model fitting, which seems to describe the data well. The model is comprehensively validated.

      The authors apply model-based fMRI analyses that provide a close link to behavioral results, offering an elegant way to examine individual biases.

      Weaknesses:

      The authors have adequately addressed my prior concerns.

      Thank you for reviewing our paper and providing constructive comments that helped us improve our paper.

      Reviewer #3 (Public review):

      Thank you again for reviewing the manuscript. In this revision, we will focus on addressing your concern on the potential confound between posterior probability and time in neuroimaging results. First, we will present whole-brain results of subjects’ probability estimates (Pt, their subjective posterior probability of switch) after controlling for the effect of time on probability of switch (the intertemporal prior). Second, we will compare the effect of probability estimates (Pt) on vmPFC and ventral striatum activity—which we found to correlate with Pt—with and without including intertemporal prior in the GLM. These results will be summarized in a new figure (Figure 4).

      Finally, to address that you were not able to locate vmPFC and ventral striatum from the Tables of activation, we will add slice-by-slice image of the whole-brain results on Pt in the supplement in addition to the Tables of Activation.

      This study concerns how observers (human participants) detect changes in the statistics of their environment, termed regime shifts. To make this concrete, a series of 10 balls are drawn from an urn that contains mainly red or mainly blue balls. If there is a regime shift, the urn is changed over (from mainly red to mainly blue) at some point in the 10 trials. Participants report their belief that there has been a regime shift as a % probability. Their judgement should (mathematically) depend on the prior probability of a regime shift (which is set at one of three levels) and the strength of evidence (also one of three levels, operationalized as the proportion of red balls in the mostly-blue urn and vice versa). Participants are directly instructed of the prior probability of regime shift and proportion of red balls, which are presented on-screen as numerical probabilities. The task therefore differs from most previous work on this question in that probabilities are instructed rather than learned by observation, and beliefs are reported as numerical probabilities rather than being inferred from participants' choice behaviour (as in many bandit tasks, such as Behrens 2007 Nature Neurosci).

      The key behavioural finding is that participants over-estimate the prior probability of regime change when it is low, and under estimate it when it is high; and participants over-estimate the strength of evidence when it is low and under-estimate it when it is high. In other words participants make much less distinction between the different generative environments than an optimal observer would. This is termed 'system neglect'. A neuroeconomic-style mathematical model is presented and fit to data.

      Functional MRI results how that strength of evidence for a regime shift (roughly, the surprise associated with a blue ball from an apparently red urn) is associated with activity in the frontal-parietal orienting network. Meanwhile at time-points where the probability of a regime shift is high, there is activity in another network including vmPFC. Both networks show individual differences effects, such that people who were more sensitive to strength of evidence and prior probability show more activity in the frontal-parietal and vmPFC-linked networks respectively.

      Strengths

      (1) The study provides a different task for looking at change-detection and how this depends on estimates of environmental volatility and sensory evidence strength, in which participants are directly and precisely informed of the environmental volatility and sensory evidence strength rather than inferring them through observation as in most previous studies

      (2) Participants directly provide belief estimates as probabilities rather than experimenters inferring them from choice behaviour as in most previous studies

      (3) The results are consistent with well-established findings that surprising sensory events activate the frontal-parietal orienting network whilst updating of beliefs about the word ('regime shift') activates vmPFC.

      Weaknesses

      (1) The use of numerical probabilities (both to describe the environments to participants, and for participants to report their beliefs) may be problematic because people are notoriously bad at interpreting probabilities presented in this way, and show poor ability to reason with this information (see Kahneman's classic work on probabilistic reasoning, and how it can be improved by using natural frequencies). Therefore the fact that, in the present study, people do not fully use this information, or use it inaccurately, may reflect the mode of information delivery.

      In the response to this comment the authors have pointed out their own previous work showing that system neglect can occur even when numerical probabilities are not used. This is reassuring but there remains a large body of classic work showing that observers do struggle with conditional probabilities of the type presented in the task.

      Thank you. Yes, people do struggle with conditional probabilities in many studies. However, as our previous work suggested (Massey and Wu, 2005), system-neglect was likely not due to response mode (having to enter probability estimates or making binary predictions, and etc.).

      (2) Although a very precise model of 'system neglect' is presented, many other models could fit the data.

      For example, you would get similar effects due to attraction of parameter estimates towards a global mean - essentially application of a hyper-prior in which the parameters applied by each participant in each block are attracted towards the experiment-wise mean values of these parameters. For example, the prior probability of regime shift ground-truth values [0.01, 0.05, 0.10] are mapped to subjective values of [0.037, 0.052, 0.069]; this would occur if observers apply a hyper-prior that the probability of regime shift is about 0.05 (the average value over all blocks). This 'attraction to the mean' is a well-established phenomenon and cannot be ruled out with the current data (I suppose you could rule it out by comparing to another dataset in which the mean ground-truth value was different).

      We thank the reviewer for this comment. We do not disagree that there are alternative models that can describe over- and underreactions seen in the dataset. However, we do wish to point out that since we began with the normative Bayesian model, the natural progression in case the normative model fails to capture data is to modify the starting model. It is under this context that we developed the system-neglect model. It was a simple extension (a parameterized version) of the normative Bayesian model.

      Regarding the hyperprior idea, even if the participants have a hyperprior, there has to be some function that describes/implements attraction to the mean. Having a hyperprior itself does not imply attraction to this hyperprior. We therefore were not sure why the hyperprior itself can produce attraction to the mean.

      We do look further into the possibility of attraction to the mean. First, as suggested by the reviewer, we looked into another dataset with different mean ground-truth value. In Massey and Wu (2005), the transition probabilities were [0.02 0.05 0.1 0.2], which is different from the current study [0.01 0.05 0.1], and there they also found over- and underreactions as well. Second, we reason that for the attraction to the mean idea to work subjects need to know the mean of the system parameters. This would take time to develop because we did not tell subjects about the mean. If this is caused by attraction to the mean, subjects’ behavior would be different in the early stage of the experiment where they had little idea about the mean, compared with the late stage of the experiment where they knew about the mean. We will further analyze and compare participants’ data at the beginning of the experiment with data at the end of the experiment.

      More generally, any model in which participants don't fully use the numerical information they were given would produce apparent 'system neglect'. Four qualitatively different example reasons are: 1. Some individual participants completely ignored the probability values given. 2. Participants did not ignore the probability values given, but combined them with a hyperprior as above. 3. Participants had a reporting bias where their reported beliefs that a regime-change had occurred tend to be shifted towards 50% (rather than reporting 'confident' values such 5% or 95%). 4. Participants underweighted probability outliers, resulting in underweighting of evidence in the 'high signal diagnosticity' environment (10.1016/j.neuron.2014.01.020 )

      We thank the reviewer for pointing out these potential explanations. Again, we do not disagree that any model in which participants don’t fully use numerical information they were given would produce system neglect. It is hard to separate ‘not fully using numerical information’ from ‘lack of sensitivity to the numerical information’. We will respond in more details to the four example reasons later.

      In summary I agree that any model that fits the data would have to capture the idea that participants don't differentiate between the different environments as much as they should, but I think there are a number of qualitatively different reasons why they might do this - of which the above are only examples - hence I find it problematic that the authors present the behaviour as evidence for one extremely specific model.

      Again, we do not disagree with the reviewer on the modeling statement. However, we also wish to point out that the system-neglect model we had is a simple extension of the normative Bayesian model. Had we gone to a non-Bayesian framework, we would have faced the criticism of why we simply do not consider a simple extension of the starting model. In response, we will add a section in Discussion summarizing our exchange on this matter.

      (3) Despite efforts to control confounds in the fMRI study, including two control experiments, I think some confounds remain.

      For example, a network of regions is presented as correlating with the cumulative probability that there has been a regime shift in this block of 10 samples (Pt). However, regardless of the exact samples shown, Pt always increases with sample number (as by the time of later samples, there have been more opportunities for a regime shift)? To control for this the authors include, in a supplementary analysis, an 'intertemporal prior.' I would have preferred to see the results of this better-controlled analysis presented in the main figure. From the tables in the SI it is very difficult to tell how the results change with the includion of the control regressors.

      Thank you. In response, we will add a new figure, now Figure 4, showing the results of Pt and delta Pt from GLM-2 where we added the intertemporal prior as a regressor to control for temporal confounds. We compared Pt and delta Pt results in vmPFC and ventral striatum between GLM-1 and GLM-2. We also will show the results of intertemporal prior on vmPFC and ventral striatum under GLM-2.

      On the other hand, two additional fMRI experiments are done as control experiments and the effect of Pt in the main study is compared to Pt in these control experiments. Whilst I admire the effort in carrying out control studies, I can't understand how these particular experiment are useful controls. For example, in experiment 3 participants simply type in numbers presented on the screen - how can we even have an estimate of Pt from this task?

      We thank the reviewer for this comment. On the one hand, the effect of Pt we see in brain activity can be simply due to motor confounds and the purpose of Experiment 3 was to control for them. Our question was, if subjects saw the similar visual layout and were just instructed to press buttons to indicate two-digit numbers, would we observe the vmPFC, ventral striatum, and the frontoparietal network like what we did in the main experiment (Experiment 1)?

      On the other hand, the effect of Pt can simply reflect probability estimates of that the current regime is the blue regime, and therefore not particularly about change detection. In Experiment 2, we tested that idea, namely whether what we found about Pt was unique to change detection. In Experiment 2, subjects estimated the probability that the current regime is the blue regime (just as they did in Experiment 1) except that there were no regime shifts involved. In other words, it is possible that the regions we identified were generally associated with probability estimation and not particularly about probability estimates of change. We used Experiment 2 to examine whether this were true.

      To make the purpose of the two control experiments clearer, we updated the paragraph describing the control experiments on page 9:

      “To establish the neural representations for regime-shift estimation, we performed three fMRI experiments ( subjects for each experiment, 90 subjects in total). Experiment 1 was the main experiment, while Experiments 2 to 3 were control experiments that ruled out two important confounds (Fig. 1E). The control experiments were designed to clarify whether any effect of subjects’ probability estimates of a regime shift, , in brain activity can be uniquely attributed to change detection. Here we considered two major confounds that can contribute to the effect of . First, since subjects in Experiment 1 made judgments about the probability that the current regime is the blue regime (which corresponded to probability of regime change), the effect of  did not particularly have to do with change detection. To address this issue, in Experiment 2 subjects made exactly the same judgments as in Experiment 1 except that the environments were stationary (no transition from one regime to another was possible), as in Edwards (1968) classic “bookbag-and-poker chip” studies. Subjects in both experiments had to estimate the probability that the current regime is the blue regime, but this estimation corresponded to the estimates of regime change only in Experiment 1. Therefore, activity that correlated with probability estimates in Experiment 1 but not in Experiment 2 can be uniquely attributed to representing regime-shift judgments. Second, the effect of  can be due to motor preparation and/or execution, as subjects in Experiment 1 entered two-digit numbers with button presses to indicate their probability estimates. To address this issue, in Experiment 3 subjects performed a task where they were presented with two-digit numbers and were instructed to enter the numbers with button presses. By comparing the fMRI results of these experiments, we were therefore able to establish the neural representations that can be uniquely attributed to the probability estimates of regime-shift.”

      To further make sure that the probability-estimate signals in Experiment 1 were not due to motor confounds, we implemented an action-handedness regressor in the GLM, as we described below on page 19:

      “Finally, we note that in GLM-1, we implemented an “action-handedness” regressor to directly address the motor-confound issue, that higher probability estimates preferentially involved right-handed responses for entering higher digits. The action-handedness regressor was parametric, coding -1 if both finger presses involved the left hand (e.g., a subject pressed “23” as her probability estimate when seeing a signal), 0 if using one left finger and one right finger (e.g., “75”), and 1 if both finger presses involved the right hand (e.g., “90”). Taken together, these results ruled out motor confounds and suggested that vmPFC and ventral striatum represent subjects’ probability estimates of change (regime shifts) and belief revision.”

      (4) The Discussion is very long, and whilst a lot of related literature is cited, I found it hard to pin down within the discussion, what the key contributions of this study are. In my opinion it would be better to have a short but incisive discussion highlighting the advances in understanding that arise from the current study, rather than reviewing the field so broadly.

      Thank you. We thank the reviewer for pushing us to highlight the key contributions. In response, we added a paragraph at the beginning of Discussion to better highlight our contributions:

      “In this study, we investigated how humans detect changes in the environments and the neural mechanisms that contribute to how we might under- and overreact in our judgments. Combining a novel behavioral paradigm with computational modeling and fMRI, we discovered that sensitivity to environmental parameters that directly impact change detection is a key mechanism for under- and overreactions. This mechanism is implemented by distinct brain networks in the frontal and parietal cortices and in accordance with the computational roles they played in change detection. By introducing the framework in system neglect and providing evidence for its neural implementations, this study offered both theoretical and empirical insights into how systematic judgment biases arise in dynamic environments.”

      **Recommendations for the authors:

      Reviewer #3 (Recommendations for the authors):**

      Thank you for pointing out the inclusion of the intertemporal prior in glm2, this seems like an important control that would address my criticism. Why not present this better-controlled analysis in the main figure, rather than the results for glm1 which has no effective control of the increasing posterior probability of a reversal with time?

      Thank you for this suggestion. We added a new figure (Figure 4) that showed results from GLM-2. In this new figure, we showed whole-brain results on Pt and delta Pt, ROI results of vmPFC and ventral striatum on Pt, delta Pt, and intertemporal prior.

      The reason we kept results from GLM-1 (Figure 3) was primarily because we wanted to compare the effect of Pt between experiments under identical GLM. In other words, the regressors in GLM-1 was identical across all 3 experiments. In Experiments 1 and 2, Pt and delta Pt were respectively probability estimates and belief updates that current regime was the Blue regime. In Experiment 3, Pt and delta Pt were simply the number subjects were instructed to press (Pt) and change in number between successive periods (delta Pt).

      As a further point I could not navigate the tables of fMRI activations in SI and recommend replacing or supplementing these with images. For example I cannot actually find a vmPFC or ventral striatum cluster listed for the effect of Pt in GLM1 (version in table S1), which I thought were the main results? Beyond that, comparing how much weaker (or not) those results are when additional confound regressors are included in GLM2 seems impossible.

      The vmPFC and ventral striatum were part of the cluster labeled as Central Opercular cortex. In response, we will provide information about coordinates on the local maxima within the cluster. We will also add slice-by-slice images showing the effect of Pt.


      The following is the authors’ response to the original reviews

      eLife Assessment

      This study offers valuable insights into how humans detect and adapt to regime shifts, highlighting distinct contributions of the frontoparietal network and ventromedial prefrontal cortex to sensitivity to signal diagnosticity and transition probabilities. The combination of an innovative task design, behavioral modeling, and model-based fMRI analyses provides a solid foundation for the conclusions; however, the neuroimaging results have several limitations, particularly a potential confound between the posterior probability of a switch and the passage of time that may not be fully controlled by including trial number as a regressor. The control experiments intended to address this issue also appear conceptually inconsistent and, at the behavioral level, while informing participants of conditional probabilities rather than requiring learning is theoretically elegant, such information is difficult to apply accurately, as shown by well-documented challenges with conditional reasoning and base-rate neglect. Expressing these probabilities as natural frequencies rather than percentages may have improved comprehension. Overall, the study advances understanding of belief updating under uncertainty but would benefit from more intuitive probabilistic framing and stronger control of temporal confounds in future work.

      We thank the editors for the assessment and we appreciate your efforts in reviewing the paper. The editors added several limitations in the assessment based on the new reviewer 3 in this round, which we would like to clarify below.

      With regard to temporal confounds, we clarified in the main text and response to Reviewer 3 that we had already addressed the potential confound between posterior probability of a switch and passage of time in GLM-2 with the inclusion of intertemporal prior. After adding intertemporal prior in the GLM, we still observed the same fMRI results on probability estimates. In addition, we did two other robustness checks, which we mentioned in the manuscript.

      With regard to response mode (probability estimation rather than choice or indicating natural frequencies), we wish to point out that the in previous research by Massey and Wu (2005), which the current study was based on, the concern of participants showing system-neglect tendencies due to the mode of information delivery, namely indicating beliefs through reporting probability estimates rather than through choice or other response mode was addressed. Massy and Wu (2005, Study 3) found the same biases when participants performed a choice task that did not require them to indicate probability estimates.

      With regard to the control experiments, the control experiments in fact were not intended to address the confounds between posterior probability and passage of time. Rather, they aimed to address whether the neural findings were unique to change detection (Experiment 2) and to address visual and motor confounds (Experiment 3). These and the results of the control experiments were mentioned on page 18-19.

      We also wish to highlight that we had performed detailed model comparisons after reviewer 2’s suggestions. Although reviewer 2 was unable to re-review the manuscript, we believe this provides insight into the literature on change detection. See “Incorporating signal dependency into system-neglect model led to better models for regime-shift detection” (p.27-30). The model comparison showed that system-neglect models that incorporate signal dependency are better models than the original system-neglect model in describing participants probability estimates. This suggests that people respond to change-consistent and change-inconsistent signals differently when judging whether the regime had changed. This was not reported in previous behavioral studies and was largely inspired by the neural finding on signal dependency in the frontoparietal cortex. It indicates that neural findings can provide novel insights into computational modeling of behavior.

      To better highlight and summarize our key contributions, we added a paragraph at the beginning of Discussion:

      “In this study, we investigated how humans detect changes in the environments and the neural mechanisms that contribute to how we might under- and overreact in our judgments. Combining a novel behavioral paradigm with computational modeling and fMRI, we discovered that sensitivity to environmental parameters that directly impact change detection is a key mechanism for under- and overreactions. This mechanism is implemented by distinct brain networks in the frontal and parietal cortices and in accordance with the computational roles they played in change detection. By introducing the framework in system neglect and providing evidence for its neural implementations, this study offered both theoretical and empirical insights into how systematic judgment biases arise in dynamic environments.”    

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study examines human biases in a regime-change task, in which participants have to report the probability of a regime change in the face of noisy data. The behavioral results indicate that humans display systematic biases, in particular, overreaction in stable but noisy environments and underreaction in volatile settings with more certain signals. fMRI results suggest that a frontoparietal brain network is selectively involved in representing subjective sensitivity to noise, while the vmPFC selectively represents sensitivity to the rate of change.

      Strengths:

      - The study relies on a task that measures regime-change detection primarily based on descriptive information about the noisiness and rate of change. This distinguishes the study from prior work using reversal-learning or change-point tasks in which participants are required to learn these parameters from experiences. The authors discuss these differences comprehensively.

      - The study uses a simple Bayes-optimal model combined with model fitting, which seems to describe the data well. The model is comprehensively validated.

      - The authors apply model-based fMRI analyses that provide a close link to behavioral results, offering an elegant way to examine individual biases.

      We thank the reviewer for the comments.

      Weaknesses:

      The authors have adequately addressed most of my prior concerns.

      We thank the reviewer for recognizing our effort in addressing your concerns.

      My only remaining comment concerns the z-test of the correlations. I agree with the non-parametric test based on bootstrapping at the subject level, providing evidence for significant differences in correlations within the left IFG and IPS.

      However, the parametric test seems inadequate to me. The equation presented is described as the Fisher z-test, but the numerator uses the raw correlation coefficients (r) rather than the Fisher-transformed values (z). To my understanding, the subtraction should involve the Fisher z-scores, not the raw correlations.

      More importantly, the Fisher z-test in its standard form assumes that the correlations come from independent samples, as reflected in the denominator (which uses the n of each independent sample). However, in my opinion, the two correlations are not independent but computed within-subject. In such cases, parametric tests should take into account the dependency. I believe one appropriate method for the current case (correlated correlation coefficients sharing a variable [behavioral slope]) is explained here:

      Meng, X.-l., Rosenthal, R., & Rubin, D. B. (1992). Comparing correlated correlation coefficients. Psychological Bulletin, 111(1), 172-175. https://doi.org/10.1037/0033-2909.111.1.172

      It should be implemented here:

      Diedenhofen B, Musch J (2015) cocor: A Comprehensive Solution for the Statistical Comparison of Correlations. PLoS ONE 10(4): e0121945. https://doi.org/10.1371/journal.pone.0121945

      My recommendation is to verify whether my assumptions hold, and if so, perform a test that takes correlated correlations into account. Or, to focus exclusively on the non-parametric test.

      In any case, I recommend a short discussion of these findings and how the authors interpret that some of the differences in correlations are not significant.

      Thank you for the careful check. Yes. This was indeed a mistake from us. We also agree that the two correlations are not independent. Therefore, we modified the test that accounts for dependent correlations by following Meng et al. (1992) suggested by the reviewer. We updated in the Methods section on p.56-57:

      “In the parametric test, we adopted the approach of Meng et al. (1992) to statistically compare the two correlation coefficients. This approach specifically tests differences between dependent correlation coefficients according to the following equation

      Where N is the number of subjects, z<sub>ri</sub> is the Fisher z-transformed value of r<sub>i</sub>,(r<sub>1</sub> = r<sub>blue</sub> and r<sub>2</sub> = r<sub>red</sub>), and r<sub>x</sub> is the correlation between the neural sensitivity at change-consistent signals and change-inconsistent signals. The computation of h is based on the following equations

      Where is the mean of the , and f should be set to 1 if > 1.”

      We updated on the Results section on p.29:

      “Since these correlation coefficients were not independent, we compared them using the test developed in Meng et al. (1992) (see Methods). We found that among the five ROIs in the frontoparietal network, two of them, namely the left IFG and left IPS, the difference in correlation was significant (one-tailed z test; left IFG: z = 1.8908, p = 0.0293; left IPS: z = 2.2584, p = 0.0049). For the remaining three ROIs, the difference in correlation was not significant (dmPFC: z = 0.9522, p = 0.1705; right IFG: z = 0.9860, p = 0.1621; right IPS: z = 1.4833, p = 0.0690).”

      We added a Discussion on these results on p.41:

      “Interestingly, such sensitivity to signal diagnosticity was only present in the frontoparietal network when participants encountered change-consistent signals. However, while most brain areas within this network responded in this fashion, only the left IPS and left IFG showed a significant difference in coding individual participants’ sensitivity to signal diagnosticity between change-consistent and change-inconsistent signals. Unlike the left IPS and left IFG, we observed in dmPFC a marginally significant correlation with behavioral sensitivity at change-inconsistent signals as well. Together, these results indicate that while different brain areas in the frontoparietal network responded similarly to change-consistent signals, there was a greater degree of heterogeneity in responding to change-inconsistent signals.”

      Reviewer #3 (Public review):

      This study concerns how observers (human participants) detect changes in the statistics of their environment, termed regime shifts. To make this concrete, a series of 10 balls are drawn from an urn that contains mainly red or mainly blue balls. If there is a regime shift, the urn is changed over (from mainly red to mainly blue) at some point in the 10 trials. Participants report their belief that there has been a regime shift as a % probability. Their judgement should (mathematically) depend on the prior probability of a regime shift (which is set at one of three levels) and the strength of evidence (also one of three levels, operationalized as the proportion of red balls in the mostly-blue urn and vice versa). Participants are directly instructed of the prior probability of regime shift and proportion of red balls, which are presented on-screen as numerical probabilities. The task therefore differs from most previous work on this question in that probabilities are instructed rather than learned by observation, and beliefs are reported as numerical probabilities rather than being inferred from participants' choice behaviour (as in many bandit tasks, such as Behrens 2007 Nature Neurosci).

      The key behavioural finding is that participants over-estimate the prior probability of regime change when it is low, and under estimate it when it is high; and participants over-estimate the strength of evidence when it is low and under-estimate it when it is high. In other words participants make much less distinction between the different generative environments than an optimal observer would. This is termed 'system neglect'. A neuroeconomic-style mathematical model is presented and fit to data.

      Functional MRI results how that strength of evidence for a regime shift (roughly, the surprise associated with a blue ball from an apparently red urn) is associated with activity in the frontal-parietal orienting network. Meanwhile, at time-points where the probability of a regime shift is high, there is activity in another network including vmPFC. Both networks show individual differences effects, such that people who were more sensitive to strength of evidence and prior probability show more activity in the frontal-parietal and vmPFC-linked networks respectively.

      We thank the reviewer for the overall descriptions of the manuscript.

      Strengths

      (1) The study provides a different task for looking at change-detection and how this depends on estimates of environmental volatility and sensory evidence strength, in which participants are directly and precisely informed of the environmental volatility and sensory evidence strength rather than inferring them through observation as in most previous studies

      (2) Participants directly provide belief estimates as probabilities rather than experimenters inferring them from choice behaviour as in most previous studies

      (3) The results are consistent with well-established findings that surprising sensory events activate the frontal-parietal orienting network whilst updating of beliefs about the word ('regime shift') activates vmPFC.

      Thank you for these assessments.

      Weaknesses

      (1) The use of numerical probabilities (both to describe the environments to participants, and for participants to report their beliefs) may be problematic because people are notoriously bad at interpreting probabilities presented in this way, and show poor ability to reason with this information (see Kahneman's classic work on probabilistic reasoning, and how it can be improved by using natural frequencies). Therefore the fact that, in the present study, people do not fully use this information, or use it inaccurately, may reflect the mode of information delivery.

      We appreciate the reviewer’s concern on this issue. The concern was addressed in Massey and Wu (2005) as participants performed a choice task in which they were not asked to provide probability estimates (Study 3 in Massy and Wu, 2005). Instead, participants in Study 3 were asked to predict the color of the ball before seeing a signal. This was a more intuitive way of indicating his or her belief about regime shift. The results from the choice task were identical to those found in the probability estimation task (Study 1 in Massey and Wu). We take this as evidence that the system-neglect behavior the participants showed was less likely to be due to the mode of information delivery.

      (2) Although a very precise model of 'system neglect' is presented, many other models could fit the data.

      For example, you would get similar effects due to attraction of parameter estimates towards a global mean - essentially application of a hyper-prior in which the parameters applied by each participant in each block are attracted towards the experiment-wise mean values of these parameters. For example, the prior probability of regime shift ground-truth values [0.01, 0.05, 0.10] are mapped to subjective values of [0.037, 0.052, 0.069]; this would occur if observers apply a hyper-prior that the probability of regime shift is about 0.05 (the average value over all blocks). This 'attraction to the mean' is a well-established phenomenon and cannot be ruled out with the current data (I suppose you could rule it out by comparing to another dataset in which the mean ground-truth value was different).

      We thank the reviewer for this comment. It is true that the system-neglect model is not entirely inconsistent with regression to the mean, regardless of whether the implementation has a hyper prior or not. In fact, our behavioral measure of sensitivity to transition probability and signal diagnosticity, which we termed the behavioral slope, is based on linear regression analysis. In general, the modeling approach in this paper is to start from a generative model that defines ideal performance and consider modifying the generative model when systematic deviations in actual performance from the ideal is observed. In this approach, a generative Bayesian model with hyper priors would be more complex to begin with, and a regression to the mean idea by itself does not generate a priori predictions.

      More generally, any model in which participants don't fully use the numerical information they were given would produce apparent 'system neglect'. Four qualitatively different example reasons are: 1. Some individual participants completely ignored the probability values given. 2. Participants did not ignore the probability values given, but combined them with a hyperprior as above. 3. Participants had a reporting bias where their reported beliefs that a regime-change had occurred tend to be shifted towards 50% (rather than reporting 'confident' values such 5% or 95%). 4. Participants underweighted probability outliers resulting in underweighting of evidence in the 'high signal diagnosticity' environment (10.1016/j.neuron.2014.01.020)

      In summary I agree that any model that fits the data would have to capture the idea that participants don't differentiate between the different environments as much as they should, but I think there are a number of qualitatively different reasons why they might do this - of which the above are only examples - hence I find it problematic that the authors present the behaviour as evidence for one extremely specific model.

      Thank you for raising this point. The modeling principle we adopt is the following. We start from the normative model—the Bayesian model—that defined what normative behavior should look like. We compared participants’ behavior with the Bayesian model and found systematic deviations from it. To explain those systematic deviations, we considered modeling options within the confines of the same modeling framework. In other words, we considered a parameterized version of the Bayesian model, which is the system-neglect model and examined through model comparison the best modeling choice. This modeling approach is not uncommon in economics and psychology. For example, Kahneman and Tversky adopted this approach when proposing prospect theory, a modification of expected utility theory where expected utility theory can be seen as one specific model for how utility of an option should be computed.

      (3) Despite efforts to control confounds in the fMRI study, including two control experiments, I think some confounds remain.

      For example, a network of regions is presented as correlating with the cumulative probability that there has been a regime shift in this block of 10 samples (Pt). However, regardless of the exact samples shown, doesn't Pt always increase with sample number (as by the time of later samples, there have been more opportunities for a regime shift)? Unless this is completely linear, the effect won't be controlled by including trial number as a co-regressor (which was done).

      Thank you for raising this concern. Yes, Pt always increases with sample number regardless of evidence (seeing change-consistent or change-inconsistent signals). This is captured by the ‘intertemporal prior’ in the Bayesian model, which we included as a regressor in our GLM analysis (GLM-2), in addition to Pt. In short, GLM-1 had Pt and sample number. GLM-2 had Pt, intertemporal prior, and sample number, among other regressors. And we found that, in both GLM-1 and GLM-2, both vmPFC and ventral striatum correlated with Pt.

      To make this clearer, we updated the main text to further clarify this on p.18:

      “We examined the robustness of P<sub>t</sub> representations in these two regions in several follow-up analyses. First, we implemented a GLM (GLM-2 in Methods) that, in addition to P<sub>t</sub>, included various task-related variables contributing to P<sub>t</sub> as regressors (Fig. S7 in SI). Specifically, to account for the fact that the probability of regime change increased over time, we included the intertemporal prior as a regressor in GLM-2. The intertemporal prior is the natural logarithm of the odds in favor of regime shift in the t-th period, where q is transition probability and t = 1,…,10 is the period (see Eq. 1 in Methods). It describes normatively how the prior probability of change increased over time regardless of the signals (blue and red balls) the subjects saw during a trial. Including it along with P<sub>t</sub> would clarify whether any effect of P<sub>t</sub> can otherwise be attributed to the intertemporal prior. Second, we implemented a GLM that replaced P<sub>t</sub> with the log odds of P<sub>t</sub>, ln (P<sub>t</sub>/(1-P<sub>t</sub>)) (Fig. S8 in SI). Third, we implemented a GLM that examined  separately on periods when change-consistent (blue balls) and change-inconsistent (red balls) signals appeared (Fig. S9 in SI). Each of these analyses showed the same pattern of correlations between P<sub>t</sub> and activation in vmPFC and ventral striatum, further establishing the robustness of the P<sub>t</sub> findings.”

      On the other hand, two additional fMRI experiments are done as control experiments and the effect of Pt in the main study is compared to Pt in these control experiments. Whilst I admire the effort in carrying out control studies, I can't understand how these particular experiment are useful controls. For example in experiment 3 participants simply type in numbers presented on the screen - how can we even have an estimate of Pt from this task?

      We thank the reviewer for this comment. On the one hand, the effect of Pt we see in brain activity can be simply due to motor confounds and the purpose of Experiment 3 was to control for them. Our question was, if subjects saw the similar visual layout and were just instructed to press buttons to indicate two-digit numbers, would we observe the vmPFC, ventral striatum, and the frontoparietal network like what we did in the main experiment (Experiment 1)?

      On the other hand, the effect of Pt can simply reflect probability estimates of that the current regime is the blue regime, and therefore not particularly about change detection. In Experiment 2, we tested that idea, namely whether what we found about Pt was unique to change detection. In Experiment 2, subjects estimated the probability that the current regime is the blue regime (just as they did in Experiment 1) except that there were no regime shifts involved. In other words, it is possible that the regions we identified were generally associated with probability estimation and not particularly about probability estimates of change. We used Experiment 2 to examine whether this were true.

      To make the purpose of the two control experiments clearer, we updated the paragraph describing the control experiments on page 9:

      “To establish the neural representations for regime-shift estimation, we performed three fMRI experiments (n\=30 subjects for each experiment, 90 subjects in total). Experiment 1 was the main experiment, while Experiments 2 to 3 were control experiments that ruled out two important confounds (Fig. 1E). The control experiments were designed to clarify whether any effect of subjects’ probability estimates of a regime shift, P<sub>t</sub>, in brain activity can be uniquely attributed to change detection. Here we considered two major confounds that can contribute to the effect of . First, since subjects in Experiment 1 made judgments about the probability that the current regime is the blue regime (which corresponded to probability of regime change), the effect of P<sub>t</sub> did not particularly have to do with change detection. To address this issue, in Experiment 2 subjects made exactly the same judgments as in Experiment 1 except that the environments were stationary (no transition from one regime to another was possible), as in Edwards (1968) classic “bookbag-and-poker chip” studies. Subjects in both experiments had to estimate the probability that the current regime is the blue regime, but this estimation corresponded to the estimates of regime change only in Experiment 1. Therefore, activity that correlated with probability estimates in Experiment 1 but not in Experiment 2 can be uniquely attributed to representing regime-shift judgments. Second, the effect of P<sub>t</sub> can be due to motor preparation and/or execution, as subjects in Experiment 1 entered two-digit numbers with button presses to indicate their probability estimates. To address this issue, in Experiment 3 subjects performed a task where they were presented with two-digit numbers and were instructed to enter the numbers with button presses. By comparing the fMRI results of these experiments, we were therefore able to establish the neural representations that can be uniquely attributed to the probability estimates of regime-shift.”

      To further make sure that the probability-estimate signals in Experiment 1 were not due to motor confounds, we implemented an action-handedness regressor in the GLM, as we described below on page 19:

      “Finally, we note that in GLM-1, we implemented an “action-handedness” regressor to directly address the motor-confound issue, that higher probability estimates preferentially involved right-handed responses for entering higher digits. The action-handedness regressor was parametric, coding -1 if both finger presses involved the left hand (e.g., a subject pressed “23” as her probability estimate when seeing a signal), 0 if using one left finger and one right finger (e.g., “75”), and 1 if both finger presses involved the right hand (e.g., “90”). Taken together, these results ruled out motor confounds and suggested that vmPFC and ventral striatum represent subjects’ probability estimates of change (regime shifts) and belief revision.”

      (4) The Discussion is very long, and whilst a lot of related literature is cited, I found it hard to pin down within the discussion, what the key contributions of this study are. In my opinion it would be better to have a short but incisive discussion highlighting the advances in understanding that arise from the current study, rather than reviewing the field so broadly.

      Thank you. We thank the reviewer for pushing us to highlight the key contributions. In response, we added a paragraph at the beginning of Discussion to better highlight our contributions:

      “In this study, we investigated how humans detect changes in the environments and the neural mechanisms that contribute to how we might under- and overreact in our judgments. Combining a novel behavioral paradigm with computational modeling and fMRI, we discovered that sensitivity to environmental parameters that directly impact change detection is a key mechanism for under- and overreactions. This mechanism is implemented by distinct brain networks in the frontal and parietal cortices and in accordance with the computational roles they played in change detection. By introducing the framework in system neglect and providing evidence for its neural implementations, this study offered both theoretical and empirical insights into how systematic judgment biases arise in dynamic environments.”

      Recommendations for the authors:

      Reviewer #3 (Recommendations for the authors):

      Many of the figures are too tiny - the writing is very small, as are the pictures of brains. I'd suggest adjusting these so they will be readable without enlarging.

      Thank you. We apologize for the poor readability of the figures. We had enlarged the figures (Fig. 5 in particular) and their font size to make them more readable.

    1. Author response:

      General Response

      We thank the reviewers for their positive assessment of our work and for acknowledging the timeliness of the problem and the novelty of using domain adaptation to address model mismatch. We appreciate the constructive feedback regarding validation and clarity. In the revised manuscript, we will address these points as follows:

      (1) Systematic Validation: We will design and perform systematic in silico experiments to evaluate the method beyond the single in vivo dataset , including robustness tests regarding recording length and network synchrony.

      (2) Recurrent Networks & Failure Analysis: We will test our method on synthetic datasets generated from highly recurrent networks and analyze exactly when the method breaks as a function of mismatch magnitude.

      (3) Method Comparisons: We will report the Matthews Correlation Coefficient (MCC) for the approach by English et al. (2017) and expand our comparison and discussion of GLM-based methods.

      (4) Clarifications: We will rigorously define the dataset details (labeling, recording methodology), mathematical notation, and machine learning terminology ('data', 'labels').

      (5) Discussion of Limitations: We will explicitly discuss the challenges and limitations inherent in generalizing to more recurrently connected regions.

      Below are our more detailed responses:

      Public Reviews:

      Reviewer #1 (Public review):

      Weaknesses:

      (1) The validation of the approach is incomplete: due to its very limited size, the single ground-truth dataset considered does not provide a sufficient basis to draw a strong conclusion. While the authors correctly note that this is the only dataset of its kind, the value of this validation is limited compared to what could be done by carefully designing in silico experiments.

      We thank the reviewer for acknowledging the scarcity of suitable in vivo ground-truth datasets and the limitations this poses. We agree that additional validation is necessary to draw strong conclusions. In the revised manuscript, we will systematically design and perform in silico experiments for evaluations beyond the single in vivo dataset.

      (2) Surprisingly, the authors fail to compare their method to the approach originally proposed for the data they validate on (English et al., 2017).

      We agree that this is an essential comparison. We will report the Matthews Correlation Coefficient (MCC) result of the approach by English et al. (2017) on the spontaneous period of the recording.

      (3) The authors make a commendable effort to study the method's robustness by pushing the limits of the dataset. However, the logic of the robustness analysis is often unclear, and once again, the limited size of the dataset poses major limitations to the authors.

      We appreciate the reviewer recognizing our initial efforts to evaluate robustness. In our original draft, we tested recording length, network model choices, and analyzed failure cases. However, we agree that the limited real data restricts the scope of these tests. To address this, we will perform more systematic robustness tests on the newly generated synthetic datasets in the revised version, allowing us to evaluate performance under a wider range of conditions.

      (4) The lack of details concerning both the approach and the validation makes it challenging for the reader to establish the technical soundness of the study.

      We will revise the manuscript thoroughly to better present the methodology of our framework and the validation pipelines. We will ensure that the figures and text clearly articulate the technical details required to assess the soundness of the study.

      Although in the current form this study does not provide enough basis to judge the impact of DeepDAM in the broader neuroscience community, it nevertheless puts forward a valuable and novel idea: using domain adaptation to mitigate the problem of model mismatch. This approach might be leveraged in future studies and methods to infer connectivity.

      We thank the reviewer again for acknowledging the novelty and importance of our work.

      Reviewer #2 (Public review):

      While the validation data set was well chosen and of high quality, it remains a single dataset and also remains a non-recurrent network. The authors acknowledge this in the discussion, but I wanted to chime in to say that for the method to be more than convincing, it would need to have been tested on more datasets. It should be acknowledged that the problem becomes more complicated in a recurrent excitatory network, and thus the method may not work as well in the cortex or in CA3.

      We will carefully revise our text to specifically discuss this limitation and the challenges inherent in generalizing to more recurrently connected regions. Furthermore, to empirically address this concern, we will test our method extensively on synthetic datasets generated from highly recurrent networks to quantify performance in these regimes.

      While the data is shown to work in this particular dataset (plus the two others at the end), I was left wondering when the method breaks. And it should break if the models are sufficiently mismatched. Such a question can be addressed using synthetic-synthetic models. This was an important intuition that I was missing, and an important check on the general nature of the method that I was missing.

      We thank the reviewer for this insight regarding the general nature of the method. While we previously analyzed failure cases regarding strong covariation and low spike counts, we agree that a systematic analysis of mismatch magnitude is missing. Building on our planned experiments with synthetic data, we will analyze and discuss exactly when the method breaks as a function of the mismatch magnitude between datasets.

      While the choice of state-of-the-art is good in my opinion, I was looking for comments on the methods prior to that. For instance, methods such based on GLMs have been used by the Pillow, Paninski, and Truccolo groups. I could not find a decent discussion of these methods in the main text and thought that both their acknowledgement and rationale for dismissing were missing.

      As the reviewer noted, we extensively compared our method with a GLM-based method (GLMCC) and CoNNECT, whose superiority over other GLM-based methods, such as extend GLM method (Ren et al., 2020, J Neurophysiol), have already been demonstrated in their papers (Endo et al., Sci Rep, 2021). However, we acknowledge that the discussion of the broader GLM literature was insufficient. To make the comparison more thorough, we will conduct comparisons with additional GLM-based methods and include a detailed discussion of these approaches.

      Endo, D., Kobayashi, R., Bartolo, R., Averbeck, B. B., Sugase-Miyamoto, Y., Hayashi, K., ... & Shinomoto, S. (2021). A convolutional neural network for estimating synaptic connectivity from spike trains. Scientific Reports, 11(1), 12087.

      Ren, N., Ito, S., Hafizi, H., Beggs, J. M., & Stevenson, I. H. (2020). Model-based detection of putative synaptic connections from spike recordings with latency and type constraints. Journal of Neurophysiology, 124(6), 1588-1604.

      While most of the text was very clear, I thought that page 11 was odd and missing much in terms of introductions. Foremost is the introduction of the dataset, which is never really done. Page 11 refers to 'this dataset', while the previous sentence was saying that having such a dataset would be important and is challenging. The dataset needs to be properly described: what's the method for labeling, what's the brain area, what were the spike recording methodologies, what is meant by two labeling methodologies, what do we know about the idiosyncrasies of the particular network the recording came from (like CA1 is non-recurrent, so which connections)? I was surprised to see 'English et al.' cited in text only on page 13 since their data has been hailed from the beginning.

      Further elements that needed definition are the Nsyn and i, which were not defined in the cortex of Equation 2-3: I was not sure if it referred to different samples or different variants of the synthetic model. I also would have preferred having the function f defined earlier, as it is defined for Equation 3, but appears in Equation 2.

      When the loss functions are described, it would be important to define 'data' and 'labels' here. This machine learning jargon has a concrete interpretation in this context, and making this concrete would be very important for the readership.

      We thank the reviewer for these constructive comments on the writing. We will clarify the introduction of the dataset (labeling method, brain area, recording methodology) and ensure all mathematical terms (such as Nsyn, i, and function f) and machine learning terminology (definitions of 'data' and 'labels' in this context) are rigorously defined upon first use in the revised manuscript.

      While I appreciated that there was a section on robustness, I did not find that the features studied were the most important. In this context, I was surprised that the other datasets were relegated to supplementary, as these appeared more relevant.

      Robustness is an important aspect of our framework to demonstrate its applicability to real experimental scenarios. We specifically analyzed how synchrony between neurons, the number of recorded spikes and the choice of the network influence the performance of our method. We also agree that these aspects are limited by the one dataset we evaluated on. Therefore, we will test the robustness of our method more systematically on synthetic datasets.

      With more extensive analysis on synthetic datasets, we believe that the results on inferring biophysical properties of single neuron and microcircuit models remain in the supplement, such that the main figures focus purely on synaptic connectivity inference.

      Some of the figures have text that is too small. In particular, Figure 2 has text that is way too small. It seemed to me that the pseudo code could stand alone, and the screenshot of the equations did not need to be repeated in a figure, especially if their size becomes so small that we can't even read them.

      We will remove the pseudo-code and equations from Figure 2 to improve readability. The pseudo-code will be presented as a distinct box in the main text.

    1. Author response:

      Thank you very much for the constructive feedback on our manuscript, "Simple Methods to Acutely Measure Multiple Timing Metrics among Sexual Repertoire of Male Drosophila," and for the opportunity to address the reviewers' comments. We appreciate the time and effort the reviewers have invested in evaluating our work, and we agree that their suggestions will significantly strengthen the manuscript.

      We are currently working diligently to address all the concerns raised in the public reviews and recommendations. Below is an outline of the major revisions we plan to implement in the revised version:

      (1) Statistical Rigor and Analysis

      We acknowledge the statistical limitations pointed out by Reviewer #2. We will re-analyze the multi-group data in Figures 3 and 4 using One-way and Two-way ANOVA with appropriate post-hoc tests (e.g., Tukey's HSD), respectively, to properly account for multiple comparisons and interaction effects between genotype and training conditions.

      (2) Comparison with Existing Tools

      As suggested by both reviewers, we will provide a detailed comparison of DrosoMating with established automated tracking systems (e.g., FlyTracker, JAABA, Ctrax),and specific use cases where DrosoMating offers distinct advantages in terms of cost, accessibility, and ease of use for high-throughput screening.

      (3) Control for Locomotor Activity

      To address the potential confound of general locomotor deficits in w1118 and y1 mutants, we will calculate and present general locomotion metrics (e.g., average velocity, total distance traveled) from our tracking data to dissociate motor defects from specific courtship deficits.

      (4) Software Capabilities and Cross-Species Applicability

      We will clarify how DrosoMating handles fly identification during mating (including occlusion management). We will also discuss or test the software's applicability across different *Drosophila* species, as requested.

      (5) Minor Corrections

      We will address all textual errors, standardize terminology (e.g., "Mating Duration" vs. "Copulation Duration"), improve figure legibility, and provide complete statistical details for all figures.

      We believe these revisions will substantially improve the rigor, clarity, and utility of our manuscript. We aim to resubmit the revised version within the standard timeframe and will ensure the preprint is updated accordingly.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This fundamental study identifies a new mechanism that involves a mycobacterial nucleomodulin manipulation of the host histone methyltransferase COMPASS complex to promote infection. Although other intracellular pathogens are known to manipulate histone methylation, this is the first report demonstrating the specific targeting of the COMPASS complex by a pathogen. The rigorous experimental design using state-of-the art bioinformatic analysis, protein modeling, molecular and cellular interaction, and functional approaches, culminating with in vivo infection modeling, provides convincing, unequivocal evidence that supports the authors' claims. This work will be of particular interest to cellular microbiologists working on microbial virulence mechanisms and effectors, specifically nucleomodulins, and cell/cancer biologists that examine COMPASS dysfunction in cancer biology.

      Strengths:

      (1) The strengths of this study include the rigorous and comprehensive experimental design that involved numerous state-of-the-art approaches to identify potential nucleomodulins, define molecular nucleomodulin-host interactions, cellular nucleomodulin localization, intracellular survival, and inflammatory gene transcriptional responses, and confirmation of the inflammatory and infection phenotype in a small animal model.

      (2) The use of bioinformatic, cellular, and in vivo modeling that are consistent and support the overall conclusions is a strength of the study. In addition, the rigorous experimental design and data analysis, including the supplemental data provided, further strengthen the evidence supporting the conclusions.

      Weaknesses:

      (1) This work could be stronger if the MgdE-COMPASS subunit interactions that negatively impact COMPASS complex function were better defined. Since the COMPASS complex consists of many enzymes, examining the functional impact on each of the components would be interesting.

      We thank the reviewer for this insightful comment. A biochemistry assays could be helpful to interpret the functional impact on each of the components by MgdE interaction. However, the purification of the COMPASS complex could be a hard task itself due to the complexity of the full COMPASS complex along with its dynamic structural properties and limited solubility.

      (2) Examining the impact of WDR5 inhibitors on histone methylation, gene transcription, and mycobacterial infection could provide additional rigor and provide useful information related to the mechanisms and specific role of WDR5 inhibition on mycobacterial infection.

      We thank the reviewer for the comment. A previous study showed that WIN-site inhibitors, such as compound C6, can displace WDR5 from chromatin, leading to a reduction in global H3K4me3 levels and suppression of immune-related gene expression (Hung et al., Nucleic Acids Res, 2018; Bryan et al., Nucleic Acids Res, 2020). These results closely mirror the functional effects we observed for MgdE, suggesting that MgdE may act as a functional mimic of WDR5 inhibition. This supports our proposed model in which MgdE disrupts COMPASS activity by targeting WDR5, thereby dampening host pro-inflammatory responses.

      (3) The interaction between MgdE and COMPASS complex subunit ASH2L is relatively undefined, and studies to understand the relationship between WDR5 and ASH2L in COMPASS complex function during infection could provide interesting molecular details that are undefined in this study.

      We thank the reviewer for the comment. In this study, we constructed single and multiple point mutants of MgdE at residues S<sup>80</sup>, D<sup>244</sup>, and H<sup>247</sup> to identify key amino acids involved in its interaction with ASH2L (Figure 5A and B; New Figure S4C). However, these mutations did not interrupt the interaction with MgdE, suggesting that more residues are involved in the interaction.

      ASH2L and WDR5 function cooperatively within the WRAD module to stabilize the SET domain and promote H3K4 methyltransferase activity with physiological conditions (Couture and Skiniotis, Epigenetics, 2013; Qu et al., Cell, 2018; Rahman et al., Proc Natl Acad Sci U S A, 2022). ASH2L interacts with RbBP5 via its SPRY domain, whereas WDR5 bridges MLL1 and RbBP5 through the WIN and WBM motifs (Chen et al., Cell Res, 2012; Park et al., Nat Commun, 2019). The interaction status between ASH2L and WDR5 during mycobacterial infection could not be determined in our current study.

      (4) The AlphaFold prediction results for all the nuclear proteins examined could be useful. Since the interaction predictions with COMPASS subunits range from 0.77 for WDR5 and 0.47 for ASH2L, it is not clear how the focus on COMPASS complex over other nuclear proteins was determined.

      We thank the reviewer for the comment. We employed AlphaFold to predict the interactions between MgdE and the major nuclear proteins. This screen identified several subunits of the SET1/COMPASS complex as high-confidence candidates for interaction with MgdE (Figure S4A). This result is consistent with a proteomic study by Penn et al. which reported potential interactions between MgdE and components of the human SET1/COMPASS complex based on affinity purification-mass spectrometry analysis (Penn et al., Mol Cell, 2018).

      Reviewer #2 (Public review):

      Summary:

      The manuscript by Chen et al addresses an important aspect of pathogenesis for mycobacterial pathogens, seeking to understand how bacterial effector proteins disrupt the host immune response. To address this question, the authors sought to identify bacterial effectors from M. tuberculosis (Mtb) that localize to the host nucleus and disrupt host gene expression as a means of impairing host immune function.

      Strengths:

      The researchers conducted a rigorous bioinformatic analysis to identify secreted effectors containing mammalian nuclear localization signal (NLS) sequences, which formed the basis of quantitative microscopy analysis to identify bacterial proteins that had nuclear targeting within human cells. The study used two complementary methods to detect protein-protein interaction: yeast two-hybrid assays and reciprocal immunoprecipitation (IP). The combined use of these techniques provides strong evidence of interactions between MgdE and SET1 components and suggests that the interactions are, in fact, direct. The authors also carried out a rigorous analysis of changes in gene expression in macrophages infected with the mgdE mutant BCG. They found strong and consistent effects on key cytokines such as IL6 and CSF1/2, suggesting that nuclear-localized MgdE does, in fact, alter gene expression during infection of macrophages.

      Weaknesses:

      There are some drawbacks in this study that limit the application of the findings to M. tuberculosis (Mtb) pathogenesis. The first concern is that much of the study relies on ectopic overexpression of proteins either in transfected non-immune cells (HEK293T) or in yeast, using 2-hybrid approaches. Some of their data in 293T cells is hard to interpret, and it is unclear if the protein-protein interactions they identify occur during natural infection with mycobacteria. The second major concern is that pathogenesis is studied using the BCG vaccine strain rather than virulent Mtb. However, overall, the key findings of the paper - that MgdE interacts with SET1 and alters gene expression are well-supported.

      We thank the reviewer for the comment. We agree that the ectopic overexpression could not completely reflect a natural status, although these approaches were adopted in many similar experiments (Drerup et al., Molecular plant, 2013; Chen et al., Cell host & microbe, 2018; Ge et al., Autophagy, 2021). Further, the MgdE localization experiment using Mtb infected macrophages will be performed to increase the evidence in the natural infection.

      We agree with the reviewer that BCG strain could not fully recapitulate the pathogenicity or immunological complexity of M. tuberculosis infection. We employed BCG as a biosafe surrogate model since it was acceptable in many related studies (Wang et al., Nat Immunol, 2025; Wang et al., Nat Commun, 2017; Péan et al., Nat Commun, 2017; Li et al., J Biol Chem, 2020).

      Reviewer #3 (Public review):

      In this study, Chen L et al. systematically analyzed the mycobacterial nucleomodulins and identified MgdE as a key nucleomodulin in pathogenesis. They found that MgdE enters into host cell nucleus through two nuclear localization signals, KRIR<sup>108-111</sup> and RLRRPR<sup>300-305</sup>, and then interacts with COMPASS complex subunits ASH2L and WDR5 to suppress H3K4 methylation-mediated transcription of pro-inflammatory cytokines, thereby promoting mycobacterial survival. This study is potentially interesting, but there are several critical issues that need to be addressed to support the conclusions of the manuscript.

      (1) Figure 2: The study identified MgdE as a nucleomodulin in mycobacteria and demonstrated its nuclear translocation via dual NLS motifs. The authors examined MgdE nuclear translocation through ectopic expression in HEK293T cells, which may not reflect physiological conditions. Nuclear-cytoplasmic fractionation experiments under mycobacterial infection should be performed to determine MgdE localization.

      We thank the reviewer for this insightful comment. In the revised manuscript, we addressed this concern by performing nuclear-cytoplasmic fractionation experiments using M. bovis BCG-infected macrophages to assess the subcellular localization of MgdE (New Figure 2F) (Lines 146–155). Nuclear-cytoplasmic fractionation experiments showed that WT MgdE and the NLS single mutants (MgdE<sup>ΔNLS1</sup> and MgdE<sup>ΔNLS2</sup>) could be detected both in the cytoplasm and in the nucleus, while the double mutant MgdE<sup>ΔNLS1-2</sup> was detectable only in the cytoplasm. These findings strongly indicate that MgdE is capable of translocating into the host cell nucleus during BCG infection, and that this nuclear localization relies on the dual NLS motifs.

      (2) Figure 2F: The authors detected MgdE-EGFP using an anti-GFP antibody, but EGFP as a control was not detected in its lane. The authors should address this technical issue.

      We thank the reviewer for this question. In the revised manuscript, we have included the uncropped immunoblot images, which clearly show the EGFP band in the corresponding lane. These have been provided in the New Figure 2E.

      (3) Figure 3C-3H: The data showing that the expression of all detected genes in 24 h is comparable to that in 4 h (but not 0 h) during WT BCG infection is beyond comprehension. The issue is also present in Figure 7C, Figure 7D, and Figure S7. Moreover, since Il6, Il1β (pro-inflammatory), and Il10 (anti-inflammatory) were all upregulated upon MgdE deletion, how do the authors explain the phenomenon that MgdE deletion simultaneously enhanced these gene expressions?

      We thank the reviewer for the comment. A relative quantification method was used in our qPCR experiments to normalize the WT expression levels in Figure 3C–3H, Figure 7C, 7D, and New Figure S6.

      The concurrent induction of both types of cytokines likely represents a dynamic host strategy to fine-tune immune responses during infection. This interpretation is supported by previous studies (Podleśny-Drabiniok et al., Cell Rep, 2025; Cicchese et al., Immunological Reviews, 2018).

      (4) Figure 5: The authors confirmed the interactions between MgdE and WDR5/ASH2L. How does the interaction between MgdE and WDR5 inhibit COMPASS-dependent methyltransferase activity? Additionally, the precise MgdE-ASH2L binding interface and its functional impact on COMPASS assembly or activity require clarification.

      We thank the reviewer for this insightful comment. We cautiously speculate that the MgdE interaction inhibits COMPASS-dependent methyltransferase activity by interfering with the integrity and stability of the COMPASS complex. Accordingly, we have incorporated the following discussion into the revised manuscript (Lines 303-315):

      “The COMPASS complex facilitates H3K4 methylation through a conserved assembly mechanism involving multiple core subunits. WDR5, a central scaffolding component, interacts with RbBP5 and ASH2L to promote complex assembly and enzymatic activity (Qu et al., 2018; Wysocka et al., 2005). It also recognizes the WIN motif of methyltransferases such as MLL1, thereby anchoring them to the complex and stabilizing the ASH2L-RbBP5 dimer (Hsu et al., Cell, 2018). ASH2L further contributes to COMPASS activation by interacting with both RbBP5 and DPY30 and by stabilizing the SET domain, which is essential for efficient substrate recognition and catalysis (Qu et al., Cell, 2018; Park et al., Nat Commun, 2019). Our work shows that MgdE binds both WDR5 and ASH2L and inhibits the methyltransferase activity of the COMPASS complex. Site-directed mutagenesis revealed that residues D<sup>224</sup> and H<sup>247</sup> of MgdE are critical for WDR5 binding, as the double mutant MgdE-D<sup>224</sup>A/H<sup>247</sup>A fails to interact with WDR5 and shows diminished suppression of H3K4me3 levels (Figure 5D).”

      Regarding the precise MgdE-ASH2L binding interface, we attempted to identify the key interaction site by introducing point mutations into ASH2L. However, these mutations did not disrupt the interaction (Figure 5A and B; New Figure S4C), suggesting that more residues are involved in the interaction.

      (5) Figure 6: The authors proposed that the MgdE-regulated COMPASS complex-H3K4me3 axis suppresses pro-inflammatory responses, but the presented data do not sufficiently support this claim. H3K4me3 inhibitor should be employed to verify cytokine production during infection.

      We thank the reviewer for the comment. We have now revised the description in lines 220-221 and lines 867-868 "MgdE suppresses host inflammatory responses probably by inhibition of COMPASS complex-mediated H3K4 methylation."

      (6) There appears to be a discrepancy between the results shown in Figure S7 and its accompanying legend. The data related to inflammatory responses seem to be missing, and the data on bacterial colonization are confusing (bacterial DNA expression or CFU assay?).

      We thank the reviewer for the comment. New Figure S6 specifically addresses the effect of MgdE on bacterial colonization in the spleens of infected mice, which was assessed by quantitative PCR rather than by CFU assay.

      We have now revised the legend of New Figure S6 as below (Lines 986-991):

      “MgdE facilitates bacterial colonization in the spleens of infected mice. Bacterial colonization was assessed in splenic homogenates from infected mice (as described in Figure 7A) by quantifying bacterial DNA using quantitative PCR at 2, 14, 21, 28, and 56 days post-infection.”

      (7) Line 112-116: Please provide the original experimental data demonstrating nuclear localization of the 56 proteins harboring putative NLS motifs.

      We thank the reviewer for the comment. We will provide this data in the New Table S3.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      There are a few concerns about specific experiments:

      Major Comments:

      (1) Questions about the exact constructs used in their microscopy studies and the behavior of their controls. GFP is used as a negative control, but in the data they provide, the GFP signal is actually nuclear-localized (for example, Figure 1c, Figure 2a). Later figures do show other constructs with clear cytoplasmic localization, such as the delta-NLS-MgdE-GFP in Figure 2D. This raises significant questions about how the microscopy images were analyzed and clouds the interpretation of these findings. It is also not clear if their microscopy studies use the mature MdgE, lacking the TAT signal peptide after signal peptidase cleavage (the form that would be delivered into the host cell) or if they are transfecting the pro-protein that still has the TAT signal peptide (a form that would present in the bacterial cell but that would not be found in the host cell). This should be clarified, and if their construct still has the TAT peptide, then key findings such as nuclear localization and NLS function should be confirmed with the mature protein lacking the signal peptide.

      We thank the reviewer for this question.  EGFP protein can passively diffuse through nuclear pores due to its smaller size (Petrovic et al., Science, 2022; Yaseen et al., Nat Commun, 2015; Bhat et al., Nucleic Acids Res, 2015). However, upon transfection with EGFP-tagged wild-type MdgE and its NLS deletion mutants (MdgE<sup>ΔNLS1</sup>, MdgE<sup>ΔNLS2</sup>, and MdgE<sup>ΔNLS1-2</sup>), we observed significantly stronger nuclear fluorescence in cells expressing wild-type MdgE compared to the EGFP protein. Notably, the MdgE<sup>ΔNLS1-2</sup>-EGFP mutant showed almost no detectable nuclear fluorescence (Figure 2C, D, and E). These results indicate that (i) MdgE-EGFP fusion protein could not enter the nucleus by passive diffusion, and (ii) EGFP does not interfere with the nuclear targeting ability of MdgE.

      We did not construct a signal peptide-deleted MgdE for transfection assays. Instead, we performed an infection experiment using recombinant M. bovis BCG strains expressing Flag-tagged wild-type MgdE. The mature MgdE protein (signal peptide cleaved) can be detected in the nucleus fractionation (New Figure 2F), suggesting that the signal peptide does not play a role for the nuclear localization of MgdE.

      (2) The localization of MdgE is not shown during actual infection. The study would be greatly strengthened by an analysis of the BCG strain expressing their MdgE-FLAG construct.

      We thank the reviewer for the comment. In the revised manuscript, we constructed M. bovis BCG strains expressing FLAG-tagged wild-type MdgE as well as NLS deletion mutants (MdgE<sup>ΔNLS1</sup>, MdgE<sup>ΔNLS2</sup>, and MdgE<sup>ΔNLS1-2</sup>). These strains were used to infect THP-1 cells, and nuclear-cytoplasmic fractionation was performed 24 hours post-infection.

      Nuclear-cytoplasmic fractionation experiments showed that WT MgdE and the NLS single mutants could be detected both in the cytoplasm and in the nucleus by immunoblotting, while the double mutant MgdE<sup>ΔNLS1-2</sup> was detectable only in the cytoplasm (New Figure 2F) (Lines 146–155). These findings indicate that MdgE is capable of entering the host cell nucleus during BCG infection, and that this nuclear localization depends on the presence of both its N-terminal and C-terminal NLS motifs.

      (3) Their pathogenesis studies suggesting a role for MdgE would be greatly strengthened by studying MdgE in virulent Mtb rather than the BCG vaccine strain. If this is not possible because of technical limitations (such as lack of a BSL3 facility), then at least a thorough discussion of studies that examined Rv1075c/MdgE in Mtb is important. This would include a discussion of the phenotype observed in a previously published study examining the Mtb Rv1075c mutant that showed a minimal phenotype in mice (PMID: 31001637) and would also include a discussion of whether Rv1075c was identified in any of the several in vivo Tn-Seq studies done on Mtb.

      We thank the reviewer for this insightful comment. In the revised manuscript, we have incorporated a more thorough discussion of prior studies that examined Rv1075c/MgdE in Mtb, including the reported minimal phenotype of an Mtb MgdE mutant in mice (PMID: 31001637) (Lines 288–294).

      In the latest TnSeq studies in M. tuberculosis, Rv1075c/MgdE was not classified as essential for in vivo survival or virulence (James et al., NPJ Vaccines, 2025; Zhang et al., Cell, 2013). However, this absence should not be interpreted as evidence of dispensability since these datasets also failed to identify some well characterized virulence factors including Rv2067c (Singh et al., Nat Commun, 2023), PtpA (Qiang et al., Nat Commun, 2023), and PtpB (Chai et al., Science, 2022) which were demonstrated to be required for the virulence of Mtb.

      Minor Comments:

      (1) Multiple figures with axes with multiple discontinuities used when either using log-scale or multiple graphs is more appropriate, including 3B, 7A.

      We sincerely thank the reviewer for pointing this out. In the revised manuscript, we have updated Figure 3B and Figure 7A.

      (2) Figure 1C - Analysis of only nuclear MFI can be very misleading because it is affected by the total expression of each construct. Ratios of nuclear to cytoplasmic MFI are a more rigorous analysis.

      We thank the reviewer for this comment. We agree that analyzing the ratio of nuclear to cytoplasmic mean fluorescence intensity (MFI) provides a more rigorous quantification of nuclear localization, particularly when comparing constructs with different expression levels. However, the analysis presented in Figure 1C was intended as a preliminary qualitative screen to identify Tat/SPI-associated proteins with potential nuclear localization, rather than a detailed quantitative assessment.

      (3) Figure 5C - Controls missing and unclear interpretation of their mutant phenotype. There is no mock or empty-vector control transfection, and their immunoblot shows a massive increase in total cellular H3K4me3 signal in the bulk population, although their prior transfection data show only a small fraction of cells are expressing MdgE. They also see a massive increase in methylation in cells transfected with the inactive mutant, but the reason for this is unclear. Together, these data raise questions about the specificity of the increasing methylation they observe. An empty vector control should be included, and the phenotype of the mutant explained.

      We thank the reviewer for this comment. In the revised manuscript, we transfected HEK293T cells with an empty EGFP vector and performed a quantitative analysis of H3K4me3 levels. The results demonstrated that, at the same time point, cells expressing MdgE showed significantly lower levels of H3K4me3 compared to both the EGFP control and the catalytically inactive mutant MdgE (D<sup>244</sup>A/H<sup>247</sup>A) (New Figure 5D) (Lines 213–216). These findings support the conclusion that MdgE specifically suppresses H3K4me3 levels in cells.

      (4) Figure S1A - The secretion assay is lacking a critical control of immunoblotting a cytoplasmic bacterial protein to demonstrate that autolysis is not releasing proteins into the culture filtrate non-specifically - a common problem with secretion assays in mycobacteria.

      We thank the reviewer for this comment. To address the concerns, we examined FLAG-tagged MgdE and the secreted antigen Ag85B in the culture supernatants by monitoring the cytoplasmic protein GlpX. The absence of GlpX in the supernatant confirmed that there was no autolysis in the experiment. We could detect MgdE-Flag in the culture supernatant (New Figure S2A), indicating that MgdE is a secreted protein.

      (5) The volcano plot of their data shows that the proteins with the smallest p-values have the smallest fold-changes. This is unusual for a transcriptomic dataset and should be explained.

      We thank the reviewer for this comment. We are not sure whether the p-value is correlated with fold-change in the transcriptomic dataset. This is probably case by case.

      Reviewer #3 (Recommendations for the authors):

      There are several minor comments:

      (1) Line 104-109: The number of proteins harboring NLS motifs and candidate proteins assigned to the four distinct pathways does not match the data presented in Table S2. Please recheck the details. Figure 1A and B, as well as Figure S1A and B, should also be corrected accordingly.

      We thank the reviewer for the comment. We have carefully checked the details and the numbers were confirmed and updated.

      (2) Please add the scale bar in all image figures, including Figure 1C, Figure 2D, Figure 5C, Figure 7B, and Figure S2.

      We thank the reviewer for this suggestion. We have now added scale bars to all relevant image figures in the revised manuscript, including Figure 1C, New Figure 2C, Figure 5C, Figure 7B, and New Figure S2B.

      (3) Please add the molecular marker in all immunoblotting figures, including Figure 2C, Figure 2F, Figure 4B, Figure 4C, Figure 5B, Figure 5D, and Figure S5.

      We thank the reviewer for this suggestion. We have now added the molecular marker in all immunoblotting figures in the revised manuscript, including New Figure 2E–F, Figure 4B–C, Figure 5B and D, Figure S2A, New Figure S2E and New Figure S4C.

      References

      Bryan AF, Wang J, Howard GC, Guarnaccia AD, Woodley CM, Aho ER, Rellinger EJ, Matlock BK, Flaherty DK, Lorey SL, Chung DH, Fesik SW, Liu Q, Weissmiller AM, Tansey WP (2020) WDR5 is a conserved regulator of protein synthesis gene expression Nucleic Acids Res 48:2924-2941.

      Chai Q, Yu S, Zhong Y, Lu Z, Qiu C, Yu Y, Zhang X, Zhang Y, Lei Z, Qiang L, Li BX, Pang Y, Qiu XB, Wang J, Liu CH (2022) A bacterial phospholipid phosphatase inhibits host pyroptosis by hijacking ubiquitin Science 378(6616):eabq0132.

      Chen C, Nguyen BN, Mitchell G, Margolis SR, Ma D, Portnoy DA (2018) The listeriolysin O PEST-like sequence co-opts AP-2-mediated endocytosis to prevent plasma membrane damage during Listeria infection Cell host & microbe 23: 786-795.

      Chen Y, Cao F, Wan B, Dou Y, Lei M (2012) Structure of the SPRY domain of human Ash2L and its interactions with RbBP5 and DPY30 Cell Res 22:598–602.

      Cicchese JM, Evans S, Hult C, Joslyn LR, Wessler T, Millar JA, Marino S, Cilfone NA, Mattila JT, Linderman JJ, Kirschner DE (2018) Dynamic balance of pro‐ and anti‐inflammatory signals controls disease and limits pathology Immunological Reviews 285: 147–167.

      Couture JF, Skiniotis G (2013) Assembling a COMPASS Epigenetics 8:349-54

      Drerup MM, Schlücking K, Hashimoto K, Manishankar P, Steinhorst L, Kuchitsu K, Kudla J (2013) The calcineurin B-like calcium sensors CBL1 and CBL9 together with their interacting protein kinase CIPK26 regulate the Arabidopsis NADPH oxidase RBOHF Molecular plant 6: 559-569.

      Ge P, Lei Z, Yu Y, Lu Z, Qiang L, Chai Q, Zhang Y, Zhao D, Li B, Pang Y, Liu C, Wang J (2021) M. tuberculosis PknG Manipulates Host Autophagy Flux to Promote Pathogen Intracellular Survival Autophagy 18: 576–94.

      Hung KH, Woo YH, Lin IY, Liu CH, Wang LC, Chen HY, Chiang BL, Lin KI (2018) The KDM4A/KDM4C/NF-κB and WDR5 epigenetic cascade regulates the activation of B cells Nucleic Acids Res 46:5547–5560.

      James KS, Jain N, Witzl K, Cicchetti N, Fortune SM, Ioerger TR, Martinot AJ, Carey AF (2025) TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity NPJ Vaccines 10:103.

      Li X, Chen L, Liao J, Hui J, Li W, He ZG (2020) A novel stress-inducible CmtR-ESX3-Zn²⁺ regulatory pathway essential for survival of Mycobacterium bovis under oxidative stress J Biol Chem 295:17083–17099.

      Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US (2019) Cryo-EM structure of the human MLL1 core complex bound to the nucleosome Nat Commun 10:5540.

      Penn BH, Netter Z, Johnson JR, Von Dollen J, Jang GM, Johnson T, Ohol YM, Maher C, Bell SL, Geiger K (2018) An Mtb-human protein-protein interaction map identifies a switch between host antiviral and antibacterial responses Mol Cell 71:637-648.e5.

      Petrovic S, Samanta D, Perriches T, Bley CJ, Thierbach K, Brown B, Nie S, Mobbs GW, Stevens TA, Liu X, Tomaleri GP, Schaus L, Hoelz A (2022) Architecture of the linker-scaffold in the nuclear pore Science 376: eabm9798.

      Podleśny-Drabiniok A, Romero-Molina C, Patel T, See WY, Liu Y, Marcora E, Goate AM (2025) Cytokine-induced reprogramming of human macrophages toward Alzheimer's disease-relevant molecular and cellular phenotypes in vitro Cell Rep 44:115909.

      Qiang L, Zhang Y, Lei Z, Lu Z, Tan S, Ge P, Chai Q, Zhao M, Zhang X, Li B, Pang Y, Zhang L, Liu CH, Wang J (2023) A mycobacterial effector promotes ferroptosis-dependent pathogenicity and dissemination Nat Commun 14:1430.

      Qu Q, Takahashi YH, Yang Y, Hu H, Zhang Y, Brunzelle JS, Couture JF, Shilatifard A, Skiniotis G (2018) Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex Cell 174:1117-1126.e12.

      Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C (2022) Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome Proc Natl Acad Sci U S A 119:e2205691119.

      Sharma G, Upadhyay S, Srilalitha M, Nandicoori VK, Khosla S 2015 The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding Nucleic Acids Res 43:3922-37.

      Singh PR, Dadireddy V, Udupa S, Kalladi SM, Shee S, Khosla S, Rajmani RS, Singh A, Ramakumar S, Nagaraja V (2023) The Mycobacterium tuberculosis methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival Nat Commun 14:8497.

      Wang J, Ge P, Qiang L, Tian F, Zhao D, Chai Q, Zhu M, Zhou R, Meng G, Iwakura Y, Gao GF, Liu CH (2017) The mycobacterial phosphatase PtpA regulates the expression of host genes and promotes cell proliferation Nat Commun 8:244.

      Wang J, Li BX, Ge PP, Li J, Wang Q, Gao GF, Qiu XB, Liu CH (2015) Mycobacterium tuberculosis suppresses innate immunity by coopting the host ubiquitin system Nat Immunol 16:237–245

      Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, Roeder RG, Brivanlou AH, Allis CD (2005) WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development Cell 121:859-72.

      Yaseen I, Kaur P, Nandicoori VK, Khosla S (2015) Mycobacteria modulate host epigenetic machinery by Rv1988 methylation of a non-tail arginine of histone H3 Nat Commun 6:8922.

      Zhang L, Kent JE, Whitaker M, Young DC, Herrmann D, Aleshin AE, Ko YH, Cingolani G, Saad JS, Moody DB, Marassi FM, Ehrt S, Niederweis M (2022) A periplasmic cinched protein is required for siderophore secretion and virulence of Mycobacterium tuberculosis Nat Commun 13:2255.

      Zhang YJ, Reddy MC, Ioerger TR, Rothchild AC, Dartois V, Schuster BM, Trauner A, Wallis D, Galaviz S, Huttenhower C, Sacchettini JC, Behar SM, Rubin EJ (2013) Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing Cell 155:1296-308.

    1. Author response:

      Reviewer #1

      We thank the reviewer for their thoughtful and constructive assessment of AutoMorphoTrack and for recognizing its potential utility as an open-source end-to-end workflow for organelle analysis.

      (1) Novelty and relationship to existing tools / FIJI workflows

      We appreciate this concern and agree that many of the underlying image-processing operations (e.g., thresholding, morphological cleanup, region properties) are well-established. Our goal with AutoMorphoTrack is not to introduce new segmentation algorithms, but rather to provide a curated, reproducible, and extensible end-to-end workflow that integrates segmentation, morphology, tracking, motility, and colocalization into a single, transparent pipeline tailored for live-cell organelle imaging.

      While an experienced user could assemble similar analyses ad hoc using FIJI or custom scripts, our contribution lies in:

      Unifying these steps into a single workflow with consistent parameterization and outputs

      Generating standardized, publication-ready visualizations and tables at each step,

      Enabling batch and longitudinal analyses across cells and conditions, and

      Lowering the barrier for users who do not routinely write custom analysis code.

      We note that the documentation-style presentation of the manuscript is intentional, as it serves both as a methods paper and a practical reference for users implementing the workflow. We agree, however, that the manuscript currently overemphasizes step-by-step execution at the expense of positioning. In revision, we will more explicitly frame AutoMorphoTrack as a workflow integration and usability contribution, rather than a fundamentally new algorithmic advance.

      We will also cite and discuss the image.sc example referenced by the reviewer, clarifying conceptual overlap and differences in scope.

      (2) Comparison to existing pipelines (Imaris, CellProfiler, CellPose, StarDist)

      We agree and thank the reviewer for highlighting this omission. In the revised manuscript, we will expand the related-work and positioning section to explicitly compare AutoMorphoTrack with established commercial (e.g., Imaris) and open-source (e.g., CellProfiler, MiNA, MitoGraph) platforms, as well as learning-based segmentation tools such as CellPose and StarDist.

      Rather than claiming superiority, we will clarify trade-offs, emphasizing that AutoMorphoTrack prioritizes:

      Transparency and parameter interpretability,

      Lightweight dependencies suitable for small live-imaging datasets

      Direct integration of morphology, tracking, and colocalization in a single workflow, and

      Ease of modification for domain-specific use cases.

      (3) AI / chatbot integration

      We appreciate this critique and agree that the current description is insufficiently precise. AutoMorphoTrack does not implement a native natural-language interface. Instead, our intent was to convey that the workflow can be executed and modified with assistance from external large language models (LLMs) in a notebook-based environment.

      In revision, we will revise this section to:

      Clearly distinguish AutoMorphoTrack’s functionality from that of external LLM tools,

      Remove any implication of a built-in AI interface, and

      Provide concrete, reproducible examples of how non-coding users may interact with the pipeline using natural-language prompts mediated by external tools.

      Reviewer #2

      We thank the reviewer for their detailed and technically rigorous evaluation. We appreciate the recognition of the workflow’s motivation and structure, and we agree that several aspects of validation, positioning, and quantitative reporting must be strengthened.

      (1) AI-assisted / natural-language functionality

      We agree with this critique. AutoMorphoTrack does not provide a native natural-language execution layer, and the manuscript currently overstates this aspect. In revision, we will explicitly scope any reference to AI assistance as external, optional support for code generation and parameter editing, with clearly documented examples and stated limitations.

      We agree that conflating external LLM capabilities with the software itself risks misleading readers, and we will correct this accordingly.

      (2) Lack of quantitative validation

      We fully agree that the current manuscript lacks formal quantitative validation. In the revised version, we will add a dedicated validation section including:

      Segmentation accuracy compared to expert annotations using overlap metrics (e.g., Dice / IoU),

      Tracking fidelity assessed using manually annotated tracks and/or synthetic ground truth,

      Sensitivity analyses for key parameters (e.g., thresholding and linking distance), and

      Explicit discussion of failure modes and quality-control indicators.

      We acknowledge that without such validation, claims of robustness are not sufficiently supported.

      (3) Benchmarking and positioning relative to existing tools

      We agree and will substantially strengthen AutoMorphoTrack’s benchmarking and positioning relative to existing platforms. Rather than framing novelty algorithmically, we will clarify that the primary contribution is a reproducible, integrated workflow designed specifically for two-organelle live imaging in neurons, with transparent parameters and standardized outputs.

      We note that our goal is not to exhaustively benchmark against all available tools, but rather to provide representative comparisons that clarify operating regimes, assumptions, and trade-offs. We will add a comparative table and/or qualitative comparison highlighting strengths, assumptions, and limitations relative to existing tools.

      (4) Core algorithms and robustness

      We agree that reliance on threshold-based segmentation introduces sensitivity to imaging conditions. In revision, we will:

      Explicitly discuss the operating regime and assumptions under which AutoMorphoTrack performs reliably,

      Clarify that the framework is modular and can accept alternative segmentation backends, and

      Include guidance on when outputs should be treated with caution.

      (5) Figure, metric, and statistical issues

      We thank the reviewer for identifying several critical issues and agree that these undermine confidence. In revision, we will correct all figure, metric-definition, and reporting inconsistencies, including:

      Resolving circularity values exceeding 1 by correcting computation and/or labeling errors,

      Revising physically invalid displacement plots and clarifying kernel-density limitations,

      Ensuring colocalization metrics are consistently defined, named, and interpreted, with explicit clarification of whether calculations are intensity- or mask-based,

      Correcting figure legends to match displayed panels, and

      Clearly reporting sample size, sampling units, and statistical assumptions, including handling of multiple comparisons where applicable.

      (6) Value-added demonstration

      We agree that the manuscript would benefit from a clearer demonstration of value-added use cases. In revision, we will include at least one realistic example showing how AutoMorphoTrack enables a complete, reproducible analysis workflow with reduced setup burden compared to manually assembling multiple tools.

      (7) Editorial suggestions

      We agree and will streamline the Results section to reduce procedural repetition and focus more on validation, limitations, and quality-control guidance.

      Reviewer #3

      We thank the reviewer for their positive assessment of clarity and organization, and for the constructive practical feedback.

      Installation issues

      We appreciate the detailed report of installation failures and acknowledge that the current packaging and distribution are inadequate. Prior to revision, we will:

      Fix the package structure to support standard installation methods,

      Ensure all required files (e.g., setup configuration, README) are correctly included,

      Test installation on clean environments across platforms, and

      Correct broken links to notebooks and documentation.

      We agree that without a functional installation pathway, the utility of the tool is severely limited.

      AI-assisted claims

      We agree with the reviewer and echo our responses above. The AI-assisted description will be clarified and appropriately scoped in the revised manuscript.

      Additional suggestions

      Color accessibility: We will revise all figures to use colorblind-safe palettes.

      Velocity–displacement diagonal: We will explicitly explain the origin of this relationship, including whether it reflects dataset properties, tracking assumptions, or minimum detectable motion.

      Integrated correlation metric: We agree that Spearman correlation is more appropriate for many of these relationships and will replace Pearson correlations accordingly.

      Supplementary movies: We agree that providing raw movies would improve interpretability and will add representative examples as supplementary material.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1(Public review):

      Summary:

      In this study, the authors distinguished afferent inputs to different cell populations in the VTA using dimensionality reduction approaches and found significantly distinct patterns between normal and drug treatment conditions. They also demonstrated negative correlations of the inputs induced by drugs with gene expression of ion channels or proteins involved in synaptic transmission and demonstrated the knockdown of one of the voltage-gated calcium ion channels caused decreased inputs.

      Weaknesses:

      (1) For quantifications of brain regions in this study, boundaries were based on the Franklin-Paxinos (FP) atlas according to previous studies (Beier KT et al 2015, Beier KT et al 2019). It has been reported significant discrepancies exist between the anatomical labels on the FP atlas and the Allen Brain Atlas (ref: Chon U et al., Nat Commun 2019). Although a summary of conversion is provided as a sheet, the authors need to describe how consistent or different the brain boundaries they defined in the manuscript with Allen Brain Atlas by adding histology images. Also, I wonder how reliable the annotations were for over a hundred of animals with manual quantification. The authors should briefly explain it rather than citing previous studies in the Material and Methods Section.

      We thank the reviewer for attention to this point; indeed, neuroanatomical detail is often overlooked in modern neuroscience, occasionally leading to spurious conclusions. We acknowledge that there are significant discrepancies in brain region definitions across atlases, which can make cross-study comparisons difficult. Here, all cells were manually quantified by Dr. Kevin Beier, as in previous studies (Beier et al., Cell 2015; Nature 2017; Cell Reports 2019; Tian et al., Cell Reports 2022; Tian et al., Neuron 2024; Hubbard et al., Neuropsychopharmacology, 2025). As such, these studies are internally consistent as relates to the definition of brain regions, which is critical here since our analysis in this manuscript relates to data quantified only by a single individual. Several brain regions were quite easy to distinguish anatomically, such as the medial habenula and lateral habenula. Others, such as the extended amygdala area, are much more difficult. We have now provided example images in Figure S1 that detail the anatomical boundaries that we used, overlayed on images of Neurotrace blue (fluorescent Nissl stain).

      (2) Regarding the ellipsoids in the PC, although it's written in the manuscript that "Ellipsoids were centered at the average coordinate of a condition and stretched one standard deviation along the primary and secondary axes", it's intuitively hard to understand in some figures such as Figure 2O, P and Figure S1. The authors need to make their data analysis methods more accessible by providing source code to the public.

      The source code is now available to the public at https://github.com/ktbartas/Bartas_et_al_eLife_2024, which is noted in the Code Availability statement. The code for generating ellipsoids is in the first notebook, `0-dataexploration-master-euclidean.ipynb`, in the function `confidence_ellipse`, which is called from `make_pca_plots` and `umap_and_heatmap`. Example plots are all live in the notebooks as can be viewed directly from GitHub.

      (3) In histology images (Figure 1B and 3K), the authors need to add dashed lines or arrows to guide the reader's attention.

      Dashed lines have been added to these figure panels as requested.

      (4) In Figure 2A and G, apparently there are significant differences in other brain regions such as NAcMed or PBN. If they are also statistically significant, the authors should note them as well and draw asterisks(*).

      We appreciate the care in ensuring that statistics are being applied and shown appropriately. In panel A (now Figure 3A), the Two-way ANOVA interaction term was not significant (p = 0.9365), we did not find it justified to do further comparisons. However, for Figure 3G, the interaction term was significant (p = 0.0001), and thus further pairwise comparisons were performed with Sidak's correction for multiple comparisons. When done, the only two brain regions that were significantly different were the DStr (p = 0.0051) and GPe (p = 0.0036). While the NAcMed and PBN visually look different, according to the corrected statistics, they were not significantly different (NAcMed p = 0.5037, PBN p = 0.8123). The notations in our original figure thus accurately reflected these statistics.

      (5) In Figure 2N about the spatial distribution of starter cells, the authors need to add histology images for each experimental condition (i.e. saline, fluoxetine, cocaine, methamphetamine, amphetamine, nicotine, and morphine) as supplement figures

      We have now provided these as Figure S2.

      (6) In the manuscript, it is necessary to explain why Cacna1e was selected among other calcium ion channels.

      We have added a sentence to the "Functional validation of link between gene expression and RABV labeling" section (lines 722-724).

      Reviewer #2 (Public review):

      The application of rabies virus (RabV)-mediated transsynaptic tracing has been widely utilized for mapping celltype-specific neural connectivities and examining potential modifications in response to biological phenomena or pharmacological interventions. Despite the predominant focus of studies on quantifying and analyzing labeling patterns within individual brain regions based on labeling abundance, such an approach may inadvertently overlook systemic alterations. There exists a considerable opportunity to integrate RabV tracing data with the global connectivity patterns and the transcriptomic signatures of labeled brain regions. In the present study, the authors take an important step towards achieving these objectives. Specifically, the authors conducted an intensive reanalysis of a previously generated large dataset of RabV tracing to the ventral tegmental area (VTA) using dimension reduction methods such as PCA and UMPA. This reaffirmed the authors' earlier conclusion that different cell types in the VTA, namely dopamine neurons (DA) and GABAergic neurons, exhibit quantitatively distinct input patterns, and a single dose of addictive drugs, such as cocaine and morphine, induced altered labeling patterns. Additionally, the authors illustrate that distinct axes of PCA can discriminate experimental variations, such as minor differences in the injection site of viral tracers, from bona fide alternations in labeling patterns caused by drugs of abuse. While the specific mechanisms underlying altered labeling in most brain regions remain unclear, whether involving synaptic strength, synaptic numbers, pre-synaptic activities, or other factors, the present study underscores the efficacy of an informatics approach in extracting more comprehensive information from the RabV-based circuit mapping data. Moreover, the authors showcased the utility of their previously devised bulk gene expression patterns inferred by the Allen Gene Expression Atlas (AGEA) and "projection portrait" derived from bulk axon mapping data sourced from the Allen Mouse Brain Connectivity Atlas. The utilization of such bulk data rests upon several limitations. For instance, the collection of axon mapping data involves an arbitrary selection of both cell type-specific and non-specific data, which might overlook crucial presynaptic partners, and often includes contamination from neighboring undesired brain regions. Concerns arise regarding the quantitativeness of AGEA, which may also include the potential oversight of key presynaptic partners. Nevertheless, the authors conscientiously acknowledged these potential limitations associated with the dataset. Notably, building on the observation of a positive correlation between the basal expression levels of Ca2+ channels and the extent of drug-induced changes in RabV labeling patterns, the authors conducted a CRISPRi-based knockdown of a single Ca2+ channel gene. This intervention resulted in a reduction of RabV labeling, supporting that the observed gene expression patterns have causality in RabV labeling efficiency. While a more nuanced discussion is necessary for interpreting this result (see below), overall I commend the authors for their efforts to leverage the existing dataset in a more meaningful way. This endeavor has the potential to contribute significantly to our understanding of the mechanisms underlying alterations in RabV labeling induced by drugs of abuse. Finally, drawing upon the aforementioned reanalysis of previous data, the authors underscored that a single administration of ketamine/xylazine anesthesia could induce enduring modifications in RabV labeling patterns for VTA DA neurons, specifically those projecting to the nucleus accumbens and amygdala. Given the potential impact of such alterations on motivational behaviors at a broader level, I fully agree that prudent consideration is warranted when employing ketamine/xylazine for the investigation of motivational behaviors in mice.

      Specific Points:

      (1) Beyond advancements in bioinformatics, readers may find it insightful to explore whether the PCA/UMPAbased approach yields novel biological insights. For example, the authors are encouraged to discuss more functional implications of PBN and LH in the context of drugs of abuse, as their labeling abundance could elucidate the PC2 axis in Fig. 2M.

      Thank you for this suggestion: we added text (Lines 787-795) discussing the LH and PBN (and GPe) specifically, but also highlighted the importance of our approach in hypothesis-generating science.

      (2) While I appreciate the experimental data on Cacna1e knockdown, I am unclear about the rationale behind specifically focusing on Cacna1e. The logic behind the statement, "This means that expression of this gene is not inhibitory towards RABV transmission," is also unclear. Loss-of-function experiments only signify the necessity or permissive functions of a gene. In this context, Cacna1e expression levels are required for efficient RabV labeling, but this neither supports nor excludes the possibility that this gene expression instructively suppresses RabV labeling/transmission, which could be assessed through gain-of-function experiments.

      We thank the reviewer for their suggestions regarding this result, and agree that a gain-of-function would be required to provide clearer evidence on this point.  We therefore understand that our original phrasing may be misleading. Thus, we have edited this section to the more conservative statement: “These results indicate that reduced levels of Cacna1e likely lower the number of RABV-labeled inputs from the NAcLat, and directly link the levels of Cacna1e and RABV input labeling” (lines 742-744) - we refrain from over-interpreting the results. As mentioned above in response to R1, we added a sentence to explain the rationale behind focusing on Cacna1e (lines 722-724).

      Reviewer #3 (Public Review):

      Summary:

      Authors mapped monosynaptic inputs to dopamine, GABA, and glutamate neurons in VTA under different anesthesia methods, and under drugs (cocaine, morphine, methamphetamine, amphetamine, nicotine, fluoxetine). They found that input patterns under different conditions are separated, and identified some key brain areas to contribute to such separation. They also searched a database for gene expression patterns that are common across input brain areas with some changes by anesthesia or drug administration.

      Strengths:

      The whole-brain approach to address drug effects is appealing and their conclusion is clear. The methodology and motivation are clearly explained.

      Weaknesses:

      While gene expression analyses may not be related to their findings on the anatomical effects of drugs, this will be a nice starting point for follow-up studies. 

      We understand and agree with the suggestion that gene expression allows us to provide correlative observations between in situ hybridization datasets and rabies mapping datasets, and that these results do not show causality. As such, future studies would be needed to assess this in more detail. We have added a line in the discussion to this effect (lines 851-853).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Recommendations for improving the writing and presentation:

      (1) There are a couple of packages available for 3D whole-brain reconstructions based on Allen Brain Atlas (eg. https://github.com/tractatus/wholebrain, https://github.com/lahammond/BrainJ), which would be helpful to align with the gene expression or other data from Allen Institute.

      This comment is related to the noted weakness we responded to previously in this rebuttal also from R1 (see comment 1), about the discrepancies between the Franklin-Paxinos atlas and Allen Brain atlas. We agree that a systematic comparison of these two atlases using a tool like wholebrain or BrainJ would be valuable for the field. However, it would be a substantial amount of work, and likely would be an independent study in itself. We believe that the resolution of these atlases was sufficient to make our key conclusions here (e.g., identify gene expression patterns that relate to drug-induced changes rabies virus labeling patterns, and develop a testable hypothesis for CRISPR-based gene editing). They are also based on the same atlases and region definitions that have been applied in our previous studies (e.g., Beier et al., Cell 2015; Beier et al., Nature 2017; Beier et al., Cell Reports 2019; Tian et al., Cell Reports 2022; Tian et al., Neuron 2024; Hubbard et al., Neuropsychophamacology 2025, etc.)  The expression of Cacna1e is relatively consistent across the NAc, as we have now detailed in Figure S13.

      (2) There are so far two kinds of rabies virus strains available in the neuroscience field (SAD-B19 or CVS-N2c). It is recommended to describe which strain was used in the Material and Methods Section because labeling efficiency and toxicity is quite different between the strains (Reardon TR et al., Neuron 2016).

      We have now noted that we used SAD B19 for all experiments (Lines 141-142).

      Minor corrections to the text and figures:

      (1)  In Figure 1A, the color differences are not clear (i.e. light gray and dark gray). The figure can be simplified.

      In addition, generally, images/figures are recommended not to be overlapped with other figures/images (Figures 2A-F, 2G-L).

      (2)  In Figures 7C and D, the authors could add enlarged views of starter cells in VTA and NAcLat.

      We have attempted to simplify schematics and figures throughout. High-magnification images of cells have been added as insets in what is now Figure 10 (formerly Figure 7).

      Reviewer #2 (Recommendations For the authors):

      The number of animals for each graph should be explicated within the figure legend. For example, Figure 1C and Figure 7E lack this information. It is also advisable to delineate the definition of error bars within the figure legend.

      We have now added mouse numbers to all figures and/or legends, as appropriate. We also indicated in the legend at the end of Figure 1 how error bars and asterisks are defined. Furthermore, we added a sentence to the methods saying that in UMAP and PCA plots each dot is an animal (lines 244-245).

      The visual representations, particularly in Figures 1 and 3, are overcrowding. Furthermore, the arrangement of figure subpanels does not consistently adhere to the sequence of explication in the main text, significantly compromising the readability of the text. The authors are encouraged to consider the possibility of segmenting dense figures into two if there exists no upper limit for the number of figure displays. To illustrate, in Figure 3Q, crucial details about experimental conditions are denoted by numerical references, owing to spatial constraints.

      We agree that the figure layout and mis-alignment with a linear read of the text was unideal. Therefore, we broke our figures, especially the original Figures 1-4, into multiple sub-figures, including both main and supplemental figures. This facilitated the use of space to rearrange the figure panels, allowing the story to be told in a linear fashion. All figures and panels should now be read in order.

      I am seeking clarification on how to interpret the term "overlap" at the bottom of figures illustrating Gene Ontology analysis.

      We have clarified the meaning of overlap in this context (lines 324-325): The ‘overlap’ term on the x-axis of these plots means the number of genes in the correlated gene lists that were also within the list of genes for the corresponding GO term.

      The authors could provide Cacna1e gene expression patterns within the NAc from the AGEA data.

      Cacna1e expression data are now provided in Figure S13.

      Additionally, the meaning of "controls" in Figure 7F, along with the "No gRNA" condition, remains ambiguous. While the text mentions "no shRNA", the involvement of shRNA in this experiment lacks clarity.

      We now clarify that the control conditions are based on previously published data where no AAVs were injected into NAcLat. This is now clarified in the legend for Figure 10F (lines 1277-1578). We also corrected “shRNA” to “gRNA” in the text.

    1. Author response:

      The following is the authors’ response to the original reviews

      We appreciate the reviewers’ insightful comments. In response, we conducted three new experiments, summarized in Author response table 1. After the table, we provide detailed responses to each comment.

      Author response table 1.

      Summary of new experiments and results.

      Reviewer #1 (Public review):

      The authors show that corticotropin-releasing factor (CRF) neurons in the central amygdala (CeA) and bed nucleus of the stria terminalis (BNST) monosynaptically target cholinergic interneurons (CINs) in the dorsal striatum of rodents. Functionally, activation of CRFR1 receptors increases CIN firing rate, and this modulation was reduced by pre-exposure to ethanol. This is an interesting finding, with potential significance for alcohol use disorders, but some conclusions could use additional support.

      Strengths:

      Well-conceived circuit mapping experiments identify a novel pathway by which the CeA and BNST can modulate dorsal striatal function by controlling cholinergic tone. Important insight into how CRF, a neuropeptide that is important in mediating aspects of stress, affective/motivational processes, and drug-seeking, modulates dorsal striatal function.

      Weaknesses:

      (1) Tracing and expression experiments were performed both in mice and rats (in a mostly nonoverlapping way). While these species are similar in many ways, some conclusions are based on assumptions of similarities that the presented data do not directly show. In most cases, this should be addressed in the text (but see point number 2).

      In the revised manuscript, we have clarified this limitation in the first paragraph of the Methods and the third paragraph of the Discussion and avoid cross-species claims, limiting our conclusions to the species in which each assay was performed. Specifically, we now state that while mice and rats share many conserved amygdalostriatal components, our tracing and expression studies were performed in a species-specific manner, and direct cross-species comparisons of CRF–CIN connectivity and CRFR1 expression were not assessed. We further note that future studies will be needed to determine the extent to which these observations are conserved across species as more tools become available.

      (2) Experiments in rats show that CRFR1 expression is largely confined to a subpopulation of striatal CINs. Is this true in mice, too? Since most electrophysiological experiments are done in various synaptic antagonists and/or TTX, it does not affect the interpretation of those data, but non-CIN expression of CRFR1 could potentially have a large impact on bath CRF-induced acetylcholine release.

      To address whether CRFR1 expression in striatal CINs is conserved across species, we performed new histological experiments using CRFR1-GFP mice. Striatal sections were immunostained with anti-ChAT, and we found that approximately 10% of CINs express CRFR1 (new Fig. 4D, 4E). This result indicates that, similar to rats, a subset of CINs in mice express CRFR1. However, the proportion of CRFR1<sup>+</sup> CINs is lower than the proportion of CRF-responsive CINs observed during electrophysiology experiments, suggesting that CRF may also modulate CIN activity indirectly through network or synaptic mechanisms. We have also noted in the revised Discussion that while CRFR1 expression is confirmed in a subset of CINs, the broader distribution of CRFR1 among other striatal cell types remains to be determined (third paragraph of Discussion).

      In our study, bath application of CRF increased striatal ACh release. Because striatal ACh is released primarily from CINs, and CRFR1 is an excitatory receptor, this effect is most likely mediated by CRF activation of CRFR1 on CINs, leading to enhanced CIN activity and ACh release. Although CRFR1 may also be expressed on other striatal neurons, these cell types—medium spiny neurons and GABAergic interneurons—are inhibitory. If CRF were to activate CRFR1 on these GABAergic neurons, the resulting increase in GABA release would suppress CIN activity and consequently reduce, rather than enhance, ACh release. Given that most CINs responded functionally while only a small subset expressed CRFR1, these findings imply that indirect mechanisms, such as CRF modulation of local circuits influencing CIN excitability, may also contribute to the observed increase in ACh release. Together, these data support a model in which CRF primarily enhances ACh release via activation of CRFR1-expressing CINs, while indirect network effects may further amplify this response.

      (3) Experiments in rats show that about 30% of CINs express CRFR1 in rats. Did only a similar percentage of CINs in mice respond to bath application of CRF? The effect sizes and error bars in Figure 5 imply that the majority of recorded CINs likely responded. Were exclusion criteria used in these experiments?

      We thank the reviewer for this insightful question. In our mouse cell-attached recordings, ~80% of CINs increased firing during CRF bath application, and all recorded cells were included in the analysis (no exclusions based on response direction/magnitude; cells were only required to meet standard recording-quality criteria such as stable baseline firing and seal).

      Using a CRFR1-GFP reporter mouse, we found that ~10% of striatal CINs are GFP+, suggesting that the high proportion of CRF-responsive CINs cannot be explained solely by somatic reporter-labeled CRFR1 expression. Importantly, the CRF-induced increase in CIN firing is blocked by the selective CRFR1 antagonist NBI 35695 (Fig. 5B–C), supporting a CRFR1-dependent mechanism at the circuit level. We now discuss several non-mutually exclusive explanations for this apparent discrepancy: (i) reporter lines (e.g., CRFR1-GFP) may underestimate functional CRFR1 expression, particularly for low-level or compartmentalized receptor pools; (ii) bath-applied CRF may act indirectly via CRFR1 on presynaptic afferents, thereby enhancing excitatory drive onto CINs; and (iii) electrical coupling among CINs could allow direct effects in a subset of CINs to propagate through the CIN network (Ren, Liu et al. 2021). We added this discussion to the revised manuscript (fourth paragraph of the Discussion).

      (4) The conclusion that prior acute alcohol exposure reduces the ability of subsequent alcohol exposure to suppress CIN activity in the presence of CRF may be a bit overstated. In Figure 6D (no ethanol preexposure), ethanol does not fully suppress CIN firing rate to baseline after CRF exposure. The attenuated effect of CRF on CIN firing rate after ethanol pre-treatment (6E) may just reduce the maximum potential effect that ethanol can have on firing rate after CRF, due to a lowered starting point. It is possible that the lack of significant effect of ethanol after CRF in pre-treated mice is an issue of experimental sensitivity. Related to this point, does pre-treatment with ethanol reduce the later CIN response to acute ethanol application (in the absence of CRF)?

      In the revised manuscript, we have tempered our interpretation in the final Results section and throughout the Discussion to emphasize that ethanol pre-exposure attenuates, rather than abolishes, the CRFinduced increase in CIN firing. We also note the reviewer’s important point that in Figure 6D, ethanol does not fully suppress firing to baseline after CRF exposure, consistent with a partial effect. Regarding the reviewer’s question, our experiments were specifically designed to test interactions between CRF and ethanol, so we did not assess whether ethanol pre-treatment alters subsequent responses to ethanol alone. We now explicitly acknowledge CRF-dependent and CRF-independent effects of ethanol on CIN activity as an important point for future studies to disentangle (sixth paragraph of the Discussion). For example, comparing ethanol responses with and without prior ethanol without any treatment with CRF could resolve this question.

      (5) More details about the area of the dorsal striatum being examined would be helpful (i.e., a-p axis).

      We now provide more detail regarding the anterior–posterior axis of the dorsal striatum examined. Most recordings and imaging were performed in the posterior dorsomedial striatum (pDMS), corresponding to coronal slices posterior to the crossing of the anterior commissure and anterior to the tail of the striatum (starting around 0.62 mm and ending at −1.3 mm relative to the Bregma). While our primary focus was on posterior slices, some anterior slices were included to increase the sample size. These details have been added to the Methods (Last sentence of the ‘Histology and cell counting’ section and of the ‘Slice electrophysiology’ section).

      Reviewer #2 (Public review):

      Essoh and colleagues present a thorough and elegant study identifying the central amygdala and BNST as key sources of CRF input to the dorsal striatum. Using monosynaptic rabies tracing and electrophysiology, they show direct connections to cholinergic interneurons. The study builds on previous findings that CRF increases CIN firing, extending them by measuring acetylcholine levels in slices and applying optogenetic stimulation of CRF+ fibers. It also uncovers a novel interaction between alcohol and CRF signaling in the striatum, likely to spark significant interest and future research.

      Strengths:

      A key strength is the integration of anatomical and functional approaches to demonstrate these projections and assess their impact on target cells, striatal cholinergic interneurons.

      Weaknesses:

      (1) The nature of the interaction between alcohol and CRF actions on cholinergic neurons remains unclear. Also, further clarification of the ACh sensor used and others is required

      We have clarified the nature of the interaction between alcohol and CRF signaling in CINs and have provided additional details regarding the acetylcholine sensor used. These issues are addressed in detail in our responses to the specific comments below.

      Reviewer #2 (Recommendations for the authors):

      (1) The interaction between the effects of alcohol and CRF is a novel and important part of this study. When considering possible mechanisms underlying the findings in the discussion, there is no mention of occlusion. Given that incubation with alcohol produced a similar increase in firing of CINs as CRF, occlusion could be a parsimonious explanation for the observed interaction. Have the author considered blocking the effects of alcohol on CIN with CRF-R1 antagonist? Another experiment that could address the occlusion would be to test if alcohol also increases ACh levels as it did CRF.

      We thank the reviewer for proposing occlusion as a potential mechanism underlying the interaction between alcohol and CRF. We agree that, in principle, alcohol-induced endogenous CRF release could occlude subsequent exogenous CRF-mediated potentiation of CIN firing, and we carefully considered this possibility.

      However, several observations from our data argue against occlusion driven by acute alcohol exposure or withdrawal in this preparation. First, as shown in Fig. 6A, bath application of alcohol transiently reduced CIN firing, and firing recovered to baseline levels after washout without any rebound increase. Second, in Fig. 6D–E, the baseline firing rates under control conditions and following alcohol pretreatment were comparable, indicating that acute alcohol exposure and short-term withdrawal did not produce a sustained increase in CIN excitability. Together, these results suggest that acute withdrawal in slices is less likely to trigger substantial endogenous CRF release capable of occluding subsequent exogenous CRF effects.

      While we and others have previously reported increased spontaneous CIN firing following prolonged in vivo alcohol exposure and extended withdrawal periods (e.g., 21 days), short-term withdrawal (e.g., 1 day) does not robustly alter baseline CIN firing (Ma, Huang et al. 2021, Huang, Chen et al. 2024). Consistent with these prior findings, the absence of a rebound or elevated baseline firing in the present slice experiments discouraged further pursuit of an endogenous CRF occlusion mechanism under acute conditions.

      We also considered experimentally testing occlusion by blocking CRFR1 signaling during alcohol pre-treatment. However, this approach is technically challenging in slice recordings, as CRFR1 antagonists require prolonged incubation (~1 hour) during alcohol exposure. Because it is unclear whether endogenous CRF release is triggered by alcohol incubation itself or by withdrawal, the antagonist would need to remain present throughout both the incubation and withdrawal periods. This leaves insufficient time for complete washout of the CRFR1 antagonist prior to subsequent bath application of exogenous CRF to assess its effects on CIN firing. Consequently, residual antagonist presence would confound the interpretation of the exogenous CRF response.

      Finally, regarding the possibility that alcohol increases acetylcholine release, we did not observe alcohol-induced increases in CIN firing in slices, arguing against elevated ACh signaling under these conditions. Consistent with prior work (Ma, Huang et al. 2021, Huang, Chen et al. 2024), alcohol-induced increases in CIN excitability and cholinergic signaling appear to depend on prolonged in vivo exposure and extended withdrawal rather than acute slice-level manipulations.

      We have now incorporated discussion of occlusion as a potential mechanism (seventh paragraph) and clarified why our data and technical considerations argue against it in the present study. We thank the reviewer for this wonderful suggestion, which we will test in future in vivo studies.

      (2) Retrograde monosynaptic tracing of inputs to CIN. Results state the finding of labeling in all previously reported area..." Can the authors report these areas? A list in the text or a bar plot, if there is quantification, will suffice. This formation will serve as important validation and replication of previous findings.

      We thank the reviewer for this constructive suggestion. We agree that summarizing the anatomical sources of CIN input provides important validation of our tracing results. In the revised Results, we now list the major input regions observed, including the striatum itself, cortex (e.g., cingulate cortex, motor cortex, somatosensory cortex), thalamus (e.g., parafascicular thalamic nucleus, centrolateral thalamic nucleus), globus pallidus, and midbrain (first paragraph of the Results). Quantitative analysis of relative input strength will be presented in a separate study that expands on these findings. Here, we limit the current manuscript to the functional characterization of CRF and alcohol modulation of CINs.

      (3) Given the difference in connectivity among striatal subregions, it would be important to describe in more detail the injection site in the results and figures. In the figure, for example, you might want to include the AP coordinates, given that it is such a zoomed-in image, it is hard to tell how anterior/posterior the site is. I imagine that the picture is a representative image of the injection site, but maybe having a side image with overlay of injection sites in all the animals used, would help.

      The anterior–posterior (AP) coordinates for representative images have been included in the panels and reiterated more clearly in the revised Results section and figure legends. In the legend for Figure 3B, a list of AP coordinates for each animal used for Figure 3A-3E has been added.

      (4) Figure 1D inset, there seem to be some double-labeled cells in the zoomed in BNST images. The authors might want to comment on this. It seemed far from the injection site. Do D1-MSN so far away show connectivity to CINs?

      Upon closer inspection of the BNST images, we noted a small number of double-labeled cells were indeed present, consistent with prior reports that a subset of D1R-expressing neurons (~10%) has been reported previously in our lab in the BNST, with the majority being D2R-expressing neurons (Lu, Cheng et al. 2021). Given the BNST’s anatomical proximity to the dorsal striatum, it is plausible that some D1Rexpressing neurons in this region provide monosynaptic input to CINs, highlighting a potential ventral-to-dorsal connection that merits further study.

      (5) Can the author provide quantification of the onset delay of the optogenetic evoked CRF+ axon responses onto CINs? The claim of monosynaptic connectivity is well supported by the TTX/4AP experiment but additional information on the timing will strengthen that conclusion.

      We thank the reviewer for this insightful suggestion. Quantifying the onset latency of optogenetically evoked CRFMsup+</sup> axon responses onto CINs provides valuable confirmation of monosynaptic connectivity. To address this, we performed new latency measurements under the same recording conditions as the TTX/4-AP experiments. The average onset latency from the start of the optical stimulation was 5.85 ± 0.37 ms (new Figure 3J), consistent with direct monosynaptic transmission.

      As an additional reference, we analyzed latency data from a separate project in which we optogenetically stimulated cholinergic interneurons and recorded synaptic responses in medium spiny neurons. This circuit, known to involve disynaptic transmission from CINs to MSNs via nAChR-expressing interneurons (Autor response image 1) (English, Ibanez-Sandoval et al. 2011), exhibited a significantly longer latency (18.34 ± 0.70 ms; t<sub>(29)</sub> = 10.3, p < 0.001) compared to CRF⁺ CeA/BNST inputs to CINs (5.85 ± 0.37 ms). Together, these results further support that CRF⁺ axons form direct functional synapses onto CINs.

      Author response image 1.

      Latency of disynaptic transmission from CINs to MSNs via interneurons A) Schematic illustrating optogenetic stimulation of Chrimson-expressing CINs, leading to excitation of nAChRexpressing interneurons that release GABA onto recorded MSNs. B) Sample trace of disynaptic transmission (left) and bar graph summarizing onset latency (right) from light stimulation to synaptic response onset (n = 23 neurons from 3 mice).

      (6) The ACh sensor reported is "AAV-GRABACh4m" but the reference is for GRAB-ACh3.0. Also, BrainVTA has GRAB-ACh4.3. Is this the vector? Could you please check the name of the construct and report the corresponding reference, as well as clarify the meaning of the additional "m". They have a mutant version of the GRAB-ACH that researchers use for control, and of course, you want to use it as a control, but not for the test experiment.

      GRAB-ACh4m is the correct acetylcholine sensor used in this study. The ACh4 series (including ACh4h, ACh4m, and ACh4l; personal communication with Dr. Yulong Li’s lab) represents an updated generation following GRAB-ACh3.0. Although the ACh4 family has not yet been formally published, these constructs are publicly available through BrainVTA (https://www.brainvta.tech/plus/view.php?aid=2680).

      The suffix “m” does not indicate a mutant control; rather, it denotes a medium-affinity variant within the ACh4 sensor family. Importantly, the mutant (non-responsive) control sensor is only available for GRAB-ACh3.0 (ACh3.0mut) and does not exist for the ACh4 series.

      Our laboratory has previously used GRAB-ACh4m in multiple peer-reviewed publications (Huang, Chen et al. 2024, Gangal, Iannucci et al. 2025, Purvines, Gangal et al. 2025), and its use has also been reported by independent groups in recent preprints (Potjer, Wu et al. 2025, Touponse, Pomrenze et al. 2025). We have now clarified the construct name, its relationship to GRAB-ACh3.0, in the Methods ‘Reagents’ section, and we have corrected the reference accordingly.

      (7) Are CRF-R1+ CINs equally abundant in the DMS and DLS? From the image in Figure 4, it seems that a larger percentage of CINs are CRFR1+ in the DLS than in DMS. Is this true? The authors probably already have this data, or it should be easy to get, and it could be additional information that was not studied before.

      We did not perform a quantitative comparison of CRFR1+ CIN abundance between the DMS and DLS in the present study. While the representative images in Figure 4 may appear to suggest regional differences, these panels were selected to illustrate labeling quality rather than relative density and should not be interpreted as evidence of unequal distribution. We have clarified this point in the revised Discussion (last sentence of the third paragraph) and note that future studies will be needed to systematically evaluate potential regional differences in CRFR1 expression, which could have important implications for dorsal striatal function.

      (8) The manuscript states several times that there are no CRF+ neurons in the dorsal striatum. At the same time, there are reports of the CRF+ neuron in the ventral striatum and its role in learning. Could the authors include mention of the studies by the Lemos group (10.1016/j.biopsych.2024.08.006)

      We have revised the Discussion section to clarify that our findings pertain specifically to the dorsal striatum and now acknowledge the presence and functional relevance of CRF+ neurons in the ventral striatum, citing the Lemos group’s study (fifth paragraph of the Discussion).

      (9) For the histology analysis, please express cell counts as "density", not just number of cells, by providing an area (e.g., "number of cell/ µm2").

      In the revised manuscript, all histological outcomes have been recalculated as cell density (cells/mm<sup>2</sup>) by normalizing raw cell counts to the measured area of each region of interest (ROI). Figures that previously displayed absolute counts now present densities (cells/mm<sup>2</sup>), with corresponding updates made to figure legends and text. We note one exception in Figure 4B, where the comparison between the total number of CINs and CRFR1+ CINs is best represented as cell counts rather than normalized values, as the counting was conducted in the same area (within the same ROI) of the dorsostriatal subregion.

      (10) Figure 2C, we can see there are some labeled fibers in the striatum cut. Would it be possible to get a better confocal image?

      Figure 2C has been replaced with a higher-quality confocal image captured at the same magnification and scale. The updated image provides improved clarity and resolution, ensuring accurate visualization of labeled CRF+ fibers, but not cell bodies, within the striatum.

      (11) The ACh measurements in the slice are very informative and an important addition. I first thought that these experiments with the GRAB-ACh sensor were performed in ChAT-eGFP mice. After reading more carefully, I realized they were done in wild-type mice. Would you include the wildtype label in the figure as well? The ChATeGFP BAC transgenic line was reported to have enhanced ACh packaging and increased ACh release, which could have magnified the signals. So, it is important to highlight the experiments were done in wildtype mice.

      We now label with ‘WT mice’ and note in the legend that all GRAB-ACh experiments were performed in wild-type mice, not ChAT-eGFP, to avoid confounds in ACh release. We thank the reviewer for this important suggestion.

      Reviewer #3 (Public review):

      The authors demonstrate that CRF neurons in the extended amygdala form GABAergic synapses onto cholinergic interneurons and that CRF can excite these neurons. The evidence is strong, however, the authors fail to make a compelling connection showing CRF released from these extended amygdala neurons is mediating any of these effects. Further, they show that acute alcohol appears to modulate this action, although the effect size is not particularly robust.

      Strengths:

      This is an exciting connection from the extended amygdala to the striatum that provides a new direction for how these regions can modulate behavior. The work is rigorous and well done.

      Weaknesses:

      (1) While the authors show that opto stim of these neurons can increase firing, this is not shown to be CRFR1 dependent. In addition, the effects of acute ethanol are not particularly robust or rigorously evaluated. Further, the opto stim experiments are conducted in an Ai32 mouse, so it is impossible to determine if that is from CEA and BNST, vs. another population of CRF-containing neurons. This is an important caveat.

      We added recordings with the CRFR1 antagonist antalarmin. Light-evoked increases in CIN firing were abolished under CRFR1 blockade, linking the effect to CRFR1 (Figure 5J, 5K). We also clarify that CRFCre;Ai32 does not isolate CeA versus BNST sources, so we temper regional claims and highlight this as a limitation. The acute ethanol effects are modest but consistent; we expanded the discussion of dose and preparation constraints in acute slice physiology and note that in vivo studies will be needed to define the network-level impact.

      Reviewer #3 (Recommendations for the authors):

      (1) The authors could bring some of this data together by examining CRFR1 dependence of optical stimulationinduced increases in firing. Further, the authors have devoted significant effort to exploring how the BNST and CEA project to the CIN, yet their ephys does not explore site-specific infusion of ChR2 into either region. How are we to be sure it is not some other population of CRF neurons mediating this effect? The alcohol data does not appear particularly robust, but I think if the authors wanted to, they could explore other concentrations. Mostly I think it is important to discuss the limitations of acute alcohol on 5a brain slice.

      We thank the reviewer for these thoughtful comments, which helped us strengthen the mechanistic interpretation of the CRF-CIN interaction. In the revised manuscript, we have addressed each point as follows:

      - CRFR1 dependence of optogenetically evoked responses: We performed new recordings in which optogenetic stimulation of CRF⁺ terminals in the dorsal striatum was conducted in the presence of the CRFR1 antagonist antalarmin. The increase in CIN firing evoked by light stimulation was abolished under CRFR1 blockade, confirming that this effect is mediated through CRFR1 activation (new Figure 5J, 5K, third paragraph of the corresponding Result section). These results directly link the functional effects of CRF⁺ terminal activation to CRFR1 signaling on CINs.

      - CeA vs. BNST projection specificity: The reviewer is correct that CeA and BNST projections were not analyzed separately. As unknown pathways, our experiment was designed to first establish the monosynaptic connections between CeA/BNST CRF neurons to striatal CINs. Future studies would further explore the specific contribution of each site. However, our data exclude the possibility of other CRF neurons as we selectively infused Cre-dependent opsins into both CeA and BNST of CRF-Cre mice (Figure 3G-3J).

      - Limitations of acute slice experiments: We have expanded the Discussion (sixth paragraph) to acknowledge that acute slice physiology cannot fully capture the dynamic and network-level effects of ethanol observed in vivo. While this preparation enables mechanistic precision, factors such as washout, diffusion constraints, and the absence of systemic feedback may underestimate ethanol’s impact on CINs. We now explicitly note this limitation and highlight the need for in vivo studies to examine behavioral and circuit-level implications of CRF–alcohol interactions.

      Collectively, these revisions clarify the CRFR1 dependence of CRF<sup>+</sup> terminal effects and reaffirm that both CeA and BNST projections contribute to CIN modulation while addressing the methodological limitations of the slice preparation.

      Reviewer #4 Public Review):

      This manuscript presents a compelling and methodologically rigorous investigation into how corticotropin-releasing factor (CRF) modulates cholinergic interneurons (CINs) in the dorsal striatum - a brain region central to cognitive flexibility and action selection-and how this circuit is disrupted by alcohol exposure. Through an integrated series of anatomical, optogenetic, electrophysiological, and imaging experiments, the authors uncover a previously uncharacterized CRF⁺ projection from the central amygdala (CeA) and bed nucleus of the stria terminalis (BNST) to dorsal striatal CINs.

      Strengths:

      Key strengths of the study include the use of state-of-the-art monosynaptic rabies tracing, CRF-Cre transgenic models, CRFR1 reporter lines, and functional validation of synaptic connectivity and neurotransmitter release. The finding that CRF enhances CIN excitability and acetylcholine (ACh) release via CRFR1, and that this effect is attenuated by acute alcohol exposure and withdrawal, provides important mechanistic insight into how stress and alcohol interact to impair striatal function. These results position CRF signaling in CINs as a novel contributor to alcohol use disorder (AUD) pathophysiology, with implications for relapse vulnerability and cognitive inflexibility associated with chronic alcohol intake. The study is well-structured, with a clear rationale, thorough methodology, and logical progression of results. The discussion effectively contextualizes the findings within broader addiction neuroscience literature and suggests meaningful future directions, including therapeutic targeting of CRFR1 signaling in the dorsal striatum.

      Weaknesses:

      (1) Minor areas for improvement include occasional redundancy in phrasing, slightly overlong descriptions in the abstract and significance sections, and a need for more concise language in some places. Nevertheless, these do not detract from the manuscript's overall quality or impact. Overall, this is a highly valuable contribution to the fields of addiction neuroscience and striatal circuit function, offering novel insights into stress-alcohol interactions at the cellular and circuit level, which requires minor editorial revisions.

      We have streamlined the abstract and significance statement, reduced redundancy, and improved conciseness throughout the text. We appreciate the reviewer’s feedback, which has helped us further strengthen the clarity and readability of the manuscript.

      Reviewer #4 (Recommendations for the authors):

      (1) Line 29-30: Slightly verbose. Consider: "Alcohol relapse is associated with corticotropin-releasing factor (CRF) signaling and altered reward pathway function, though the precise mechanisms are unclear."

      The sentence has been revised as recommended to improve clarity and conciseness in the introductory section (Lines 31-32).

      (2) Lines 39-43: Good synthesis, but could better emphasize the novelty of identifying a CRF-CIN pathway.

      The abstract has been revised to more clearly emphasize the novelty of identifying a CRF-CIN pathway and its functional significance (Line 42-43).

      (3) Lines 66-68: Consider integrating clinical relevance more directly, e.g., "AUD affects over 14 million adults in the U.S., with relapse often triggered by stress...".

      The introduction has been revised to more directly emphasize the clinical relevance of alcohol use disorder, including its high prevalence and the role of stress in relapse, thereby underscoring the translational significance of our findings (Lines 68-69).

      (4) Line 83: Repetition of "goal-directed learning, habit formation, and behavioral flexibility" appears multiple times; consider variety.

      We have varied the phrasing in the Introduction to avoid redundancy. Specifically, in place of repeating “goal-directed learning, habit formation, and behavioral flexibility,” we now use alternative terms such as “action selection,” “habitual responding,” and “cognitive flexibility,” depending on the context.

      (5) Lines 107-116: Clarify why both rats and mice were used-do they serve different experimental purposes?

      We now explain that each species was used for complementary experimental purposes. Rats were used for histological validation of CRFR1 expression using the CRFR1-Cre-tdTomato line, which has been extensively characterized in this species. Mice were used for the majority of electrophysiological, optogenetic, and GRAB-ACh sensor experiments due to the availability of well-established transgenic CRF-Cre-driver lines. This division allowed us to leverage the most appropriate tools in each species to address different aspects of the study. We have clarified this rationale in the Methods (first paragraph of the “Animals” section) and Discussion (third paragraph).

      (6) Electrophysiology section: The distinction between acute exposure vs. withdrawal could be further emphasized.

      To better highlight the distinction between acute alcohol exposure and withdrawal, we have clarified the timing and context of each condition within the Results section for Figure 6. Specifically, we now distinguish the immediate suppressive effects of alcohol observed during bath application (acute exposure) from the subsequent changes in CIN firing measured after washout (withdrawal). These revisions clarify the temporal dynamics and functional implications of CRF–alcohol interactions in our experimental design.

      (7) Lines 227-229: Reword for clarity: "Significantly more BNST neurons projected to CINs compared to the CeA...".

      The sentence has been reworded to clarify as recommended (Lines 247-248).

      (8) Lines 373-374: Consider connecting the CRF-CIN circuit to behavioral inflexibility in AUD more directly.

      We have modified the sentence (Lines 390-395) to more explicitly link alcohol-induced dysregulation of the CRF–CIN circuit to behavioral inflexibility in AUD, consistent with the established role of CINs in action selection and cognitive flexibility.

      (9) Lines 387-389: This is an excellent point about stress resilience; consider expanding with examples or potential implications.

      We thank the reviewer for this insightful suggestion. In the revised Discussion (sixth paragraph), we expanded this section to more directly connect alcohol-induced disruption of CRF–CIN signaling with impaired stress resilience and behavioral inflexibility. Specifically, we now note that such dysregulation may compromise stress resilience mechanisms mediated by CRF–cholinergic interactions in the striatum and related corticostriatal circuits. We further discuss how impaired CIN responsiveness could blunt adaptive behavioral adjustments under stress, biasing animals toward habitual or compulsive alcohol seeking. This addition highlights the broader implication that alcohol-induced alterations in CRF–CIN signaling may contribute to relapse vulnerability by undermining adaptive stress coping.

      References

      English, D. F., O. Ibanez-Sandoval, E. Stark, F. Tecuapetla, G. Buzsaki, K. Deisseroth, J. M. Tepper and T. Koos (2011). "GABAergic circuits mediate the reinforcement-related signals of striatal cholinergic interneurons." Nat Neurosci 15(1): 123–130.

      Gangal, H., J. Iannucci, Y. Huang, R. Chen, W. Purvines, W. T. Davis, A. Rivera, G. Johnson, X. Xie, S. Mukherjee, V. Vierkant, K. Mims, K. O'Neill, X. Wang, L. A. Shapiro and J. Wang (2025). "Traumatic brain injury exacerbates alcohol consumption and neuroinflammation with decline in cognition and cholinergic activity." Transl Psychiatry 15(1): 403.

      Huang, Z., R. Chen, M. Ho, X. Xie, H. Gangal, X. Wang and J. Wang (2024). "Dynamic responses of striatal cholinergic interneurons control behavioral flexibility." Sci Adv 10(51): eadn2446.

      Lu, J. Y., Y. F. Cheng, X. Y. Xie, K. Woodson, J. Bonifacio, E. Disney, B. Barbee, X. H. Wang, M. Zaidi and J. Wang (2021). "Whole-Brain Mapping of Direct Inputs to Dopamine D1 and D2 Receptor-Expressing Medium Spiny Neurons in the Posterior Dorsomedial Striatum." Eneuro 8(1).

      Ma, T., Z. Huang, X. Xie, Y. Cheng, X. Zhuang, M. J. Childs, H. Gangal, X. Wang, L. N. Smith, R. J. Smith, Y. Zhou and J. Wang (2021). "Chronic alcohol drinking persistently suppresses thalamostriatal excitation of cholinergic neurons to impair cognitive flexibility." J Clin Invest 132(4): e154969.

      Potjer, E. V., X. Wu, A. N. Kane and J. G. Parker (2025). "Parkinsonian striatal acetylcholine dynamics are refractory to L-DOPA treatment." bioRxiv.

      Purvines, W., H. Gangal, X. Xie, J. Ramos, X. Wang, R. Miranda and J. Wang (2025). "Perinatal and prenatal alcohol exposure impairs striatal cholinergic function and cognitive flexibility in adult offspring." Neuropharmacology 279: 110627.

      Ren, Y., Y. Liu and M. Luo (2021). "Gap Junctions Between Striatal D1 Neurons and Cholinergic Interneurons." Front Cell Neurosci 15: 674399.

      Touponse, G. C., M. B. Pomrenze, T. Yassine, V. Mehta, N. Denomme, Z. Zhang, R. C. Malenka and N. Eshel (2025). "Cholinergic modulation of dopamine release drives effortful behavior." bioRxiv.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary: 

      This study presents an interesting behavioral paradigm and reveals interactive effects of social hierarchy and threat type on defensive behaviors. However, addressing the aforementioned points regarding methodological detail, rigor in behavioral classification, depth of result interpretation, and focus of the discussion is essential to strengthen the reliability and impact of the conclusions in a revised manuscript. 

      Strengths: 

      The paper is logically sound, featuring detailed classification and analysis of behaviors, with a focus on behavioral categories and transitions, thereby establishing a relatively robust research framework. 

      Weaknesses: 

      Several points require clarification or further revision. 

      (1) Methods and Terminology Regarding Social Hierarchy: 

      The study uses the tube test to determine subordinate status, but the methodological description is quite brief. Please provide a more detailed account of the experimental procedure and the criteria used for determination. 

      We will add more details about how the tube test was performed in the revised manuscript.

      The dominance hierarchy is established based on pairs of mice. However, the use of terms like "group cohesion" - typically applied to larger groups - to describe dyadic interactions seems overstated. Please revise the terminology to more accurately reflect the pairwise experimental setup.

      Thanks for the comment. We agree that the term “group cohesion” can be misleading and will replace it with “social engagement”.

      (2) Criteria and Validity of Behavioral Classification: 

      The criteria for classifying mouse behaviors (e.g., passive defense, active defense) are not sufficiently clear. Please explicitly state the operational definitions and distinguishing features for each behavioral category. 

      Passive defense was defined as an immobility-based defensive strategy characterized by suppression of locomotor activity. This category included freezing and tail rattling, which in our study involved minimal body displacement aside from rapid tail vibration. Active defense was defined as movement- or posture-dependent defensive strategy, encompassing behaviors that involved locomotor engagement or spatial repositioning relative to the threat, including approach, investigation, withdrawal, and stretch-attend. We will clarify this in the revised manuscript.

      How was the meaningfulness and distinctness of these behavioral categories ensured to avoid overlap? For instance, based on Figure 3E, is "active defense" synonymous with "investigative defense," involving movement to the near region followed by return to the far region? This requires clearer delineation. 

      Defensive behaviors in the rat exposure paradigm were grouped into two categories: passive and active defense, each comprising distinct behaviors. All the manually annotated behaviors were mutually exclusive; that is, each video frame was assigned a single behavioral label to avoid overlap across behaviors. Active defense includes four behaviors: approach, investigation, withdrawal, and stretch-attend. We will clarify these points in the revised manuscript.

      The current analysis focuses on a few core behaviors, while other recorded behaviors appear less relevant. Please clarify the principles for selecting or categorizing all recorded behaviors.

      Thank you for pointing this out. In the current study, we focused primarily on defensive and social behaviors. We also included several neutral solitary behaviors related to anxiety and defensive state, such as sniffing, grooming, and rearing, which were consistently expressed across animals and closely linked to our main findings. We will clarify this rationale in the revised manuscript.

      (3) Interpretation of Key Findings and Mechanistic Insights:

      Looming exposure increased the proportion of proactive bouts in the dominant zone but decreased it in the subordinate zone (Figure 4G), with a similar trend during rat exposure. Please provide a potential explanation for this consistent pattern. Does this consistency arise from shared neural mechanisms, or do different behavioral strategies converge to produce similar outputs under both threats?

      Thanks for bringing up this important question. The consistent increase in proactive bouts in dominant mice across both paradigms suggests a consistent rank-dependent reorganization of dyadic interaction under threats. We propose that this convergence reflects a shared neural mechanism that links defensive state with social-rank information, potentially mediated by overlapping hypothalamic and prefrontal circuits. We will expand the Discussion to incorporate this explanation.

      (4) Support for Claims and Study Limitations:

      The manuscript states that this work addresses a gap by showing defensive responses are jointly shaped by threat type and social rank, emphasizing survival-critical behaviors over fear or stress alone. However, it is possible that the behavioral differences stem from varying degrees of danger perception rather than purely strategic choices. This warrants a clear description and a deeper discussion to address this possibility.

      We thank the reviewer for this insightful comment. We agree that, in principle, behavioral differences could arise from variations in perceived danger rather than strategic choice. In humans, decisions can sometimes reflect value-based strategies that override perceived danger. In contrast, under naturalistic threat conditions, mice likely rely predominantly on danger perception to make behavioral decisions, and such responses are expected to be consistent with value-based strategies shaped by natural selection. In the revised manuscript, we will expand the Discussion to address the role of threat perception and its relationship to decision-making in our behavioral paradigms.

      The Discussion section proposes numerous brain regions potentially involved in fear and social regulation. As this is a behavioral study, the extensive speculation on specific neural circuitry involvement, without supporting neuroscience data, appears insufficiently grounded and somewhat vague. It is recommended to focus the discussion more on the implications of the behavioral findings themselves or to explicitly frame these neural hypotheses as directions for future research.

      We will revise the Discussion to focus more directly on behavioral findings and add explicit neural hypotheses as potential future directions.

      Reviewer #2 (Public review):

      Summary:

      The authors investigate how dominance hierarchy shapes defensive strategies in mice under two naturalistic threats: a transient visual looming stimulus and a sustained live rat. By comparing single versus paired testing, they report that social presence attenuates fear and that dominant and subordinate mice exhibit different patterns of defensive and social behaviors depending on threat type. The work provides a rich behavioral dataset and a potentially useful framework for studying hierarchical modulation of innate fear.

      Strengths:

      (1) The study uses two ecologically meaningful threat paradigms, allowing comparison across transient and sustained threat contexts.

      (2) Behavioral quantification is detailed, with manual annotation of multiple behavior types and transition-matrix level analysis.

      (3) The comparison of dominant versus subordinate pairs is novel in the context of innate fear.

      (4) The manuscript is well-organized and clearly written.

      (5) Figures are visually informative and support major claims.

      Weaknesses:

      Lack of neural mechanism insights.

      The current study focused on behavior. In the revised manuscript, we will incorporate a discussion of potential neural mechanisms and highlight this as an important direction for future work.

      Reviewer #3 (Public review):

      Summary:

      This study examines how dominance hierarchy influences innate defensive behaviors in pair-housed male mice exposed to two types of naturalistic threats: a transient looming stimulus and a sustained live rat. The authors show that social presence reduces fear-related behaviors and promotes active defense, with dominant mice benefiting more prominently. They also demonstrate that threat exposure reinforces social roles and increases group cohesion. The work highlights the bidirectional interaction between social structure and defensive behavior.

      Strengths:

      This study makes a valuable contribution to behavioral neuroscience through its well-designed examination of socially modulated fear. A key strength is the use of two ethologically relevant threat paradigms - a transient looming stimulus and a sustained live predator, enabling a nuanced comparison of defensive behaviors. The experimental design is robust, systematically comparing animals tested alone versus with their cage mate to cleanly isolate social effects. The behavioral analysis is sophisticated, employing detailed transition maps that reveal how social context reshapes behavioral sequences, going beyond simple duration measurements. The finding that social modulation is rank-dependent adds significant depth, linking social hierarchy to adaptive defense strategies. Furthermore, the demonstration that threat exposure reciprocally enhances social cohesion provides a compelling systems-level perspective. Together, these elements establish a strong behavioral framework for future investigations into the neural circuits underlying socially modulated innate fear.

      Weaknesses:

      The study exhibits several limitations. The neural mechanism proposed is speculative, as the study provides no causal evidence.

      Establishing causal evidence for neural mechanisms is beyond the scope of the current behavioral study. We highlight this as an important direction for future work.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This paper investigates the control signals that drive event model updating during continuous experience. The authors apply predictions from previously published computational models to fMRI data acquired while participants watched naturalistic video stimuli. They first examine the time course of BOLD pattern changes around human-annotated event boundaries, revealing pattern changes preceding the boundary in anterior temporal and then parietal regions, followed by pattern stabilization across many regions. The authors then analyze time courses around boundaries generated by a model that updates event models based on prediction error and another that uses prediction uncertainty. These analyses reveal overlapping but partially distinct dynamics for each boundary type, suggesting that both signals may contribute to event segmentation processes in the brain.

      Strengths:

      (1) The question addressed by this paper is of high interest to researchers working on event cognition, perception, and memory. There has been considerable debate about what kinds of signals drive event boundaries, and this paper directly engages with that debate by comparing prediction error and prediction uncertainty as candidate control signals.

      (2) The authors use computational models that explain significant variance in human boundary judgments, and they report the variance explained clearly in the paper.

      (3) The authors' method of using computational models to generate predictions about when event model updating should occur is a valuable mechanistic alternative to methods like HMM or GSBS, which are data-driven.

      (4) The paper utilizes an analysis framework that characterizes how multivariate BOLD pattern dissimilarity evolves before and after boundaries. This approach offers an advance over previous work focused on just the boundary or post-boundary points.

      We appreciate this reviewer’s recognition of the significance of this research problem, and of the value of the approach taken by this paper.

      Weaknesses:

      (1) While the paper raises the possibility that both prediction error and uncertainty could serve as control signals, it does not offer a strong theoretical rationale for why the brain would benefit from multiple (empirically correlated) signals. What distinct advantages do these signals provide? This may be discussed in the authors' prior modeling work, but is left too implicit in this paper.

      We added a brief discussion in the introduction highlighting the complementary advantages of prediction error and prediction uncertainty, and cited prior theoretical work that elaborates on this point. Specifically, we now note that prediction error can act as a reactive trigger, signaling when the current event model is no longer sufficient (Zacks et al., 2007). In contrast, prediction uncertainty is framed as proactive, allowing the system to prepare for upcoming changes even before they occur (Baldwin & Kosie, 2021; Kuperberg, 2021). Together, this makes clearer why these two signals could each provide complementary benefits for effective event model updating.

      "One potential signal to control event model updating is prediction error—the difference between the system’s prediction and what actually occurs. A transient increase in prediction error is a valid indicator that the current model no longer adequately captures the current activity. Event Segmentation Theory (EST; Zacks et al., 2007) proposes that event models are updated when prediction error increases beyond a threshold, indicating that the current model no longer adequately captures ongoing activity. A related but computationally distinct proposal is that prediction uncertainty (also termed "unpredictability") can serve as a control signal (Baldwin & Kosie, 2021). The advantage of relying on prediction uncertainty to detect event boundaries is that it is inherently proactive: the cognitive system can start looking for cues about what might come next before the next event starts (Baldwin & Kosie, 2021; Kuperberg, 2021). "

      (2) Boundaries derived from prediction error and uncertainty are correlated for the naturalistic stimuli. This raises some concerns about how well their distinct contributions to brain activity can be separated. The authors should consider whether they can leverage timepoints where the models make different predictions to make a stronger case for brain regions that are responsive to one vs the other.

      We addressed this concern by adding an analysis that explicitly tests the unique contributions of prediction error– and prediction uncertainty–driven boundaries to neural pattern shifts. In the revised manuscript, we describe how we fit a combined FIR model that included both boundary types as predictors and then compared this model against versions with only one predictor. This allowed us to identify the variance explained by each boundary type over and above the other. The results revealed two partially dissociable sets of brain regions sensitive to error- versus uncertainty-driven boundaries (see Figure S1), strengthening our argument that these signals make distinct contributions.

      "To account for the correlation between uncertainty-driven boundaries and error-driven boundaries, we also fitted a FIR model that predicted pattern dissimilarity from both types of boundaries (combined FIR) for each parcel. Then, we performed two likelihood ratio tests: combined FIR to error FIR, which measures the unique contribution of uncertainty boundaries to pattern dissimilarity, and combined FIR to uncertainty FIR, which measures the unique contribution of error boundaries to pattern dissimilarity. The analysis also revealed two dissociable sets of brain regions associated with each boundary type (see Figure S1)."

      (3) The authors refer to a baseline measure of pattern dissimilarity, which their dissimilarity measure of interest is relative to, but it's not clear how this baseline is computed. Since the interpretation of increases or decreases in dissimilarity depends on this reference point, more clarity is needed.

      We clarified how the FIR baseline is estimated in the methods section. Specifically, we now explain that the FIR coefficients should be interpreted relative to a reference level, which reflects the expected dissimilarity when timepoints are far from an event boundary. This makes it clear what serves as the comparison point for observed increases or decreases in dissimilarity.

      "The coefficients from the FIR model indicate changes relative to baseline, which can be conceptualized as the expected value when far from event boundaries."

      (4) The authors report an average event length of ~20 seconds, and they also look at +20 and -20 seconds around each event boundary. Thus, it's unclear how often pre- and post-boundary timepoints are part of adjacent events. This complicates the interpretations of the reported time courses.

      This is related to reviewer's 2 comment, and it will be addressed below.

      (5) The authors describe a sequence of neural pattern shifts during each type of boundary, but offer little setup of what pattern shifts we might expect or why. They also offer little discussion of what cognitive processes these shifts might reflect. The paper would benefit from a more thorough setup for the neural results and a discussion that comments on how the results inform our understanding of what these brain regions contribute to event models.

      We thank the reviewer for this advice on how better to set the context for the different potential outcomes of the study. We expanded both the introduction and discussion to better set up expectations for neural pattern shifts and to interpret what these shifts may reflect. In the introduction, we now describe prior findings showing that sensory regions tend to update more quickly than higher-order multimodal regions (Baldassano et al., 2017; Geerligs et al., 2021, 2022), and we highlight that it remains unclear whether higher-order updates precede or follow those in lower-order regions. We also note that our analytic approach is well-suited to address this open question. In the discussion, we then interpret our results in light of this framework. Specifically, we describe how we observed early shifts in higher-order areas such as anterior temporal and prefrontal cortex, followed by shifts in parietal and dorsal attention regions closer to event boundaries. This pattern runs counter to the traditional bottom-up temporal hierarchy view and instead supports a model of top-down updating, where high-level representations are updated first and subsequently influence lower-level processing (Friston, 2005; Kuperberg, 2021). To make this interpretation concrete, we added an example: in a narrative where a goal is reached midway—for instance, a mystery solved before the story formally ends—higher-order regions may update the event representation at that point, and this updated model then cascades down to shape processing in lower-level regions. Finally, we note that the widespread stabilization of neural patterns after boundaries may signal the establishment of a new event model.

      Excerpt from Introduction:

      “More recently, multivariate approaches have provided insights into neural representations during event segmentation. One prominent approach uses hidden Markov models (HMMs) to detect moments when the brain switches from one stable activity pattern to another (Baldassano et al., 2017) during movie viewing; these periods of relative stability were referred to as "neural states" to distinguish them from subjectively perceived events. Sensory regions like visual and auditory cortex showed faster transitions between neural states. Multi-modal regions like the posterior medial cortex, angular gyrus, and intraparietal sulcus showed slower neural state shifts, and these shifts aligned with subjectively reported event boundaries. Geerligs et al. (2021, 2022) employed a different analytical approach called Greedy State Boundary Search (GSBS) to identify neural state boundaries. Their findings echoed the HMM results: short-lived neural states were observed in early sensory areas (visual, auditory, and somatosensory cortex), while longer-lasting states appeared in multi-modal regions, including the angular gyrus, posterior middle/inferior temporal cortex, precuneus, anterior temporal pole, and anterior insula. Particularly prolonged states were found in higher-order regions such as lateral and medial prefrontal cortex.

      The previous evidence about evoked responses at event boundaries indicates that these are dynamic phenomena evolving over many seconds, with different brain areas showing different dynamics (Ben-Yakov & Henson, 2018; Burunat et al., 2024; Kurby & Zacks, 2018; Speer et al., 2007; Zacks, 2010). Less is known about the dynamics of pattern shifts at event boundaries (e.g. whether shifts observed in higher-order regions precedes or follow shifts observed in lower-level regions), because the HMM and GSBS analysis methods do not directly provide moment-by-moment measures of pattern shifts. Both the spatial and temporal aspects of evoked responses and pattern shifts at event boundaries have the potential to provide evidence about two potential control processes (error-driven and uncertainty-driven) for event model updating.”

      Excerpt from Discussion:

      “We first characterized the neural signatures of human event segmentation by examining both univariate activity changes and multivariate pattern changes around subjectively identified event boundaries. Using multivariate pattern dissimilarity, we observed a structured progression of neural reconfiguration surrounding human-identified event boundaries. The largest pattern shifts were observed near event boundaries (~4.5s before) in dorsal attention and parietal regions; these correspond with regions identified by Geerligs et. al as shifting their patterns on a fast to intermediate timescale (2022). We also observed smaller pattern shifts roughly 12 seconds prior to event boundaries in higher-order regions within anterior temporal cortex and prefrontal cortex, and these are slow-changing regions identified by Geerligs et. al (2022). This is puzzling. One prevalent proposal, based on the idea of a cortical hierarchy of increasing temporal receptive windows (TRWs), suggests that higher-order regions should update representations after lower-order regions do (Chang et al., 2021). In this view, areas with shorter TRWs (e.g., word-level processors) pass information upward, where it is integrated into progressively larger narrative units (phrases, sentences, events). This proposal predicts neural shifts in higher-order regions to follow those in lower-order regions. By contrast, our findings indicate the opposite sequence. Our findings suggest that the brain might engage in top-down event representation updating, with changes in coarser-grain representations propagating downward to influence finer-grain representations. (Friston, 2005; Kuperberg, 2021). For example, in a narrative where the main goal is achieved midway—such as a detective solving a mystery before the story formally ends—higher-order regions might update the overarching event representation at that point, and this updated model could then cascade down to reconfigure how lower-level regions process the remaining sensory and contextual details. In the period after a boundary (around +12 seconds), we found widespread stabilization of neural patterns across the brain, suggesting the establishment of a new event model. Future work could focus on understanding the mechanisms behind the temporal progression of neural pattern changes around event boundaries.”

      Reviewer #2 (Public review):

      Summary:

      Tan et al. examined how multivoxel patterns shift in time windows surrounding event boundaries caused by both prediction errors and prediction uncertainty. They observed that some regions of the brain show earlier pattern shifts than others, followed by periods of increased stability. The authors combine their recent computational model to estimate event boundaries that are based on prediction error vs. uncertainty and use this to examine the moment-to-moment dynamics of pattern changes. I believe this is a meaningful contribution that will be of interest to memory, attention, and complex cognition research.

      Strengths:

      The authors have shown exceptional transparency in terms of sharing their data, code, and stimuli, which is beneficial to the field for future examinations and to the reproduction of findings. The manuscript is well written with clear figures. The study starts from a strong theoretical background to understand how the brain represents events and has used a well-curated set of stimuli. Overall, the authors extend the event segmentation theory beyond prediction error to include prediction uncertainty, which is an important theoretical shift that has implications in episodic memory encoding, the use of semantic and schematic knowledge, and attentional processing.

      We thank the reader for their support for our use of open science practices, and for their appreciation of the importance of incorporating prediction uncertainty into models of event comprehension.

      Weaknesses:

      The data presented is limited to the cortex, and subcortical contributions would be interesting to explore. Further, the temporal window around event boundaries of 20 seconds is approximately the length of the average event (21.4 seconds), and many of the observed pattern effects occur relatively distal from event boundaries themselves, which makes the link to the theoretical background challenging. Finally, while multivariate pattern shifts were examined at event boundaries related to either prediction error or prediction uncertainty, there was no exploration of univariate activity differences between these two different types of boundaries, which would be valuable.

      The fact that we observed neural pattern shifts well before boundaries was indeed unexpected, and we now offer a more extensive interpretation in the discussion section. Specifically, we added text noting that shifts emerged in higher-order anterior temporal and prefrontal regions roughly 12 seconds before boundaries, whereas shifts occurred in lower-level dorsal attention and parietal regions closer to boundaries. This sequence contrasts with the traditional bottom-up temporal hierarchy view and instead suggests a possible top-down updating mechanism, in which higher-order representations reorganize first and propagate changes to lower-level areas (Friston, 2005; Kuperberg, 2021). (See excerpt for Reviewer 1’s comment #5.)

      With respect to univariate activity, we did not find strong differences between error-driven and uncertainty-driven boundaries. This makes the multivariate analyses particularly informative for detecting differences in neural pattern dynamics. To support further exploration, we have also shared the temporal progression of univariate BOLD responses on OpenNeuro (BOLD_coefficients_brain_animation_pe_SEM_bold.html and BOLD_coefficients_brain_animation_uncertainty_SEM_bold.html in the derivatives/figures/brain_maps_and_timecourses/ directory; https://doi.org/10.18112/openneuro.ds005551.v1.0.4) for interested researchers.

      Reviewer #3 (Public review):

      Summary:

      The aim of this study was to investigate the temporal progression of the neural response to event boundaries in relation to uncertainty and error. Specifically, the authors asked (1) how neural activity changes before and after event boundaries, (2) if uncertainty and error both contribute to explaining the occurrence of event boundaries, and (3) if uncertainty and error have unique contributions to explaining the temporal progression of neural activity.

      Strengths:

      One strength of this paper is that it builds on an already validated computational model. It relies on straightforward and interpretable analysis techniques to answer the main question, with a smart combination of pattern similarity metrics and FIR. This combination of methods may also be an inspiration to other researchers in the field working on similar questions. The paper is well written and easy to follow. The paper convincingly shows that (1) there is a temporal progression of neural activity change before and after an event boundary, and (2) event boundaries are predicted best by the combination of uncertainty and error signals.

      We thank the reviewer for their thoughtful and supportive comments, particularly regarding the use of the computational model and the analysis approaches.

      Weaknesses:

      (1) The current analysis of the neural data does not convincingly show that uncertainty and prediction error both contribute to the neural responses. As both terms are modelled in separate FIR models, it may be that the responses we see for both are mostly driven by shared variance. Given that the correlation between the two is very high (r=0.49), this seems likely. The strong overlap in the neural responses elicited by both, as shown in Figure 6, also suggests that what we see may mainly be shared variance. To improve the interpretability of these effects, I think it is essential to know whether uncertainty and error explain similar or unique parts of the variance. The observation that they have distinct temporal profiles is suggestive of some dissociation,but not as convincing as adding them both to a single model.

      We appreciate this point. It is closely related to Reviewer 1's comment 2; please refer to our response above.

      (2) The results for uncertainty and error show that uncertainty has strong effects before or at boundary onset, while error is related to more stabilization after boundary onset. This makes me wonder about the temporal contribution of each of these. Could it be the case that increases in uncertainty are early indicators of a boundary, and errors tend to occur later?

      We also share the intuition that increases in uncertainty are early indicators of a boundary, and errors tend to occur later. If that is the case, we would expect some lags between prediction uncertainty and prediction error. We examined lagged correlation between prediction uncertainty and prediction error, and the optimal lag is 0 for both uncertainty-driven and error-driven models. This indicates that when prediction uncertainty rises, prediction error also simultaneously rises.

      Author response image 1.

      (3) Given that there is a 24-second period during which the neural responses are shaped by event boundaries, it would be important to know more about the average distance between boundaries and the variability of this distance. This will help establish whether the FIR model can properly capture a return to baseline.

      We have added details about the distribution of event lengths. Specifically, we now report that the mean length of subjectively identified events was 21.4 seconds (median 22.2 s, SD 16.1 s). For model-derived boundaries, the average event lengths were 28.96 seconds for the uncertainty-driven model and 24.7 seconds for the error-driven model.

      " For each activity, a separate group of 30 participants had previously segmented each movie to identify fine-grained event boundaries (Bezdek et al., 2022). The mean event length was 21.4 s (median 22.2 s, SD 16.1 s). Mean event lengths for uncertainty-driven model and error-driven model were 28.96s, and 24.7s, respectively (Nguyen et al., 2024)."

      (4) Given that there is an early onset and long-lasting response of the brain to these event boundaries, I wonder what causes this. Is it the case that uncertainty or errors already increase at 12 seconds before the boundaries occur? Or if there are other makers in the movie that the brain can use to foreshadow an event boundary? And if uncertainty or errors do increase already 12 seconds before an event boundary, do you see a similar neural response at moments with similar levels of error or uncertainty, which are not followed by a boundary? This would reveal whether the neural activity patterns are specific to event boundaries or whether these are general markers of error and uncertainty.

      We appreciate this point; it is similar to reviewer 2’s comment 2. Please see our response to that comment above.

      (5) It is known that different brain regions have different delays of their BOLD response. Could these delays contribute to the propagation of the neural activity across different brain areas in this study?

      Our analyses use ±20 s FIR windows, and the key effects we report include shifts ~12s before boundaries in higher-order cortex and ~4.5s pre-boundary in dorsal attention/parietal areas. Given the literature above, region-dependent BOLD delays are much smaller (~1–2s) than the temporal structure we observe (Taylor et al., 2018), making it unlikely that HRF lag alone explains our multi-second, region-specific progression.

      (6) In the FIR plots, timepoints -12, 0, and 12 are shown. These long intervals preclude an understanding of the full temporal progression of these effects.

      For page length purposes, we did not include all timepoints. We uploaded a brain animation of all timepoints and coefficients for each parcel in Openneuro (PATTERN_coefficients_brain_animation_human_fine_pattern.html and PATTERN_coefficients_lines_human_fine.html in the derivatives/figures/brain_maps_and_timecourses/ directory; https://doi.org/10.18112/openneuro.ds005551.v1.0.4) for interested researchers.

      References

      Taylor, A. J., Kim, J. H., & Ress, D. (2018). Characterization of the hemodynamic response function across the majority of human cerebral cortex. NeuroImage, 173, 322–331. https://doi.org/10.1016/j.neuroimage.2018.02.061

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer 1

      Minor

      The main substance of my previous comment I suppose targeted a deeper issue - namely whether such a result is reflecting a resolution to a 'neural prediction' puzzle or a 'perceptual prediction' puzzle. Of course, these results tell us a great deal about a potential resolution for how dampening and sharpening might co-exist in the brain - but in the absence of corresponding perceptual effects (or a lack of correlation between neural and perceptual variables - as outlined in this revision) I do wonder if any claims about implications for perception might need moderation or caveating. To be honest, I don't think the authors *need* to make any more changes along these lines for this paper to be acceptable - it is more an issue they might wish to consider themselves when contextualizing their findings.

      Thank you for the thoughtful comment. We have now added a caveat to the relevant section of the discussion to make it clearer that we are discussing neural results, not perceptual results (p.20, lines 378-379).

      I am also happy with the changes that the authors have made justifying which claims can and cannot made based on a statistical decoding test against 'chance' in a single condition using t-tests. I was perhaps a little unclear when I spoke about 'comparisons against 0' in my original review, when the key issue (as the authors have intuited!) is about comparisons against 'chance' (where e.g., 0% decoding above chance is the same thing as 'chance'!). The authors are of course correct in the amendment they have made on p.29 to make clear this is a 'fixed effects analysis' - though I still worry this could be a little cryptic for the average reader. I am not suggesting that the authors run more analyses, or revise any conclusions, but I think it would be more transparent if a note was added along the lines of "while the fixed effects approach (one-sample t-test) enables us to establish whether some consistent informative patterns are detectable in these particular subjects, the results from our paired t-tests support inference to the wider population".

      This sentence has been added for increased transparency (p. 27, lines 544-547).

      Reviewer 3

      Major

      (1) In the previous round of comments, I noted that: "I am not fully convinced that Figures 3A/B and the associated results support the idea that early learning stages result in dampening and later stages in sharpening. The inference made requires, in my opinion, not only a significant effect in one-time bin and the absence of an effect in other bins. Instead to reliably make this inference one would need a contrast showing a difference in decoding accuracy between bins, or ideally an analysis not contingent on seemingly arbitrary binning of data, but a decrease (or increase) in the slope of the decoding accuracy across trials. Moreover, the decoding analyses seem to be at the edge of SNR, hence making any interpretation that depends on the absence of an effect in some bins yet more problematic and implausible". The authors responded: "we fitted a logarithmic model to quantify the change of the decoding benefit over trials, then found the trial index for which the change of the logarithmic fit was < 0.1%. Given the results of this analysis and to ensure a sufficient number of trials, we focused our further analyses on bins 1-2". However, I do not see how this new analysis addresses the concern that the conclusion highlights differences in decoding performance between bins 1 and 2, yet no contrast between these bins are performed. While I appreciate the addition of the new model, in my current understanding it does not solve the problem I raised. I still believe that if the authors wish to conclude that an effect differs between two bins they must contrast these directly and/or use a different appropriate analysis approach.

      Relatedly, the logarithmic model fitting and how it justifies the focus on analysis bin 1-2 needs to be explained better, especially the rationale of the analysis, the choice of parameters (e.g., why logarithmic, why change of logarithmic fit < 0.1% as criterion, etc), and why certain inferences follow from this analysis. Also, the reporting of the associated results seems rather sparse in the current iteration of the manuscript.

      We thank the reviewer for this important point. Following your suggestion, we conducted additional post-hoc tests directly comparing the first and second bins. We found significant differences between bins in the invalid trials, but not the valid trials, suggesting that sharpening/dampening effects are condition specific. This is discussed in the manuscript on p.14, lines 268-271; p.15, 280-284; p.20, lines 382-386.

      A logarithmic analysis was chosen as learning is usually found to be a nonlinear process; learning effects occur rapidly before stabilising relatively early, as seen in Fig. 2D. This is consistent with other research which found that logarithmic fits efficiently describe learning curves in statistical learning (Kang et al., 2023; Siegelman et al., 2018; Choi et al., 2020). By utilising a change of logarithmic fit at <0.1% as a criterion, it is ensured that virtually zero learning took place after that point, allowing us to focus our analysis on learning effects as they developed and providing a more accurate model of representational change. This is explained in the manuscript on p.13, lines 250-251; p.27-28, lines 557-563.

      (2) A critical point the authors raise is that they investigate the buildup of expectations during training. They go on to show that the dampening effect disappears quickly, concluding: "the decoding benefit of invalid predictions [...] disappeared after approximately 15 minutes (or 50 trials per condition)". Maybe the authors can correct me, but my best understanding is as follows: Each bin has 50 trials per condition. The 2:1 condition has 4 leading images, this would mean ~12 trials per leading stimulus, 25% of which are unexpected, so ~9 expected trials per pair. Bin 1 represents the first time the participants see the associations. Therefore, the conclusion is that participants learn the associations so rapidly that ~9 expected trials per pair suffice to not only learn the expectations (in a probabilistic context) but learn them sufficiently well such that they result in a significant decoding difference in that same bin. If so, this would seem surprisingly fast, given that participants learn by means of incidental statistical learning (i.e. they were not informed about the statistical regularities). I acknowledge that we do not know how quickly the dampening/sharpening effects develop, however surprising results should be accompanied with a critical evaluation and exceptionally strong evidence (see point 1). Consider for example the following alternative account to explain these results. Category pairs were fixed across and within participants,i.e. the same leading image categories always predicted the same trailing image categories for all participants. Some category pairings will necessarily result in a larger representational overlap (i.e., visual similarity, etc.) and hence differences in decoding accuracy due to adaptation and related effects. For example, house  barn will result in a different decoding performance compared to coffee cup  barn, simply due to the larger visual and semantic similarity between house and barn compared to coffee cup and barn. These effects should occur upon first stimulus presentation, independent of statistical learning, and may attenuate over time e.g., due to increasing familiarity with the categories (i.e., an overall attenuation leading to smaller between condition differences) or pairs.

      We apologise for the confusion, there are 50 expected trials per bin per condition. The trial breakdown is as follows. Each participant completed 1728 trials, split equally across 3 mappings (two 2:1 maps and one 1:2 map), giving 1152 trials in the 2:1 mapping. Stimuli were expected in 75% of trials (864), leaving 216 per bin, and 54 per leading image in each bin. We have clarified this in the script (p.14, line 267; p.15, line 280). This is in line with similar studies in the field (e.g. Han et al., 2019).

      (3) In response to my previous comment, why the authors think their study may have found different results compared to multiple previous studies (e.g. Han et al., 2019; Kumar et al., 2017; Meyer and Olson, 2011), particularly the sharpening to dampening switch, the authors emphasize the use of non-repeated stimuli (no repetition suppression and no familiarity confound) in their design. However, I fail to see how familiarity or RS could account for the absence of

      sharpening/dampening inversion in previous studies.

      First, if the authors argument is about stimulus novelty and familiarity as described by Feuerriegel et al., 2021, I believe this point does not apply to the cited studies. Feuerriegel et al., 2021 note: "Relative stimulus novelty can be an important confound in situations where expected stimulus identities are presented often within an experiment, but neutral or surprising stimuli are presented only rarely", which indeed is a critical confound. However, none of the studies (Han et al., 2019; Richter et al., 2018; Kumar et al., 2017; Meyer and Olson, 2011) contained this confound, because all stimuli served as expected and unexpected stimuli, with the expectation status solely determined by the preceding cue. Thus, participants were equally familiar with the images across expectation conditions.

      Second, for a similar reason the authors argument for RS accounting for the different results does not hold either in my opinion. Again, as Feuerriegel et al. 2021 correctly point out: "Adaptation-related effects can mimic ES when the expected stimuli are a repetition of the last-seen stimulus or have been encountered more recently than stimuli in neutral expectation conditions." However, it is critical to consider the precise design of previous studies. Taking again the example of Han et al., 2019; Kumar et al., 2017; Meyer and Olson, 2011. To my knowledge none of these studies contained manipulations that would result in a more frequent or recent repetition of any specific stimulus in the expected compared to unexpected condition. The crucial manipulation in all these previous studies is not that a single stimulus or stimulus feature (which could be subject to familiarity or RS) determines the expectation status, but rather the transitional probability (i.e. cue-stimulus pairing) of a particular stimulus given the cue. Therefore, unless I am missing something critical, simple RS seems unlikely to differ between expectation condition in the previous studies and hence seems implausible to account for differences in results compared to the current study.

      Moreover, studies cited by the authors (e.g. Todorovic & de Lange, 2012) showed that RS and ES are separable in time, again making me wonder how avoiding stimulus repetition should account for the difference in the present study compared to previous ones. I am happy to be corrected in my understanding, but with the currently provided arguments by the authors I do not see how RS and familiarity can account for the discrepancy in results.

      The reviewer is correct in that the studies cited (Han et al., 2019; Kumar et al., 2017; Meyer and Olson, 2011) ensure that participants are equally familiar with the images across expectation conditions. Where the present study differs is that participants are not familiar with individual exemplars at all. Han et al., 2019 used a pool of 30 individual images, and subjects underwent exposure sessions lasting two hours each daily for 34 days prior to testing. Kumar et al., 2017 used a pool of 12 images with subjects being exposed to each sequential pair 816 times over the course of the training period. Meyer & Olsen, 2011 used pure tones at five different pitch levels. While familiarity of stimuli across conditions was controlled for in these studies in the sense that familiarity was constant across conditions, novelty was not controlled for. The present study uses a pool of ~3500 images, which are unrepeated across trials.

      Feuerriegel et al., 2021 also points out: “There are also effects of adaptation that are dependent on the recent stimulation history extending beyond the last encountered stimulus and long-lag repetition effects that occur when the first and second presentation of a stimulus is separated by tens or even hundreds of intervening images”. Bearing this in mind, and given the very small pool of stimuli being used by Han et al., 2019; Kumar et al., 2017; Meyer and Olson, 2011, it stands to reason that these studies may still have built-in but unaccounted for effects relating to the repetition of exemplars. Thus, our avoidance of those possible confounds, in addition to foregoing any prior training, may elicit differing results. Furthermore, as pointed out by Walsh et al. 2020, methodological heterogeneity (such as subject training) can produce contrasting results as PP makes divergent predictions regarding the properties of prediction error given different permutations of variables such as training, transitional probabilities, and conditional probabilities. In our case, the use of differing methodology was intentional. These issues have been discussed in more detail on p.5, lines 112-115; p.19, lines 368-377; p.20, lines 378-379).

      Minor

      (1) The authors note in their reply to my previous questions that: "As mentioned above, we opted to target our ERP analyses on Oz due to controversies in the literature regarding univariate effects of ES (Feuerriegel et al., 2021)". This might be a lack of understanding on my side, but how are concerns about the reliability of ES, as outlined by Feuerriegel et al. (2021), an argument for restricting analyses to 1 EEG channel (Oz)? Could one not argue equally well that precisely because of these concerns we should be less selective and instead average across multiple (occipital) channels to improve the reliability of results?

      The reviewer is correct in suggesting that a cluster of occipital electrodes may be more reliable than reporting one single electrode. We have amended the analysis to examine electrodes Oz, O1, and O2 (p.9, lines 187-188; p.11, lines 197-201).

      (2) The authors provide a github link for the dataset and code. However, I doubt that github is a suitable location to share EEG data (which at present I also cannot find linked in the github repo). Do the authors plan to share the EEG data and if so where?

      Thank you for bringing this to my attention. EEG data has now been uploaded at osf.io/x7ydf and linked to the github repository (p.28, lines 569-570).

      (3) The figure text could benefit from additional information; e.g. Fig.1C and Fig.3 do not clarify what the asterisk indicates; p < ? with or without multiple comparison correction?

      Thank you for pointing out this oversight, the figure texts have been amended (p. 9, line 168; p.16, line 289).

  2. Jan 2026
    1. Author response:

      We thank all reviewers for their comments. We appreciate the acknowledgement that the paper is important and that results support the major conclusions. We are planning to address the specific concerns as noted by the reviewers in the following way:

      Public Reviews:

      Reviewer #2 (Public review):

      (1) The authors generate a new tool, a Gal4 knock-in of the jam2b locus, to track EGFP-expressing cells over time and follow the developmental trajectory of jam2b-expressing cells. Figure 1 characterizes the line. However, it lacks quantification, e.g., how many etv2-expressing cells also show EGFP expression or the contribution of EGFP-expressing cells to different types of blood vessels. This type of quantification would be useful, as it would also allow for comparison of their findings to their previous data examining the contribution of SVF cells to different types of blood vessels. All the authors state that at 30 hpf, EGFP-expressing cells can be seen in the vasculature (apparently the PCV).

      It is not clear why the authors do not use a nuclear marker for both ECs (as they did in their previous publication) and for jam2b-expressing cells. UAS:nEGFP and UAS:NLS-mcherry (e.g. pt424tg) transgenic lines are available. This would circumvent the problem the authors encounter with the strong fluorescence visible in the yolk extension. It would also facilitate quantifying the contribution of jam2b cells to different types of blood vessels.

      We agree with the importance of quantification. We had performed quantification of jam2b<sup>Gt(2A-Gal4)</sup>;UAS:GFP contribution to different vascular beds, which was shown in Suppl. Fig. S3. We will clarify this in the revision. We also agree that nuclear GFP or mCherry would help to visualize and quantify cells. Unfortunately, we do not have nuclear UAS:GFP or UAS:mCherry line in our possession, and it will take too long to import it for the standard revision timeline. We are working on the construct, and will attempt to establish the line; therefore we are hoping to clarify these results with the nuclear line in the revised manuscript.

      (2) The time-lapse movie in Figure 2 is not very informative, as it just provides a single example of a dividing cell contributing to the PCV. Also, quantifications are needed. As SVF cells appear to expand significantly after their initial specification, it would be informative to know how many cell divisions and which types of blood vessels jam2b-expressing cells contribute to. Can the authors observe cells that give rise to different types of blood vessels? Jam2b expression in LPM cells apparently precedes expression of etv2. Is etv2 needed for maintenance, or do Jam2b-expressing cells contribute to different types of tissues in etv2 mutant embryos? Comparing time-lapse analysis in wildtype and etv2 mutant embryos would address this question.

      The time-lapse was meant to serve as an illustration and confirmation of jam2b cell contribution to vasculature. As noted above, Suppl. Fig. S3 provides quantification of jam2b cell contribution to different vascular beds. We had previously performed detailed time-lapse analysis and quantification of SVF cell migration to PCV, SIA and SIV using etv2-2A-Venus line (Metikala et al 2022, Dev Cell), which has some of the same (or similar) information. It is very challenging to obtain this data using jam2b reporter line due to extensive and bright GFP expression in the mesothelial layer over the yolk and yolk extension; for that reason we can only trace some GFP cells but not all of them. Regarding etv2 requirement for jam2b maintenance, we intend to address this question by analyzing jam2b cell contribution in etv2 MO injected embryos, which recapitulates the phenotype in jam2b mutants.

      (3) In Figure 3, the authors generate UAS:Cre and UAS:Cre-ERT2 transgenic lines to lineage trace the jam2b-expressing cells. It is again not clear why the authors do not use a responder line containing nuclear-localized fluorescent proteins to circumvent the strong expression of fluorescent proteins in the yolk extension. It is also unclear why the two transgenic lines give very different results regarding the number of cells being labelled. The ERT2 fusions label around 3 cells in the SIA, while the Cre line labels only about 1.5 cells per embryo, with very little contribution of labelled cells to other blood vessels. One would expect the Cre line requiring tamoxifen induction to label fewer cells when compared to the constitutive Cre line. What is the reason for this discrepancy? Are the lines single integration? Is there silencing? This needs to be better characterized, also regarding the reproducibility of the experiments. If the Cre lines were to be multiple copy integrations, outcrossing the line might lead to lower expression levels in future generations. 

      It is also not clear how the authors conclude from these findings that "SVF cells show major contribution to the SIA and SIV" when only 1.5 or 3 cells of the SIA are labelled, with even fewer cells labelled in other blood vessels. They speculate that this might be due to low recombination efficiency, a question they then set out to answer using photoconversion of etv2:KAEDE expressing cells, an experiment that they also performed in their 2014 and 2022 publications. To check for low recombination efficiency, the authors could examine the expression of Cre mRNA in their transgenic embryos. Do many more jam2b expressing cells express Cre mRNA than they observe in their switch lines? They could also compare their experiments using Cre recombinase with those using EGFP expression in jam2b cells. EGFP is relatively stable, and the time frames the authors analyze are short. As no quantification of EGFP-expressing cells is provided in Figure 1, this comparison is currently not possible. Do these two different approaches answer different questions here? 

      The reviewer brings up important points, we appreciate that. Unfortunately, we do not have a nuclear switch line in our possession, and it is not possible to obtain it in the normal manuscript revision time line. Regarding UAS:Cre and UAS:CreERT2 lines, they both show rather similar labeling, with most labeled cells present in the SIA. The difference in cell number (1.5 versus 3) is likely due to different levels of Cre expression, which may vary dependent on the integration site. The lines most likely are multi-copy integrations, which can be helpful, as this would result in higher Cre expression. We will address the silencing question by performing in situ hybridization or HCR analysis for Cre or CreERT2 and comparing it with endogenous jam2b expression, as the reviewer suggested. We have noticed that the switch line used, actb2:loxP-BFP-loxP-dsRed, exhibits lower recombination frequency compared to other switch lines (we used it because it was compatible with endothelial fli1:GFP line). We will attempt to answer this question by crossing to other switch lines, which may exhibit higher recombination frequency. In principle, UAS:GFP and switch lines should produce a similar result, except that GFP decays over time and therefore our initial expectation was that switch lines may produce a more accurate result. However, this may not be the case due to low recombination efficiency, which we will attempt to address in the revision.

      (4) Concerning the etv2:KAEDE photoconversion experiments: The percentages the authors report for SVF cells' contribution to the SIV and SIA differ from their previous study (Dev Cell, 2022). In that publication, SVF cells contributed 28% to the SIA and 48% to the SIV. In the present study, the numbers are close to 80% for both vessels. The difference is that the previous study analyzed 2dpf old embryos and the new one 4dpf old embryos. Do SVF-derived cells proliferate more than PCV-derived cells, or is there another explanation for this change in percentage contribution? 

      These numbers refer to different experiments; we apologize for the confusion. As reported earlier in Metikala et 2022, 28% of SVF cells contributed to the SIA and 48% to the SIV by 3 dpf (not 2 dpf; only PCV analysis was done at 2 dpf); SIA and SIV analysis was done based on time-lapse image analysis of etv2-2A-Venus line at 3 dpf, shown in Fig. 3C in Metikala et al. However, this only refers to SVF cell contribution. It does not mean that 28% or 48% cells in SIA or SIV are derived from SVF. The total fraction of SIA and SIV cells that are derived from SVF has not been quantified in the previous study, because that would require accurate tracking of all SVF cells, which is experimentally challenging. Etv2:Kaede experiment is slighly different, because it reports newly formed cells after 24 hpf. It cannot tell if new cells are all derived from SVF cells, although we are not aware of any other source of new endothelial cells at these stages. In the previous study by Metikala et al 2022, we reported ~22 newly formed SIA and ~50 newly formed cells in SIV by 3 dpf (Fig. 1 in Metikala et al 2022), although the entire number of cells was not quantified, therefore the percentage was not known. In the current study, we attempted to estimate the entire percentage of green only Kaede cells, which was close to 80% in both SIA or SIV at 4 dpf. Please note that this estimate was performed in the posterior portion of SIA and SIV that overlies the yolk extension and where SVF cells are observed. We did not quantify cells in the anterior SIV portion, which forms the basket over the yolk.

      (5) Single-cell sequencing data: Why do the authors not show jam2b expression in their single-cell sequencing data? They sorted for (presumably) jam2b-expressing cells and hypothesize that jam2b expression in ECs at this time point is important for the generation of intestinal vasculature. Do ECs in cluster 15 express jam2b? Why are no other top marker genes (tal1, etv2, egfl7, npas4l) included in the dot blot in Figure 5b?

      We appreciate the suggestion and will include additional marker genes as well as jam2b in the revised version of the manuscript.

      (6) Concerns about cell autonomy of mutant phenotypes: The authors need to perform in situ hybridization to characterize jam2a expression. Can it be seen in SVF cells? The double mutants show a clear phenotype in intestinal vessel development; however, it is unclear whether this is due to a cell-autonomous function of jam2a/b within SVF cells. The authors need to address this issue, as jam2b and potentially also jam2a are expressed within the tissue surrounding the forming SVF. For instance, do transplanted mutant cells contribute to the intestinal vasculature to the same extent as wild-type cells do?

      jam2a expression has been characterized in the previous studies and it is shown in the Suppl. Fig. S4E. It is primarily enriched in the skeletal muscle. However, our single-cell RNA-seq analysis shows that SVF cells also express jam2a. We will include additional data on jam2a expression in the revised manuscript. We agree that transplation to address cell autonomy is an important experiment, yet there are some practical challenges to it. Jam2a,jam2b mutant phenotype is only partially penetrant, and about 50% reduction in SVF cell number, as well as partial SIA and SIV phenotypes are observed. Only a small number of transplanted cells may contribute to intestinal vasculature, therefore it may be challenging to see the differences, given the partial penetrance. In an attempt to address cell -autonomy question, we will try a different approach. We will overexpress jam2b labeled with 2A-mCherry, and test if it can rescue the mutant phenotype in cell autonomous manner. Overexpression will be done in a mosaic manner, with higher number of cells labeled than in a typical transplantation experiment.

      (7) Finally, the authors analyze the phenotypes of hand2 mutants and their impact on the expression of jam2b and etv2. They observe a reduction in jam2b and etv2 expression in SVF cells. However, they do not show the vascular phenotypes of hand2 mutants. Is the formation of the SIA and SIV disturbed? Is hand2 cell autonomously needed in ECs? The authors suggest that hand2 controls SVF development through the regulation of jam2b. However, they also show that jam2b mutants do not have a phenotype on their own. Clearly, hand2, if it were to be required in ECs, regulates other genes important for SVF development. These might then regulate jam2b expression. The clear linear relationship, as the title suggests, is not convincingly shown by the data.

      As suggested, we will add the analysis of SIA and SIV in hand2 mutants during the revision process. We could not assess that easily because the line was not maintained in vascular fli1:GFP background. We do not know if hand2 is required cell-autonomously. This is an important question, but it may be answered better in a separate study. Regarding hand2-jam2b axis, it is very clear that jam2b expression in the posterior lateral plate mesoderm is completely lost in hand2 mutants, except for its more anterior domain over the yolk. This does support the idea that hand2 functions upstream of jam2b. However, the relationship may not be necessarily direct. We agree that hand2 may regulate additional genes involved in SVF cell development. We will attempt to clarify this relationship and test if jam2b overexpression may rescue hand2 mutant phenotype.

      Reviewer #3 (Public review):

      (1) Overall molecular mechanisms of Jam2 function are not fully uncovered in the study. How do the adhesion molecules Jam2a and Jam2b regulate SVF cell formation? Are they responsible for migration, adhesion or fate determination of these structures? The authors should provide a more in-depth study of the jam2a, jam2b mutations and assess the processes affected in these mutants. Combining these mutants with etv2:Kaede can also provide a stronger causative link between their functions and defects in SVF formation.

      Our data argue that the initial SVF cell specification (based on etv2 expression) is reduced in jam2a;jam2b mutants. We do not know if the migration or fate determination of the remaining SVF cells is also affected, although this may be more challenging to answer, as there are only few SVF cells remaining. We agree that further mechanistic studies of jam2a,jam2b function are needed. However, we think that this would be better addressed in a separate study. We are currently raising mutants crossed into fli1:Kaede line, which should confirm that there are fewer new cells that emerge after Kaede photoconversion in jam2a,jam2b mutants.

      (2) Have the authors tested the specificity of the jam2b knock-in reporter line? This is an important experiment, as many of the conclusions derive from lineage tracing and fluorescence reporting from this knock-in line. One suggestion is to cross the jam2b:GFP or jam2b:Gal4, UAS:GFP line to the generated jam2b mutants, and examine the expression pattern of these lines. Considering that the ISH experiment showed lack of jam2b expression, the reporter line should not be expressed in the jam2b mutants.

      We show in Suppl. Fig. 2 that jam2b<sup>Gt(2A-Gal4)</sup>;UAS:GFP knock-in line has similar expression pattern as jam2b mRNA by in situ hybridization, which argues for its specificity. In the revision, we plan to use HCR analysis to confirm than jam2b mRNA is expressed in the same cells as jam2b<sup>Gt(2A-Gal4)</sup>;UAS:GFP, as an additional evidence for its specificity. Unfortunately, it is not feasible to cross jam2b knock-in line into jam2b mutants, as suggested by the reviewer. Because jam2b knock-in line targets the endogenous jam2b genomic locus, which is very close in the genome to jam2b promoter deletion in jam2b mutants, the recombination frequency would be very low, and we would not get double jam2b knock-in and knock-out events in the same chromosome.

      (3) The rationale behind the regeneration study is not clear, and the mechanisms underlying the phenotype are not well described. How do the authors explain the phenotype with the impaired regeneration, and what is the significance of this finding as it relates to SVF formation and function? 

      We apologize for this omission. This experiment was more thouroughly described in our previous study by Metikala et al 2022. In that study we showed that when endothelial cells are ablated by treating with MTZ from 6 to 45 hpf, this results in ablation of all vascular endothelial cells except for SVF cells, because they originate later than other cells. We subsequently showed that these SVF cells can partially form PCV and intestinal vasculature, helping them regenerate, which was confirmed by time-lapse imaging. In the current study, we tested if jam2a; jam2b double mutants show defects in such vascular regeneration. Indeed, regeneration after cell ablation was reduced, which correlated with reduction in SVF cell number. This argues that jam2a/b function is required for SVF cell emergence and vascular recovery after endothelial cell ablation. We will provide better description of this experiment and discuss interpretations in the revised manuscript.

      (4) The authors need to include representative images of jam2b>CreERT2 with 4-OH activation at different timepoints in Figure 3.

      Yes, thanks for noting this; these images will be included in the revised manuscript.

      (5) The etv2:Kaede photoconversion experiment to show that the majority of intestinal vasculature derives after 24 hours needs to be supplemented with additional data on photoconverted post-24-hour-old endothelial cells, with the expectation that the majority of intestinal endothelial cells at 4 days will then be labeled with red Kaede. In addition, there have been data that show the red Kaede protein is not stable past several days in vivo, and 3 days might be sufficient for the removal or degradation of this photoconverted protein. Thus, the statement that intestinal vasculature forms largely by new vasculogenesis might be too strong based on existing data.

      It is apparent from Fig. 4B that many other vessels, such as the dorsal aorta and many intersegmental vessels show robust red Kaede expression at 4 dpf, arguing that there is sufficient photoconverted Kaede present at this stage, and its degradation is unlikely to be the reason. However, we are planning to include additional control experiments, as suggested by the reviewer, to make this argument stronger.

      (6) To strengthen the claim that hand2 acts upstream of jam2b, the authors can perform combinatorial genetic epistatic analysis and examine whether jam2b mutations worsen hand2 homozygous or heterozygous effects on the SVF. Similarly, overexpressing jam2b might rescue the loss of SVF/etv2 expression in hand2 mutants. 

      We appreciate this suggestion. Double epistatic analysis, while informative, can be tricky. In this case, we are dealing with jam2a; jam2b redundancy and also the maternal effect. It may take a while considerable effort to generate different combinations of tripple mutant lines (jam2a,jam2b,hand2), and it is unclear whether double or tripple heterozygous embryos will show any defects to clarify their epistatic relationship. Instead, as suggested, we are planning to overexpress jam2b in wild-type and hand2 mutants to address this point.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Wu and colleagues aimed to explain previous findings that adolescents, compared to adults, show reduced cooperation following cooperative behaviour from a partner in several social scenarios. The authors analysed behavioural data from adolescents and adults performing a zero-sum Prisoner's Dilemma task and compared a range of social and non-social reinforcement learning models to identify potential algorithmic differences. Their findings suggest that adolescents' lower cooperation is best explained by a reduced learning rate for cooperative outcomes, rather than differences in prior expectations about the cooperativeness of a partner. The authors situate their results within the broader literature, proposing that adolescents' behaviour reflects a stronger preference for self-interest rather than a deficit in mentalising.

      Strengths:

      The work as a whole suggests that, in line with past work, adolescents prioritise value accumulation, and this can be, in part, explained by algorithmic differences in weighted value learning. The authors situate their work very clearly in past literature, and make it obvious the gap they are testing and trying to explain. The work also includes social contexts that move the field beyond non-social value accumulation in adolescents. The authors compare a series of formal approaches that might explain the results and establish generative and modelcomparison procedures to demonstrate the validity of their winning model and individual parameters. The writing was clear, and the presentation of the results was logical and wellstructured.

      We thank the reviewer for recognizing the strengths of our work.

      Weaknesses:

      (Q1) I also have some concerns about the methods used to fit and approximate parameters of interest. Namely, the use of maximum likelihood versus hierarchical methods to fit models on an individual level, which may reduce some of the outliers noted in the supplement, and also may improve model identifiability.

      We thank the reviewer for this suggestion. Following the comment, we added a hierarchical Bayesian estimation. We built a hierarchical model with both group-level (adolescent group and adult group) and individual-level structures for the best-fitting model. Four Markov chains with 4,000 samples each were run, and the model converged well (see Figure supplement 7)

      We then analyzed the posterior parameters for adolescents and adults separately. The results were consistent with those from the MLE analysis (see Figure 2—figure supplement 5). These additional results have been included in the Appendix Analysis section (also see Figure supplement 5 and 7). In addition, we have updated the code and provided the link for reference. We appreciate the reviewer’s suggestion, which improved our analysis.

      (Q2) There was also little discussion given the structure of the Prisoner's Dilemma, and the strategy of the game (that defection is always dominant), meaning that the preferences of the adolescents cannot necessarily be distinguished from the incentives of the game, i.e. they may seem less cooperative simply because they want to play the dominant strategy, rather than a lower preferences for cooperation if all else was the same.

      We thank the reviewer for this comment and agree that adolescents’ lower cooperation may partly reflect a rational response to the incentive structure of the Prisoner’s Dilemma.

      However, our computational modeling explicitly addressed this possibility. Model 4 (inequality aversion) captures decisions that are driven purely by self-interest or aversion to unequal outcomes, including a parameter reflecting disutility from advantageous inequality, which represents self-oriented motives. If participants’ behavior were solely guided by the payoff-dominant strategy, this model should have provided the best fit. However, our model comparison showed that Model 5 (social reward) performed better in both adolescents and adults, suggesting that cooperative behavior is better explained by valuing social outcomes beyond payoff structures.

      Besides, if adolescents’ lower cooperation is that they strategically respond to the payoff structure by adopting defection as the more rewarding option. Then, adolescents should show reduced cooperation across all rounds. Instead, adolescents and adults behaved similarly when partners defected, but adolescents cooperated less when partners cooperated and showed little increase in cooperation even after consecutive cooperative responses. This pattern suggests that adolescents’ lower cooperation cannot be explained solely by strategic responses to payoff structures but rather reflects a reduced sensitivity to others’ cooperative behavior or weaker social reciprocity motives. We have expanded our Discussion to acknowledge this important point and to clarify how the behavioral and modeling results address the reviewer’s concern.

      “Overall, these findings indicate that adolescents’ lower cooperation is unlikely to be driven solely by strategic considerations, but may instead reflect differences in the valuation of others’ cooperation or reduced motivation to reciprocate. Although defection is the payoffdominant strategy in the Prisoner’s Dilemma, the selective pattern of adolescents’ cooperation and the model comparison results indicate that their reduced cooperation cannot be fully explained by strategic incentives, but rather reflects weaker valuation of social reciprocity.”

      Appraisal & Discussion:

      (Q3) The authors have partially achieved their aims, but I believe the manuscript would benefit from additional methodological clarification, specifically regarding the use of hierarchical model fitting and the inclusion of Bayes Factors, to more robustly support their conclusions. It would also be important to investigate the source of the model confusion observed in two of their models.

      We thank the reviewer for this comment. In the revised manuscript, we have clarified the hierarchical Bayesian modeling procedure for the best-fitting model, including the group- and individual-level structure and convergence diagnostics. The hierarchical approach produced results that fully replicated those obtained from the original maximumlikelihood estimation, confirming the robustness of our findings. Please also see the response to Q1.

      Regarding the model confusion between the inequality aversion (Model 4) and social reward (Model 5) models in the model recovery analysis, both models’ simulated behaviors were best captured by the baseline model. This pattern arises because neither model includes learning or updating processes. Given that our task involves dynamic, multi-round interactions, models lacking a learning mechanism cannot adequately capture participants’ trial-by-trial adjustments, resulting in similar behavioral patterns that are better explained by the baseline model during model recovery. We have added a clarification of this point to the Results:

      “The overlap between Models 4 and 5 likely arises because neither model incorporates a learning mechanism, making them less able to account for trial-by-trial adjustments in this dynamic task.”

      (Q4) I am unconvinced by the claim that failures in mentalising have been empirically ruled out, even though I am theoretically inclined to believe that adolescents can mentalise using the same procedures as adults. While reinforcement learning models are useful for identifying biases in learning weights, they do not directly capture formal representations of others' mental states. Greater clarity on this point is needed in the discussion, or a toning down of this language.

      We sincerely thank the reviewer for this professional comment. We agree that our prior wording regarding adolescents’ capacity to mentalise was somewhat overgeneralized. Accordingly, we have toned down the language in both the Abstract and the Discussion to better align our statements with what the present study directly tests. Specifically, our revisions focus on adolescents’ and adults’ ability to predict others’ cooperation in social learning. This is consistent with the evidence from our analyses examining adolescents’ and adults’ model-based expectations and self-reported scores on partner cooperativeness (see Figure 4). In the revised Discussion, we state:

      “Our results suggest that the lower levels of cooperation observed in adolescents stem from a stronger motive to prioritize self-interest rather than a deficiency in predicting others’ cooperation in social learning”.

      (Q5) Additionally, a more detailed discussion of the incentives embedded in the Prisoner's Dilemma task would be valuable. In particular, the authors' interpretation of reduced adolescent cooperativeness might be reconsidered in light of the zero-sum nature of the game, which differs from broader conceptualisations of cooperation in contexts where defection is not structurally incentivised.

      We thank the reviewer for this comment and agree that adolescents’ lower cooperation may partly reflect a rational response to the incentive structure of the Prisoner’s Dilemma. However, our behavioral and computational evidence suggests that this pattern cannot be explained solely by strategic responses to payoff structures, but rather reflects a reduced sensitivity to others’ cooperative behavior or weaker social reciprocity motives. We have expanded the Discussion to acknowledge this point and to clarify how both behavioral and modeling results address the reviewer’s concern (see also our response to Q2).

      (Q6) Overall, I believe this work has the potential to make a meaningful contribution to the field. Its impact would be strengthened by more rigorous modelling checks and fitting procedures, as well as by framing the findings in terms of the specific game-theoretic context, rather than general cooperation.

      We thank the reviewer for the professional comments, which have helped us improve our work.

      Reviewer #2 (Public review):

      Summary:

      This manuscript investigates age-related differences in cooperative behavior by comparing adolescents and adults in a repeated Prisoner's Dilemma Game (rPDG). The authors find that adolescents exhibit lower levels of cooperation than adults. Specifically, adolescents reciprocate partners' cooperation to a lesser degree than adults do. Through computational modeling, they show that this relatively low cooperation rate is not due to impaired expectations or mentalizing deficits, but rather a diminished intrinsic reward for reciprocity. A social reinforcement learning model with asymmetric learning rate best captured these dynamics, revealing age-related differences in how positive and negative outcomes drive behavioral updates. These findings contribute to understanding the developmental trajectory of cooperation and highlight adolescence as a period marked by heightened sensitivity to immediate rewards at the expense of long-term prosocial gains.

      Strengths:

      (1) Rigid model comparison and parameter recovery procedure.

      (2) Conceptually comprehensive model space.

      (3) Well-powered samples.

      We thank the reviewer for highlighting the strengths of our work.

      Weaknesses:

      (Q1) A key conceptual distinction between learning from non-human agents (e.g., bandit machines) and human partners is that the latter are typically assumed to possess stable behavioral dispositions or moral traits. When a non-human source abruptly shifts behavior (e.g., from 80% to 20% reward), learners may simply update their expectations. In contrast, a sudden behavioral shift by a previously cooperative human partner can prompt higher-order inferences about the partner's trustworthiness or the integrity of the experimental setup (e.g., whether the partner is truly interactive or human). The authors may consider whether their modeling framework captures such higher-order social inferences. Specifically, trait-based models-such as those explored in Hackel et al. (2015, Nature Neuroscience)-suggest that learners form enduring beliefs about others' moral dispositions, which then modulate trial-bytrial learning. A learner who believes their partner is inherently cooperative may update less in response to a surprising defection, effectively showing a trait-based dampening of learning rate.

      We thank the reviewer for this thoughtful comment. We agree that social learning from human partners may involve higher-order inferences beyond simple reinforcement learning from non-human sources. To address this, we had previously included such mechanisms in our behavioral modeling. In Model 7 (Social Reward Model with Influence), we tested a higher-order belief-updating process in which participants’ expectations about their partner’s cooperation were shaped not only by the partner’s previous choices but also by the inferred influence of their own past actions on the partner’s subsequent behavior. In other words, participants could adjust their belief about the partner’s cooperation by considering how their partner’s belief about them might change. Model comparison showed that Model 7 did not outperform the best-fitting model, suggesting that incorporating higher-order influence updates added limited explanatory value in this context. As suggested by the reviewer, we have further clarified this point in the revised manuscript.

      Regarding trait-based frameworks, we appreciate the reviewer’s reference to Hackel et al. (2015). That study elegantly demonstrated that learners form relatively stable beliefs about others’ social dispositions, such as generosity, especially when the task structure provides explicit cues for trait inference (e.g., resource allocations and giving proportions). By contrast, our study was not designed to isolate trait learning, but rather to capture how participants update their expectations about a partner’s cooperation over repeated interactions. In this sense, cooperativeness in our framework can be viewed as a trait-like latent belief that evolves as evidence accumulates. Thus, while our model does not include a dedicated trait module that directly modulates learning rates, the belief-updating component of our best-fitting model effectively tracks a dynamic, partner-specific cooperativeness, potentially reflecting a prosocial tendency.

      (Q2) This asymmetry in belief updating has been observed in prior work (e.g., Siegel et al., 2018, Nature Human Behaviour) and could be captured using a dynamic or belief-weighted learning rate. Models incorporating such mechanisms (e.g., dynamic learning rate models as in Jian Li et al., 2011, Nature Neuroscience) could better account for flexible adjustments in response to surprising behavior, particularly in the social domain.

      We thank the reviewer for the suggestion. Following the comment, we implemented an additional model incorporating a dynamic learning rate based on the magnitude of prediction errors. Specifically, we developed Model 9:  Social reward model with Pearce–Hall learning algorithm (dynamic learning rate), in which participants’ beliefs about their partner’s cooperation probability are updated using a Rescorla–Wagner rule with a learning rate dynamically modulated by the Pearce–Hall (PH) Error Learning mechanism. In this framework, the learning rate increases following surprising outcomes (larger prediction errors) and decreases as expectations become more stable (see Appendix Analysis section for details).

      The results showed that this dynamic learning rate model did not outperform our bestfitting model in either adolescents or adults (see Figure supplement 6). We greatly appreciate the reviewer’s suggestion, which has strengthened the scope of our analysis. We now have added these analyses to the Appendix Analysis section (also Figure Supplement 6) and expanded the Discussion to acknowledge this modeling extension and further discuss its implications.

      (Q3) Second, the developmental interpretation of the observed effects would be strengthened by considering possible non-linear relationships between age and model parameters. For instance, certain cognitive or affective traits relevant to social learning-such as sensitivity to reciprocity or reward updating-may follow non-monotonic trajectories, peaking in late adolescence or early adulthood. Fitting age as a continuous variable, possibly with quadratic or spline terms, may yield more nuanced developmental insights.

      We thank the reviewer for this professional comment. In addition to the linear analyses, we further conducted exploratory analyses to examine potential non-linear relationships between age and the model parameters. Specifically, we fit LMMs for each of the four parameters as outcomes (α+, α-, β, and ω). The fixed effects included age, a quadratic age term, and gender, and the random effects included subject-specific random intercepts and random slopes for age and gender. Model comparison using BIC did not indicate improvement for the quadratic models over the linear models for α<sup>+</sup> (ΔBIC<sub>quadratic-linear</sub> = 5.09), α<sup>-</sup>(ΔBIC<sub>quadratic-linear</sub> = 3.04), β (ΔBIC<sub>quadratic-linear</sub> = 3.9), or ω (ΔBIC<sub>quadratic-linear</sub>= 0). Moreover, the quadratic age term was not significant for α<sup>+</sup>, α<sup>−</sup>, or β (all ps > 0.10). For ω, we observed a significant linear age effect (b = 1.41, t = 2.65, p = 0.009) and a significant quadratic age effect (b = −0.03, t = −2.39, p = 0.018; see Author response image 1). This pattern is broadly consistent with the group effect reported in the main text. The shaded area in the figure represents the 95% confidence interval. As shown, the interval widens at older ages (≥ 26 years) due to fewer participants in that range, which limits the robustness of the inferred quadratic effect. In consideration of the limited precision at older ages and the lack of BIC improvement, we did not emphasize the quadratic effect in the revised manuscript and present these results here as exploratory.

      Author response image 1.

      Linear and quadratic model fits showing the relationship between age and the ω parameter, with 95% confidence intervals.

      (Q4) Finally, the two age groups compared - adolescents (high school students) and adults (university students) - differ not only in age but also in sociocultural and economic backgrounds. High school students are likely more homogenous in regional background (e.g., Beijing locals), while university students may be drawn from a broader geographic and socioeconomic pool. Additionally, differences in financial independence, family structure (e.g., single-child status), and social network complexity may systematically affect cooperative behavior and valuation of rewards. Although these factors are difficult to control fully, the authors should more explicitly address the extent to which their findings reflect biological development versus social and contextual influences.

      We appreciate this comment. Indeed, adolescents (high school students) and adults (university students) differ not only in age but also in sociocultural and socioeconomic backgrounds. In our study, all participants were recruited from Beijing and surrounding regions, which helps minimize large regional and cultural variability. Moreover, we accounted for individual-level random effects and included participants’ social value orientation (SVO) as an individual difference measure.

      Nonetheless, we acknowledge that other contextual factors, such as differences in financial independence, socioeconomic status, and social experience—may also contribute to group differences in cooperative behavior and reward valuation. Although our results are broadly consistent with developmental theories of reward sensitivity and social decisionmaking, sociocultural influences cannot be entirely ruled out. Future work with more demographically matched samples or with socioeconomic and regional variables explicitly controlled will help clarify the relative contributions of biological and contextual factors. Accordingly, we have revised the Discussion to include the following statement:

      “Third, although both age groups were recruited from Beijing and nearby regions, minimizing major regional and cultural variation, adolescents and adults may still differ in socioeconomic status, financial independence, and social experience. Such contextual differences could interact with developmental processes in shaping cooperative behavior and reward valuation. Future research with demographically matched samples or explicit measures of socioeconomic background will help disentangle biological from sociocultural influences.”

      Reviewer #3 (Public review):

      Summary:

      Wu and colleagues find that in a repeated Prisoner's Dilemma, adolescents, compared to adults, are less likely to increase their cooperation behavior in response to repeated cooperation from a simulated partner. In contrast, after repeated defection by the partner, both age groups show comparable behavior.

      To uncover the mechanisms underlying these patterns, the authors compare eight different models. They report that a social reward learning model, which includes separate learning rates for positive and negative prediction errors, best fits the behavior of both groups. Key parameters in this winning model vary with age: notably, the intrinsic value of cooperating is lower in adolescents. Adults and adolescents also differ in learning rates for positive and negative prediction errors, as well as in the inverse temperature parameter.

      Strengths:

      The modeling results are compelling in their ability to distinguish between learned expectations and the intrinsic value of cooperation. The authors skillfully compare relevant models to demonstrate which mechanisms drive cooperation behavior in the two age groups.

      We thank the reviewer’s recognition of our work’s strengths.

      Weaknesses:

      (Q1) Some of the claims made are not fully supported by the data:

      The central parameter reflecting preference for cooperation is positive in both groups. Thus, framing the results as self-interest versus other-interest may be misleading.

      We thank the reviewer for this insightful comment. In the social reward model, the cooperation preference parameter is positive by definition, as defection in the repeated rPDG always yields a +2 monetary advantage regardless of the partner’s action. This positive value represents the additional subjective reward assigned to mutual cooperation (e.g., reciprocity value) that counterbalances the monetary gain from defection. Although the estimated social reward parameter ω was positive, the effective advantage of cooperation is Δ=p×ω−2. Given participants’ inferred beliefs p, Δ was negative for most trials (p×ω<2), indicating that the social reward was insufficient to offset the +2 advantage of defection. Thus, both adolescents and adults valued cooperation positively, but adolescents’ smaller ω and weaker responsiveness to sustained partner cooperation suggest a stronger weighting on immediate monetary payoffs.

      In this light, our framing of adolescents as more self-interested derives from their behavioral pattern: even when they recognized sustained partner cooperation and held high expectations of partner cooperation, adolescents showed lower cooperative behavior and reciprocity rewards compared with adults. Whereas adults increased cooperation after two or three consecutive partner cooperations, this pattern was absent among adolescents. We therefore interpret their behavior as relatively more self-interested, reflecting reduced sensitivity to the social reward from mutual cooperation rather than a categorical shift from self-interest to other-interest, as elaborated in the Discussion.

      (Q2) It is unclear why the authors assume adolescents and adults have the same expectations about the partner's cooperation, yet simultaneously demonstrate age-related differences in learning about the partner. To support their claim mechanistically, simulations showing that differences in cooperation preference (i.e., the w parameter), rather than differences in learning, drive behavioral differences would be helpful.

      We thank the reviewer for raising this important point. In our model, both adolescents and adults updated their beliefs about partner cooperation using an asymmetric reinforcement learning (RL) rule. Although adolescents exhibited a higher positive and a lower negative learning rate than adults, the two groups did not differ significantly in their overall updating of partner cooperation probability (Fig. 4a-b). We then examined the social reward parameter ω, which was significantly smaller in adolescents and determined the intrinsic value of mutual cooperation (i.e., p×ω). This variable differed significantly between groups and closely matched the behavioral pattern.

      Following the reviewer’s suggestion, we conducted additional simulations varying one model parameter at a time while holding the others constant. The difference in mean cooperation probability between adults and adolescents served as the index (positive = higher cooperation in adults). As shown in the Author response image 2, decreases in ω most effectively reproduced the observed group difference (shaded area), indicating that age-related differences in cooperation are primarily driven by variation in the social reward parameter ω rather than by others.

      Author response image 2.

      Simulation results showing how variations in each model parameter affect the group difference in mean cooperation probability (Adults – Adolescents). Based on the bestfitting Model 8 and parameters estimated from all participants, each line represents one parameter (i.e., α+, α-, ω, β) systematically varied within the tested range (α±:0.1–0.9; ω, β:1–9) while other parameters were held constant. Positive values indicate higher cooperation in adults. Smaller ω values most strongly reproduced the observed group difference, suggesting that reduced social reward weighting primarily drives adolescents’ lower cooperation.

      (Q3) Two different schedules of 120 trials were used: one with stable partner behavior and one with behavior changing after 20 trials. While results for order effects are reported, the results for the stable vs. changing phases within each schedule are not. Since learning is influenced by reward structure, it is important to test whether key findings hold across both phases.

      We thank the reviewer for this thoughtful and professional comment. In our GLMM and LMM analyses, we focused on trial order rather than explicitly including the stable vs. changing phase factor, due to concerns about multicollinearity. In our design, phases occur in specific temporal segments, which introduces strong collinearity with trial order. In multi-round interactions, order effects also capture variance related to phase transitions.

      Nonetheless, to directly address this concern, we conducted additional robustness analyses by adding a phase variable (stable vs. changing) to GLMM1, LMM1, and LMM3 alongside the original covariates. Across these specifications, the key findings were replicated (see GLMM<sub>sup</sub>2 and LMM<sub>sup</sub>4–5; Tables 9-11), and the direction and significance of main effects remained unchanged, indicating that our conclusions are robust to phase differences.

      (Q4) The division of participants at the legal threshold of 18 years should be more explicitly justified. The age distribution appears continuous rather than clearly split. Providing rationale and including continuous analyses would clarify how groupings were determined.

      We thank the reviewer for this thoughtful comment. We divided participants at the legal threshold of 18 years for both conceptual and practical reasons grounded in prior literature and policy. In many countries and regions, 18 marks the age of legal majority and is widely used as the boundary between adolescence and adulthood in behavioral and clinical research. Empirically, prior studies indicate that psychosocial maturity and executive functions approach adult levels around this age, with key cognitive capacities stabilizing in late adolescence (Icenogle et al., 2019; Tervo-Clemmens et al., 2023). We have clarified this rationale in the Introduction section of the revised manuscript.

      “Based on legal criteria for majority and prior empirical work, we adopt 18 years as the boundary between adolescence and adulthood (Icenogle et al., 2019; Tervo-Clemmens et al., 2023).”

      We fully agree that the underlying age distribution is continuous rather than sharply divided. To address this, we conducted additional analyses treating age as a continuous predictor (see GLMM<sub>sup</sub>1 and LMM<sub>sup</sub>1–3; Tables S1-S4), which generally replicated the patterns observed with the categorical grouping. Nevertheless, given the limited age range of our sample, the generalizability of these findings to fine-grained developmental differences remains constrained. Therefore, our primary analyses continue to focus on the contrast between adolescents and adults, rather than attempting to model a full developmental trajectory.

      (Q5) Claims of null effects (e.g., in the abstract: "adults increased their intrinsic reward for reciprocating... a pattern absent in adolescents") should be supported with appropriate statistics, such as Bayesian regression.

      We thank the reviewer for highlighting the importance of rigor when interpreting potential null effects. To address this concern, we conducted Bayes factor analyses of the intrinsic reward for reciprocity and reported the corresponding BF10 for all relevant post hoc comparisons. This approach quantifies the relative evidence for the alternative versus the null hypothesis, thereby providing a more direct assessment of null effects. The analysis procedure is now described in the Methods and Materials section:

      “Post hoc comparisons were conducted using Bayes factor analyses with MATLAB’s bayesFactor Toolbox (version v3.0, Krekelberg, 2024), with a Cauchy prior scale σ = 0.707.”

      (Q6) Once claims are more closely aligned with the data, the study will offer a valuable contribution to the field, given its use of relevant models and a well-established paradigm.

      We are grateful for the reviewer’s generous appraisal and insightful comments.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) I commend the authors on a well-structured, clear, and interesting piece of work. I have several questions and recommendations that, if addressed, I believe will strengthen the manuscript.

      We thank the reviewer for commending the organization of our paper.

      (2) Introduction: - Why use a zero-sum (Prisoner's Dilemma; PD) versus a mixed-motive game (e.g. Trust Task) to study cooperation? In a finite set of rounds, the dominant strategy can be to defect in a PD.

      We thank the reviewer for this helpful comment. We agree that both the rationale for using the repeated Prisoner’s Dilemma (rPDG) and the limitations of this framework should be clarified. We chose the rPDG to isolate the core motivational conflict between selfinterest and joint welfare, as its symmetric and simultaneous structure avoids the sequential trust and reputation dependencies/accumulation inherent to asymmetric tasks such as the Trust Game (King-Casas et al., 2005; Rilling et al., 2002).

      Although a finitely repeated rPDG theoretically favors defection, extensive prior research shows that cooperation can still emerge in long repeated interactions when players rely on learning and reciprocity rather than backward induction (Rilling et al., 2002; Fareri et al., 2015). Our design employed 120 consecutive rounds, allowing participants to update expectations about partner behavior and to establish stable reciprocity patterns over time. We have added the following clarification to the Introduction:

      “The rPDG provides a symmetric and simultaneous framework that isolates the motivational conflict between self-interest and joint welfare, avoiding the sequential trust and reputation dynamics characteristic of asymmetric tasks such as the Trust Game (Rilling et al., 2002; King-Casas et al., 2005)”

      (3) Methods:

      Did the participants know how long the PD would go on for?

      Were the participants informed that the partner was real/simulated?

      Were the participants informed that the partner was going to be the same for all rounds?

      We thank the reviewer for the meticulous review work, which helped us present the experimental design and reporting details more clearly. the following clarifications: I. Participants were not informed of the total number of rounds in the rPDG. This prevented endgame expectations and avoided distraction from counting rounds, which could introduce additional effects. II. Participants were told that their partner was another human participant in the laboratory. However, the partner’s behavior was predetermined by a computer program. This design enabled tighter experimental control and ensured consistent conditions across age groups, supporting valid comparisons. III. Participants were informed that they would interact with the same partner across all rounds, aligning with the essence of a multiround interaction paradigm and stabilizing partner-related expectations. For transparency, we have clarified these points in the Methods and Materials section:

      “Participants were told that their partner was another human participant in the laboratory and that they would interact with the same partner across all rounds. However, in reality, the actions of the partner were predetermined by a computer program. This setup allowed for a clear comparison of the behavioral responses between adolescents and adults. Participants were not informed of the total number of rounds in the rPDG.”

      (4) The authors mention that an SVO was also recorded to indicate participant prosociality. Where are the results of this? Did this track game play at all? Could cooperativeness be explained broadly as an SVO preference that penetrated into game-play behaviour?

      We thank the reviewer for pointing this out. We agree that individual differences in prosociality may shape cooperative behavior, so we conducted additional analyses incorporating SVO. Specifically, we extended GLMM1 and LMM3 by adding the measured SVO as a fixed effect with random slopes, yielding GLMM<sub>sup</sub>3 and LMM<sub>sup</sub>6 (Tables 12–13). The results showed that higher SVO was associated with greater cooperation, whereas its effect on the reward for reciprocity was not significant. Importantly, the primary findings remained unchanged after controlling for SVO. These results indicate that cooperativeness in our task cannot be explained solely by a broad SVO preference, although a more prosocial orientation was associated with greater cooperation. We have reported these analyses and results in the Appendix Analysis section.

      (5) Why was AIC chosen rather an BIC to compare model dominance?

      Sorry for the lack of clarification. Both the Akaike Information Criterion (AIC, Akaike, 1974) and Bayesian Information Criterion (BIC, Schwarz, 1978) are informationtheoretic criterions for model comparison, neither of which depends on whether the models to be compared are nested to each other or not (Burnham et al., 2002). We have added the following clarification into the Methods.

      “We chose to use the AICc as the metric of goodness-of-fit for model comparison for the following statistical reasons. First, BIC is derived based on the assumption that the “true model” must be one of the models in the limited model set one compares (Burnham et al., 2002; Gelman & Shalizi, 2013), which is unrealistic in our case. In contrast, AIC does not rely on this unrealistic “true model” assumption and instead selects out the model that has the highest predictive power in the model set (Gelman et al., 2014). Second, AIC is also more robust than BIC for finite sample size (Vrieze, 2012).”

      (6) I believe the model fitting procedure might benefit from hierarchical estimation, rather than maximum likelihood methods. Adolescents in particular seem to show multiple outliers in a^+ and w^+ at the lower end of the distributions in Figure S2. There are several packages to allow hierarchical estimation and model comparison in MATLAB (which I believe is the language used for this analysis;

      see https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007043).

      We thank the reviewer for this helpful comment and for referring us to relevant methodological work (Piray et al., 2019). We have addressed this point by incorporating hierarchical Bayesian estimation, which effectively mitigates outlier effects and improves model identifiability. The results replicated those obtained with MLE fitting and further revealed group-level differences in key parameters. Please see our detailed response to Reviewer#1 Q1 for the full description of this analysis and results.

      (7) Results: Model confusion seems to show that the inequality aversion and social reward models were consistently confused with the baseline model. Is this explained or investigated? I could not find an explanation for this.

      The apparent overlap between the inequality aversion (Model 4) and social reward (Model 5) models in the recovery analysis likely arises because neither model includes a learning mechanism, making them unable to capture trial-by-trial adjustments in this dynamic task. Consequently, both were best fit by the baseline model. Please see Response to Reviewer #1 Q3 for related discussion.

      (8) Figures 3e and 3f show the correlation between asymmetric learning rates and age. It seems that both a^+ and a^- are around 0.35-0.40 for young adolescents, and this becomes more polarised with age. Could it be that with age comes an increasing discernment of positive and negative outcomes on beliefs, and younger ages compress both positive and negative values together? Given the higher stochasticity in younger ages (\beta), it may also be that these values simply represent higher uncertainty over how to act in any given situation within a social context (assuming the differences in groups are true).

      We appreciate this insightful interpretation. Indeed, both α+ and α- cluster around 0.35–0.40 in younger adolescents and become increasingly polarized with age, suggesting that sensitivity to positive versus negative feedback is less differentiated early in development and becomes more distinct over time. This interpretation remains tentative and warrants further validation. Based on this comment, we have revised the Discussion to include this developmental interpretation.

      We also clarify that in our model β denotes the inverse temperature parameter; higher β reflects greater choice precision and value sensitivity, not higher stochasticity. Accordingly, adolescents showed higher β values, indicating more value-based and less exploratory choices, whereas adults displayed relatively greater exploratory cooperation. These group differences were also replicated using hierarchical Bayesian estimation (see Response to Reviewer #1 Q1). In response to this comment, we have added a statement in the Discussion highlighting this developmental interpretation.

      “Together, these findings suggest that the differentiation between positive and negative learning rates changes with age, reflecting more selective feedback sensitivity in development, while higher β values in adolescents indicate greater value sensitivity. This interpretation remains tentative and requires further validation in future research.”

      (9) A parameter partial correlation matrix (off-diagonal) would be helpful to understand the relationship between parameters in both adolescents and adults separately. This may provide a good overview of how the model properties may change with age (e.g. a^+'s relation to \beta).

      We thank the reviewer for this helpful comment. We fully agree that a parameter partial correlation matrix can further elucidate the relationships among parameters. Accordingly, we conducted a partial correlation analysis and added the visually presented results to the revised manuscript as Figure 2-figure supplement 4.

      (10) It would be helpful to have Bayes Factors reported with each statistical tests given that several p-values fall within the 0.01 and 0.10.

      We thank the reviewer for this important recommendation. We have conducted Bayes factor analyses and reported BF10 for all relevant post hoc comparisons. We also clarified our analysis in the Methods and Materials section:

      “Post hoc comparisons were conducted using Bayes factor analyses with MATLAB’s bayesFactor Toolbox (version v3.0, Krekelberg, 2024), with a Cauchy prior scale σ = 0.707.”

      (11) Discussion: I believe the language around ruling out failures in mentalising needs to be toned down. RL models do not enable formal representational differences required to assess mentalising, but they can distinguish biases in value learning, which in itself is interesting. If the authors were to show that more complex 'ToM-like' Bayesian models were beaten by RL models across the board, and this did not differ across adults and adolescents, there would be a stronger case to make this claim. I think the authors either need to include Bayesian models in their comparison, or tone down their language on this point, and/or suggest ways in which this point might be more thoroughly investigated (e.g., using structured models on the same task and running comparisons: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087619).

      We thank the reviewer for the comments. Please see our response to Reviewer 1 (Appraisal & Discussion section) for details.

      Reviewer #2 (Recommendations for the authors):

      (1) The authors may want to show the winning model earlier (perhaps near the beginning of the Results section, when model parameters are first mentioned).

      We thank the reviewer for this suggestion. We agree that highlighting the winning model early improves clarity. Currently, we have mentioned the winning model before the beginning of the Results section. Specifically, in the penultimate paragraph of the Introduction we state:

      “We identified the asymmetric RL learning model as the winning model that best explained the cooperative decisions of both adolescents and adults.”

      Reviewer #3 (Recommendations for the authors):

      (1) In addition to the points mentioned above, I suggest the following:

      Clarify plots by clearly explaining each variable. In particular, the indices 1 vs. 1,2 vs 1,2,3 were not immediately understandable.

      We thank the reviewer for this suggestion. We agree that the indices were not immediately clear. We have revised the figure captions (Figure 1 and 4) to explicitly define these terms more clearly:

      “The x-axis represents the consistency of the partner’s actions in previous trials (t<sub>−1</sub>: last trial; t<sub>−1,2</sub>: last two trials;<sub>t−1,2,3</sub>: last three trials).”

      (2) It's unclear why the index stops at 3. If this isn't the maximum possible number of consecutive cooperation trials, please consider including all relevant data, as adolescents might show a trend similar to adults over more trials.

      We thank the reviewer for raising this point. In our exploratory analyses, we also examined longer streaks of consecutive partner cooperation or defection (up to four or five trials). Two empirical considerations led us to set the cutoff at three in the final analyses. First, the influence of partner behavior diminished sharply with temporal distance. In both GLMMs and LMMs, coefficients for earlier partner choices were small and unstable, and their inclusion substantially increased model complexity and multicollinearity. This recency pattern is consistent with learning and decision models emphasizing stronger weighting of recent evidence (Fudenberg & Levine, 2014; Fudenberg & Peysakhovich, 2016). Second, streaks longer than three were rare, especially among some participants, leading to data sparsity and inflated uncertainty. Including these sparse conditions risked biasing group estimates rather than clarifying them. Balancing informativeness and stability, we therefore restricted the index to three consecutive partner choices in the main analyses, which we believe sufficiently capture individuals’ general tendencies in reciprocal cooperation.

      (3) The term "reciprocity" may not be necessary. Since it appears to reflect a general preference for cooperation, it may be clearer to refer to the specific behavior or parameter being measured. This would also avoid confusion, especially since adolescents do show negative reciprocity in response to repeated defection.

      We thank you for this comment. In our work, we compute the intrinsic reward for reciprocity as p × ω, where p is the partner cooperation expectation and ω is the cooperation preference. In the rPDG, this value framework manifests as a reciprocity-derived reward: sustained mutual cooperation maximizes joint benefits, and the resulting choice pattern reflects a value for reciprocity, contingent on the expected cooperation of the partner. This quantity enters the trade-off between U<sub>cooperation</sub> and U<sub>defection</sub> and captures the participant’s intrinsic reward for reciprocity versus the additional monetary reward payoff of defection. Therefore, we consider the term “reciprocity” an acceptable statement for this construct.

      (4) Interpretation of parameters should closely reflect what they specifically measure.

      We thank the reviewer for pointing this out. We have refined the relevant interpretations of parameters in the current Results and Discussion sections.

      (5) Prior research has shown links between Theory of Mind (ToM) and cooperation (e.g., Martínez-Velázquez et al., 2024). It would be valuable to test whether this also holds in your dataset.

      We thank the reviewer for this thoughtful comment. Although we did not directly measure participants’ ToM, our design allowed us to estimate participants’ trial-by-trial inferences (i.e., expectations) about their partner’s cooperation probability. We therefore treat these cooperation expectations as an indirect representation for belief inference, which is related to ToM processes. To test whether this belief-inference component relates to cooperation in our dataset, we further conducted an exploratory analysis (GLMM<sub>sup</sub>4) in which participants’ choices were regressed on their cooperation expectations, group, and the group × cooperation-expectation interaction, controlling for trial number and gender, with random effects. Consistent with the ToM–cooperation link in prior research (MartínezVelázquez et al., 2024), participants’ expectations about their partner’s cooperation significantly predicted their cooperative behavior (Table 14), suggesting that decisions were shaped by social learning about others’ inferred actions. Moreover, the interaction between group and cooperation expectation was not significant, indicating that this inference-driven social learning process likely operates similarly in adolescents and adults. This aligns with our primary modeling results showing that both age groups update beliefs via an asymmetric learning process. We have reported these analyses in the Appendix Analysis section.

      (6) More informative table captions would help the reader. Please clarify how variables are coded (e.g., is female = 0 or 1? Is adolescent = 0 or 1?), to avoid the need to search across the manuscript for this information.

      We thank the reviewer for raising this point. We have added clear and standardized variable coding in the table notes of all tables to make them more informative and avoid the need to search the paper. We have ensured consistent wording and formatting across all tables.

      (7) I hope these comments are helpful and support the authors in further strengthening their manuscript.

      We thank the three reviewers for their comments, which have been helpful in strengthening this work.

      References

      (1) Fudenberg, D., & Levine, D. K. (2014). Recency, consistent learning, and Nash equilibrium. Proceedings of the National Academy of Sciences of the United States of America, 111(Suppl. 3), 10826–10829. https://doi.org/10.1073/pnas.1400987111.

      (2) Fudenberg, D., & Peysakhovich, A. (2016). Recency, records, and recaps: Learning and nonequilibrium behavior in a simple decision problem. ACM Transactions on Economics and Computation, 4(4), Article 23, 1–18. https://doi.org/10.1145/2956581

      (3) Hackel, L., Doll, B., & Amodio, D. (2015). Instrumental learning of traits versus rewards: Dissociable neural correlates and effects on choice. Nature Neuroscience, 18, 1233– 1235. https://doi.org/10.1038/nn.4080

      (4) Icenogle, G., Steinberg, L., Duell, N., Chein, J., Chang, L., Chaudhary, N., Di Giunta, L., Dodge, K. A., Fanti, K. A., Lansford, J. E., Oburu, P., Pastorelli, C., Skinner, A. T.Sorbring, E., Tapanya, S., Uribe Tirado, L. M., Alampay, L. P., Al-Hassan, S. M.,Takash, H. M. S., & Bacchini, D. (2019). Adolescents’ cognitive capacity reaches adult levels prior to their psychosocial maturity: Evidence for a “maturity gap” in a multinational, cross-sectional sample. Law and Human Behavior, 43(1), 69–85. https://doi.org/10.1037/lhb0000315

      (5) Krekelberg, B. (2024). Matlab Toolbox for Bayes Factor Analysis (v3.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.13744717

      (6) Martínez-Velázquez, E. S., Ponce-Juárez, S. P., Díaz Furlong, A., & Sequeira, H. (2024). Cooperative behavior in adolescents: A contribution of empathy and emotional regulation? Frontiers in Psychology, 15,1342458. https://doi.org/10.3389/fpsyg.2024.1342458

      (7) Tervo-Clemmens, B., Calabro, F. J., Parr, A. C., et al. (2023). A canonical trajectory of executive function maturation from adolescence to adulthood. Nature Communications, 14, 6922. https://doi.org/10.1038/s41467-023-42540-8

      (8) King-Casas, B., Tomlin, D., Anen, C., Camerer, C. F., Quartz, S. R., & Montague, P. R. (2005). Getting to know you: reputation and trust in a two-person economic exchange. Science, 308(5718), 78-83. https://doi.org/10.1126/science.1108062

      (9) Rilling, J. K., Gutman, D. A., Zeh, T. R., Pagnoni, G., Berns, G. S., & Kilts, C. D. (2002).A neural basis for social cooperation. Neuron, 35(2), 395-405. https://doi.org/10.1016/s0896-6273(02)00755-9

      (10) Fareri, D. S., Chang, L. J., & Delgado, M. R. (2015). Computational substrates of social value in interpersonal collaboration. Journal of Neuroscience, 35(21), 8170-8180. https://doi.org/10.1523/JNEUROSCI.4775-14.2015

      (11) Akaike, H. (2003). A new look at the statistical model identification. IEEE transactions on automatic control, 19(6), 716-723. https://doi.org/10.1109/TAC.1974.1100705

      (12) Schwarz, G. (1978). Estimating the dimension of a model. The annals of statistics, 461464. https://doi.org/10.1214/aos/1176344136

      (13) Burnham, K. P., & Anderson, D. R. (2002). Model selection and multimodel inference: A practical information-theoretic approach (2nd ed.). Springer.https://doi.org/10.1007/b97636

      (14) Gelman, A., & Shalizi, C. R. (2013). Philosophy and the practice of Bayesian statistics. British Journal of Mathematical and Statistical Psychology, 66(1), 8–38. https://doi.org/10.1111/j.2044-8317.2011.02037.x

      (15) Gelman, A., Carlin, J. B., Stern, H. S., Dunson, D. B., Vehtari, A., & Rubin, D. B. (2014). Bayesian data analysis (3rd ed.). Chapman and Hall/CRC. https://doi.org/10.1201/b16018

      (16) Vrieze, S. I. (2012). Model selection and psychological theory: A discussion of the differences between the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC). Psychological Methods, 17(2), 228–243. https://doi.org/10.1037/a0027127

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      This work by Reitz, Z. L. et al. developed an automated tool for high-throughput identification of microbial metallophore biosynthetic gene clusters (BGCs) by integrating knowledge of chelating moiety diversity and transporter gene families. The study aimed to create a comprehensive detection system combining chelator-based and transporter-based identification strategies, validate the tool through large-scale genomic mining, and investigate the evolutionary history of metallophore biosynthesis across bacteria.

      Major strengths include providing the first automated, high-throughput tool for metallophore BGC identification, representing a significant advancement over manual curation approaches. The ensemble strategy effectively combines complementary detection methods, and experimental validation using HPLC-HRMS strengthens confidence in computational predictions. The work pioneers a global analysis of metallophore diversity across the bacterial kingdom and provides a valuable dataset for future computational modeling.

      Some limitations merit consideration. First, ground truth datasets derived from manual curation may introduce selection bias toward well-characterized systems, potentially affecting performance assessment accuracy. Second, the model's dependence on known chelating moieties and transporter families constrains its ability to detect novel metallophore architectures, limiting discovery potential in metagenomic datasets. Third, while the proposed evolutionary hypothesis is internally consistent, it lacks direct validation and remains speculative without additional phylogenetic studies.

      The authors successfully achieved their stated objectives. The tool demonstrates robust performance metrics and practical utility through large-scale application to representative genomes. Results strongly support their conclusions through rigorous validation, including experimental confirmation of predicted metallophores via HPLC-HRMS analysis.

      The work provides a significant and immediate impact by enabling the transition from labor-intensive manual approaches to automated screening. The comprehensive phylogenetic framework advances understanding of bacterial metal acquisition evolution, informing future studies on microbial metal homeostasis. Community utility is substantial, since the tool and accompanying dataset create essential resources for comparative genomics, algorithm development, and targeted experimental validation of novel metallophores.

      We thank the reviewer for their valuable feedback. We appreciate the positive words, and agree with their listed limitations. Regarding the following comment:

      “Third, while the proposed evolutionary hypothesis is internally consistent, it lacks direct validation and remains speculative without additional phylogenetic studies.”

      We agree that additional phylogenetic analyses are needed in future studies. For the revised manuscript, we have validated our evolutionary hypotheses by additionally analyzing two gene families using the likelihood-based tool AleRax, which implements a probabilistic DTL model. The results were consistent with the eMPRess parsimony-based reconstructions, showing comparable patterns of rare duplication, moderate gene loss, and extensive horizontal transfer. Both methods identified similar lineages as the most probable origin and major recipients of transfer events. This agreement between independent reconciliation frameworks supports the reliability of our evolutionary conclusions. We have added a statement referencing this cross-method validation in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      This study presents a systematic and well-executed effort to identify and classify bacterial NRP metallophores. The authors curate key chelator biosynthetic genes from previously characterized NRP-metallophore biosynthetic gene clusters (BGCs) and translate these features into an HMM-based detection module integrated within the antiSMASH platform.

      The new algorithm is compared with a transporter-based siderophore prediction approach, demonstrating improved precision and recall. The authors further apply the algorithm to large-scale bacterial genome mining and, through reconciliation of chelator biosynthetic gene trees with the GTDB species tree using eMPRess, infer that several chelating groups may have originated prior to the Great Oxidation Event.

      Overall, this work provides a valuable computational framework that will greatly assist future in silico screening and preliminary identification of metallophore-related BGCs across bacterial taxa.

      Strengths:

      (1) The study provides a comprehensive curation of chelator biosynthetic genes involved in NRP-metallophore biosynthesis and translates this knowledge into an HMM-based detection algorithm, which will be highly useful for the initial screening and annotation of metallophore-related BGCs within antiSMASH.

      (2) The genome-wide survey across a large bacterial dataset offers an informative and quantitative overview of the taxonomic distribution of NRP-metallophore biosynthetic chelator groups, thereby expanding our understanding of their phylogenetic prevalence.

      (3) The comparative evolutionary analysis, linking chelator biosynthetic genes to bacterial phylogeny, provides an interesting and valuable perspective on the potential origin and diversification of NRP-metallophore chelating groups.

      We greatly appreciate these comments.

      Weaknesses:

      (1) Although the rule-based HMM detection performs well in identifying major categories of NRP-metallophore biosynthetic modules, it currently lacks the resolution to discriminate between fine-scale structural or biochemical variations among different metallophore types.

      We agree that this is a current limitation to the methodology. More specific metallophore structural prediction is among our future goals for antiSMASH. We have added a statement to this effect in the conclusion.

      (2) While the comparison with the transporter-based siderophore prediction approach is convincing overall, more information about the dataset balance and composition would be appreciated. In particular, specifying the BGC identities, source organisms, and Gram-positive versus Gram-negative classification would improve transparency. In the supplementary tables, the "Just TonB" section seems to include only BGCs from Gram-negative bacteria - if so, this should be clearly stated, as Gram type strongly influences siderophore transport systems.

      The reviewer raises good points here. An additional ZIP file containing all BGCs used for the manual curation was inadvertently left out of the supplemental dataset for the first version of the manuscript. We have added columns with source organisms and Gram stain (retrieved from Bacdive) to Table S2. F1 scores were similar for Gram positive and negative subsets, as seen in the new Table S2.

      We thank the reviewer for suggesting this additional analysis, and have added a brief statement in the revised manuscript.

      The “Just TonB” section (in which we tested the performance of requiring TonB without another transporter) was not used for the manuscript. We will preserve it in the revised Table S2 for transparency.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In line 43:

      "excreted" should be replace by "secreted".

      Done.

      (2) In lines 158-159:

      "we manually predicted metallophore production among a large set of BGCs."

      If they are first "annotated with default antiSMASH v6.1", then it is not entirely manual, right? I would suggest making this sentence clearer.

      We have revised the language.

      (3) In lines 165-169:

      It would be good to show the confusion matrix of these results.

      The confusion matrices are found in Table S2, columns AL-AR.

      (4) In Table 1:

      Method names (AntiSMASH rules/Transporter genes) could be misleading, since they are all AntiSMASH-based, right?

      We have adjusted the methods to clarify that while the transporter genes were detected using a modified version of antiSMASH, they are not related to our chelator-based detection rule (which is now correctly singular throughout the text).

      (5) Line 198:

      There are accidental spaces and characters inserted here.

      We could not find any accidental spaces and characters here.

      (6) Line 209:

      "In total, 3,264 NRP metallophore BGC regions were detected"

      Is this number correct? I don't see a correspondence in Table 1.

      We have added the following sentence to the Table 1 legend: “An additional 54 BGC regions were detected as NRP metallophores without meeting the requirements for the antiSMASH NRPS rule.”

      (7) Line 294:

      "From B. brennerae, we identified four catecholic compounds"

      From the bacterial cells or the culture supernatant? I think it is important to state this in a more precise way. If it is from the supernatant, it could be from EVs.

      We state in line 292 that “organic compounds were extracted from the culture supernatants”. As our goal was only to confirm the ability of the strains to produce the predicted metallophores, the precise localization (including cell pellet or EVs) was not explored.

      (8) Lines 349-357:

      These results would benefit greatly from a visualization strategy.

      Thank you, we have added a reference to the existing visualization in Fig. 5, Ring C.

      (9) Lines 452-454:

      How could clusters be de-replicated? Is there an identity equivalence scheme or similarity metric?

      The BGC regions were de-replicated with BiG-SCAPE, which uses multiple similarity metrics as described in Navarro-Muñoz et al, 2020. Clusters could be dereplicated further using a more strict cutoff.

      (10) Line 457:

      "relatively low number of published genomes."

      Could metagenome-assembled genomes help in that matter?

      This is a good question, but we find that MAGs are usually too fragmented to yield complete NRPS BGC regions. We’ve added additional sentences earlier in the discussion: “Detection rates were also lower for fragmented genomes; unfortunately, this limitation (inherent to antiSMASH itself) may hinder the identification of metallophore biosynthesis in metagenomes. As long-read sequencing of metagenomes becomes more common, we expect that detection will improve.”

      (11) Lines 514-515:

      "Adequately-performing pHMMs for Asp and His β-hydroxylase subtypes could not be constructed using the above method."

      What is the overall impact of this discrepancy in the methodology for these specific groups?

      The phylogeny-based methodology was used to reduce false positives. We expect this method will have improved precision at the possible expense of recall.

      (12) Lines 543-545:

      "RefSeq representative bacterial genomes were dereplicated at the genus level using R, randomly selecting one genome for each of the 330 genera determined by GTDB"

      Isn't it more of a random sampling than a dereplication? Dereplication would involve methods such as ANI computation.

      You are correct; we have adjusted the language to clarify.

      (13) Lines 559-560: "were filtered to remove clusters on contig edges."

      This sentence is confusing because networks will be mentioned soon, and they also have edges (not the edges mentioned here), and they could also be clustered (not the clusters mentioned here). Is there a way to make the terminology clearer?

      Thank you, we have adjusted the text to read “BGC regions on contig boundaries”

      (14) Line 560:

      "The resulting 2,523 BGC regions, as well as 78 previously reported BGCs "

      How many were there before filtering?

      We have added the number: 3,264

      (15) Lines 579-580:

      Confusing terminology, as mentioned in Lines 559-560.

      Adjusted as above.

      General comments and questions:

      An objective suggestion to enrich the discussion is to address the role of bacterial extracellular vesicles (EVs) as metallophore carriers. Studies show that EVs, such as outer membrane vesicles, can transport siderophores or other metallophores for iron acquisition in various bacteria, functioning as "public goods" for community-wide nutrient sharing. Highlighting this mechanism would add ecological and functional context to the manuscript. In the future, EV-associated metallophore transport could also be considered for integration into computational detection tools.

      We thank the reviewer for the suggestion; however, we do not think that such a discussion is needed. We briefly discuss the ecological function of metallophores as public goods (and public bads) in the first paragraph of the introduction. We did not find any reports that EV-associated genes co-localize with metallophore BGCs, which would be required for their presence to be a useful marker of metallophore production.

      Is there a feasible path to more generalizable detection of chelating motifs using chemistry-aware features? For example, a machine learning classifier trained on submolecular descriptors (e.g., functional groups, coordination motifs, SMARTS patterns, graph fingerprints, metal-binding propensity scores) could complement the current genome-based approach and broaden coverage beyond known metallophore families. While the discussion mentions future extensions centered on genomic features, integrating chemical information from predicted or known products (or biosynthetic logic inferred from BGC composition) could be explored. A hybrid framework-linking BGC-derived features with chemistry-derived features-may improve both recall for novel metallophore classes and precision in distinguishing true chelators from confounders, thereby increasing overall accuracy.

      We can envision a classifier that uses submolecular descriptors to predict the ability of a molecule to bind metal ions. However, starting with a BGC and accurately predicting the structure of a hitherto unknown chelating moiety will likely prove difficult.  We have added a sentence to the discussion stating that a future tool could use accessory genes to more completely predict chemical structure.

      Although the initial analysis was conducted using RefSeq genomes, what are the anticipated challenges and limitations when scaling this method for BGC prospecting in metagenome-assembled genomes (MAGs), particularly considering the inherent quality differences, assembly fragmentation, and taxonomic uncertainties that characterize MAG datasets compared to curated reference genomes?

      Please see our response to comment 10, line 457. Our pHMM-based approach is designed to be robust to organism taxonomy; however, fragmentation is a significant barrier to accurate antiSMASH-based BGC detection (including in contig-level single-isolate genomes, see Table 1).

      Reviewer #2 (Recommendations for the authors):

      (1) In the "Chemical identification of genome-predicted siderophores across taxa" section, it would be helpful to annotate the cross-species similarities between predicted metallophore BGCs and their reference clusters (Ref BGCs). As currently described, the main text seems to highlight the cross-species resolving power of BiG-SCAPE itself rather than demonstrating the taxonomic generalizability of the chelator HMM-based detection module.

      Thank you for this comment. We intended to display that the new rule is useful for detecting BGCs in unexplored taxa, but we acknowledge that there is not a great diversity in the strains we selected. We have removed “across taxa” to avoid misleading the reader and clarify our intent.

      (2) In addition to using eMPRess for gene-species reconciliation, it may be beneficial to explore or at least reference alternative reconciliation tools to validate the inferred duplication, transfer, and loss (DTL) scenarios. Incorporating such cross-method comparisons would enhance the robustness and credibility of the evolutionary conclusions.

      We appreciate this valuable suggestion. To validate the robustness of our reconciliation-based inferences, we additionally analyzed two gene families using the likelihood-based tool AleRax, which implements a probabilistic DTL model. The results were consistent with the eMPRess parsimony-based reconstructions, showing comparable patterns of rare duplication, moderate gene loss, and extensive horizontal transfer. Both methods identified similar lineages as the most probable origin and major recipients of transfer events. This agreement between independent reconciliation frameworks supports the reliability of our evolutionary conclusions. We have added a brief statement referencing this cross-method validation in the revised manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      (1) Legionella effectors are often activated by binding to eukaryote-specific host factors, including actin. The authors should test the following: a) whether Lfat1 can fatty acylate small G-proteins in vitro; b) whether this activity is dependent on actin binding; and c) whether expression of the Y240A mutant in mammalian cells affects the fatty acylation of Rac3 (Figure 6B), or other small G-proteins.

      We were not able to express and purify the full-length recombinant Lfat1 to perform fatty acylation of small GTPases in vitro. However, In cellulo overexpression of the Y240A mutant still retained ability to fatty acylate Rac3 and another small GTPase RheB (see Figure 6-figure supplement 2). We postulate that under infection conditions, actin-binding might be required to fatty acylate certain GTPases due to the small amount of effector proteins that secreted into the host cell.

      (2) It should be demonstrated that lysine residues on small G-proteins are indeed targeted by Lfat1. Ideally, the functional consequences of these modifications should also be investigated. For example, does fatty acylation of G-proteins affect GTPase activity or binding to downstream effectors?

      We have mutated K178 on RheB and showed that this mutation abolished its fatty acylation by Lfat1 (see Author response image 1 below). We were not able to test if fatty acylation by Lfat1 affect downstream effector binding.

      Author response image 1.

      (3) Line 138: Can the authors clarify whether the Lfat1 ABD induces bundling of F-actin filaments or promotes actin oligomerization? Does the Lfat1 ABD form multimers that bring multiple filaments together? If Lfat1 induces actin oligomerization, this effect should be experimentally tested and reported. Additionally, the impact of Lfat1 binding on actin filament stability should be assessed. This is particularly important given the proposed use of the ABD as an actin probe.

      The ABD domain does not form oligomer as evidenced by gel filtration profile of the ABD domain. However, we do see F-actin bundling in our in vitro -F-actin polymerization experiment when both actin and ABD are in high concentration (data not shown). Under low concentration of ABD, there is not aggregation/bundling effect of F-actin.

      (4) Line 180: I think it's too premature to refer to the interaction as having "high specificity and affinity." We really don't know what else it's binding to.

      We have revised the text and reworded the sentence by removing "high specificity and affinity."

      (5) The authors should reconsider the color scheme used in the structural figures, particularly in Figures 2D and S4.

      Not sure the comments on the color scheme of the structure figures.

      (6) In Figure 3E, the WT curve fits the data poorly, possibly because the actin concentration exceeds the Kd of the interaction. It might fit better to a quadratic.

      We have performed quadratic fitting and replaced Figure 3E.

      (7) The authors propose that the individual helices of the Lfat1 ABD could be expressed on separate proteins and used to target multi-component biological complexes to F-actin by genetically fusing each component to a split alpha-helix. This is an intriguing idea, but it should be tested as a proof of concept to support its feasibility and potential utility.

      It is a good suggestion. We plan to thoroughly test the feasibility of this idea as one of our future directions.

      (8) The plot in Figure S2D appears cropped on the X-axis or was generated from a ~2× binned map rather than the deposited one (pixel size ~0.83 Å, plot suggests ~1.6 Å). The reported pixel size is inconsistent between the Methods and Table 1-please clarify whether 0.83 Å refers to super-resolution.

      Yes, 0.83 Å is super-resolution.  We have updated in the cryoEM table

      Reviewer #2:

      Weaknesses:

      (1) The authors should use biochemical reactions to analyze the KFAT of Llfat1 on one or two small GTPases shown to be modified by this effector in cellulo. Such reactions may allow them to determine the role of actin binding in its biochemical activity. This notion is particularly relevant in light of recent studies that actin is a co-factor for the activity of LnaB and Ceg14 (PMID: 39009586; PMID: 38776962; PMID: 40394005). In addition, the study should be discussed in the context of these recent findings on the role of actin in the activity of L. pneumophila effectors.

      We have new data showed that Actin binding does not affect Lfat1 enzymatic activity. (see response to Reviewer #1). We have added this new data as Figure S7 to the paper. Accordingly, we also revised the discussion by adding the following paragraph.

      “The discovery of Lfat1 as an F-actin–binding lysine fatty acyl transferase raised the intriguing question of whether its enzymatic activity depends on F-actin binding. Recent studies have shown that other Legionella effectors, such as LnaB and Ceg14, use actin as a co-factor to regulate their activities. For instance, LnaB binds monomeric G-actin to enhance its phosphoryl-AMPylase activity toward phosphorylated residues, resulting in unique ADPylation modifications in host proteins  (Fu et al, 2024; Wang et al, 2024). Similarly, Ceg14 is activated by host actin to convert ATP and dATP into adenosine and deoxyadenosine monophosphate, thereby modulating ATP levels in L. pneumophila–infected cells (He et al, 2025). However, this does not appear to be the case for Lfat1. We found that Lfat1 mutants defective in F-actin binding retained the ability to modify host small GTPases when expressed in cells (Figure S7). These findings suggest that, rather than serving as a co-factor, F-actin may serve to localize Lfat1 via its actin-binding domain (ABD), thereby confining its activity to regions enriched in F-actin and enabling spatial specificity in the modification of host targets.”

      (2) The development of the ABD domain of Llfat1 as an F-actin domain is a nice extension of the biochemical and structural experiments. The authors need to compare the new probe to those currently commonly used ones, such as Lifeact, in labeling of the actin cytoskeleton structure.

      We fully agree with the reviewer’s insightful suggestion. However, a direct comparison of the Lfat1 ABD domain with commonly used actin probes such as Lifeact, as well as evaluation of the split α-helix probe (as suggested by Reviewer #1), would require extensive and technically demanding experiments. These are important directions that we plan to pursue in future studies.

      For all other minors, we have made corrections/changes in our revised text and figures.

    1. Author response:

      The following is the authors’ response to the current reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript by Yamamoto et al. presents a model by which the four main axes of the limb are required for limb regeneration to occur in the axolotl. A longstanding question in regeneration biology is how existing positional information is used to regenerate the correct missing elements. The limb provides an accessible experimental system by which to study the involvement of the anteroposterior, dorsoventral, and proximodistal axes in the regenerating limb. Extensive experimentation has been performed in this area using grafting experiments. Yamamoto et al. use the accessory limb model and some molecular tools to address this question. There are some interesting observations in the study. In particular, one strength the potent induction of accessory limbs in the dorsal axis with BMP2+Fgf2+Fgf8 is very interesting. Although interesting, the study makes bold claims about determining the molecular basis of DV positional cues, but the experimental evidence is not definitive and does not take into account the previous work on DV patterning in the amniote limb. Also, testing the hypothesis on blastemas after limb amputation would be needed to support the strong claims in the study.

      Strengths:

      The manuscript presents some novel new phenotypes generated in axolotl limbs due to Wnt signaling. This is generally the first example in which Wnt signaling has provided a gain of function in the axolotl limb model. They also present a potent way of inducing limb patterning in the dorsal axis by the addition of just beads loaded with Bmp2+Fgf8+Fgf2.

      Comments on revised version:

      Re-evaluation: The authors have significantly improved the manuscript and their conclusions reflect the current state of knowledge in DV patterning of tetrapod limbs. My only point of consideration is their claim of mesenchymal and epithelial expression of Wnt10b and the finding that Fgf2 and Wnt10b are lowly expressed. It is based upon the failed ISH, but this doesn't mean they aren't expressed. In interpreting the Li et al. scRNAseq dataset, conclusions depend heavily on how one analyzes and interprets it. The 7DPA sample shows a very low representation of epithelial cells compared to other time points, but this is likely a technical issue. Even the epithelial marker, Krt17, and the CT/fibroblast marker show some expression elsewhere. If other time points are included in the analysis, Wnt10b, would be interpreted as relatively highly expressed almost exclusively in the epithelium. By selecting the 7dpa timepoint, which may or may not represent the MB stage as it wasn't shown in the paper, the conclusions may be based upon incomplete data. I don't expect the authors to do more work, but it is worth mentioning this possibility. The authors have considered and made efforts to resolve previous concerns.

      We are grateful for the constructive comments. As Reviewer #1 suggested, we noted that clearer expression patterns of Wnt10b and Fgf2 may be detectable in scRNA-seq analyses at other stages, and we also clarified that low-level signals of epithelial and CT/fibroblast markers outside their expected clusters may reflect technical bias in the Discussion section. In addition, we agree with the reviewer’s point that our unsuccessful ISH experiments and the low abundance detected by RT-qPCR do not demonstrate absence of expression, and that conclusions from reanalyzing the Li et al. scRNA-seq dataset can depend strongly on analytical choices; therefore, while we focused on the 7 dpa sample because our RT-qPCR data suggested that Wnt10b and Fgf2 may be most enriched around the MB stage (the original study refers to 7 dpa as MB), we explicitly acknowledged that analyzing a single time point—especially one with a low representation of epithelial cells—may yield incomplete or stage-biased interpretations, and that inclusion of additional datasets could reveal clearer and potentially different expression patterns in the Discussion section. We also tempered our wording regarding the inferred cellular sources to avoid over-interpretation based on the current data in the Results section.

      Reviewer #2 (Public review):

      Summary:

      This study explores how signals from all sides of a developing limb, front/back and top/bottom, work together to guide the regrowth of a fully patterned limb in axolotls, a type of salamander known for its impressive ability to regenerate limbs. Using a model called the Accessory Limb Model (ALM), the researchers created early staged limb regenerates (called blastemas) with cells from different sides of the limb. They discovered that successful limb regrowth only happens when the blastema contains cells from both the top (dorsal) and bottom (ventral) of the limb. They also found that a key gene involved in front/back limb patterning, called Shh (Sonic hedgehog), is only turned on when cells from both the dorsal and ventral sides come into contact. The study identified two important molecules, Wnt10B and FGF2, that help activate Shh when dorsal and ventral cells interact. Finally, the authors propose a new model that explains how cells from all four sides of a limb, dorsal, ventral, anterior (front), and posterior (back), contribute at both the cellular and molecular level to rebuilding a properly structured limb during regeneration.

      Strengths:

      The techniques used in this study, like delicate surgeries, tissue grafting, and implanting tiny beads soaked with growth factors, are extremely difficult, and only a few research groups in the world can do them successfully. These methods are essential for answering important questions about how animals like axolotls regenerate limbs with the correct structure and orientation. To understand how cells from different sides of the limb communicate during regeneration, the researchers used a technique called in situ hybridization, which lets them see where specific genes are active in the developing limb. They clearly showed that the gene Shh, which helps pattern the front and back of the limb, only turns on when cells from both the top (dorsal) and bottom (ventral) sides are present and interacting. The team also took a broad, unbiased approach to figure out which signaling molecules are unique to dorsal and ventral limb cells. They tested these molecules individually and discovered which could substitute for actual dorsal and ventral cells, providing the same necessary signals for proper limb development. Overall, this study makes a major contribution to our understanding of how complex signals guide limb regeneration, showing how different regions of the limb work together at both the cellular and molecular levels to rebuild a fully patterned structure.

      Weaknesses:

      Because the expressional analyses are performed on thin sections of regenerating tissue, in the original manuscript, they provided only a limited view of the gene expression patterns in their experiments, opening the possibility that they could be missing some expression in other regions of the blastema. Additionally, the quantification method of the expressional phenotypes in most of the experiments did not appear to be based on a rigorous methodology. The authors' inclusion of an alternate expression analysis, qRT-PCR, on the entire blastema helped validate that the authors are not missing something in the revised manuscript.

      Overall, the number of replicates per sample group in the original manuscript was quite low (sometimes as low as 3), which was especially risky with challenging techniques like the ones the authors employ. The authors have improved the rigor of the experiment in the revised manuscript by increasing the number of replicates. The authors have not performed a power analysis to calculate the number of animals used in each experiment that is sufficient to identify possible statistical differences between groups. However, the authors have indicated that there was not sufficient preliminary data to appropriately make these quantifications.

      Likewise, in the original manuscript, the authors used an AI-generated algorithm to quantify symmetry on the dorsal/ventral axis, and my concern was that this approach doesn't appear to account for possible biases due to tissue sectioning angles. They also seem to arbitrarily pick locations in each sample group to compare symmetry measurements. There are other methods, which include using specific muscle groups and nerve bundles as dorsal/ventral landmarks, that would more clearly show differences in symmetry. The authors have now sufficiently addressed this concern by including transverse sections of the limbs annd have explained the limitations of using a landmark-based approach in their quantification strategy.

      We are grateful for the careful evaluation of the technical rigor and quantification. We have benefited from the reviewer’s earlier feedback, which guided revisions that improved the manuscript’s rigor and presentation.

      Reviewer #3 (Public review):

      Summary:

      After salamander limb amputation, the cross-section of the stump has two major axes: anterior-posterior and dorsal-ventral. Cells from all axial positions (anterior, posterior, dorsal, ventral) are necessary for regeneration, yet the molecular basis for this requirement has remained unknown. To address this gap, Yamamoto et al. took advantage of the ALM assay, in which defined positional identities can be combined on demand and their effects assessed through the outgrowth of an ectopic limb. They propose a compelling model in which dorsal and ventral cells communicate by secreting Wnt10b and Fgf2 ligands respectively, with this interaction inducing Shh expression in posterior cells. Shh was previously shown to induce limb outgrowth in collaboration with anterior Fgf8 (PMID: 27120163). Thus, this study completes a concept in which four secreted signals from four axial positions interact for limb patterning. Notably, this work firmly places dorsal-ventral interactions upstream of anterior-posterior, which is striking for a field that has been focussed on anterior-posterior communication. The ligands identified (Wnt10b, Fgf2) are different to those implicated in dorsal-ventral patterning in the non-regenerative mouse and chick models. The strength of this study is in the context of ALM/ectopic limb engineering. Although the authors attempt to assay the expression of Wnt10b and Fgf2 during limb regeneration after amputation, they were unable to pinpoint the precise expression domains of these genes beyond 'dorsal' and 'ventral' blastema. Given that experimental perturbations were not performed in regenerating limbs - almost exclusively under ALM conditions - this author finds the title "Dorsoventral-mediated Shh induction is required for axolotl limb regeneration" a little misleading.

      Strengths:

      (1) The ALM and use of GFP grafts for lineage tracing (Figures 1-3) take full advantage of the salamander model's unique ability to outgrow patterned limbs under defined conditions. As far as I am aware, the ALM has not been combined with precise grafts that assay 2 axial positions at once, as performed in Figure 3. The number of ALMs performed in this study deserves special mention, considering the challenging surgery involved.

      (2) The authors identify that posterior Shh is not expressed unless both dorsal and ventral cells are present. This echoes previous work in mouse limb development models (AER/ectoderm-mesoderm interaction) but this link between axes was not known in salamanders. The authors elegantly reconstitute dorsal-ventral communication by grafting, finding that this is sufficient to trigger Shh expression (Figure 3 - although see also section on Weaknesses).

      (3) Impressively, the authors discovered two molecules sufficient to substitute dorsal or ventral cells through electroporation into dorsal- or ventral- depleted ALMs (Figure 5). These molecules did not change the positional identity of target cells. The same group previously identified the ventral factor (Fgf2) to be a nerve-derived factor essential for regeneration. In Figure 6, the authors demonstrate that nerve-derived factors, including Fgf2, are alone sufficient to grow out ectopic limbs from a dorsal wound. Limb induction with a 3-factor cocktail without supplementing with other cells is conceptually important for regenerative engineering.

      (4) The writing style and presentation of results is very clear.

      Overall appraisal:

      This is a logical and well-executed study that creatively uses the axolotl model to advance an important framework for understanding limb patterning. The relevance of the mechanisms to normal limb regeneration are not yet substantiated, in the opinion of this reviewer. Additionally, Wnt10b and Fgf2 should be considered molecules sufficient to substitute dorsal and ventral identity (solely in terms of inducing Shh expression). It is not yet clear whether these molecules are truly necessary (loss of function would address this).

      Comments on revisions:

      Congratulations - I still find this an elegant and easy-to-read study with significant implications for the field! Linking your mechanisms to normal limb regeneration (i.e. regenerating blastema, not ALM), as well as characterising the cell populations involved, will be interesting directions for the future.

      We are grateful for the constructive comments. To mitigate the concerns raised by Reviewer #3, we cited a previous study suggesting that ALM was used as the alternative experimental system for studying limb regeneration (Nacu et al., 2016, Nature, PMID: 27120163; Satoh et al., 2007, Developmental Biology, PMID: 17959163) in the Introduction section. We are confident that our ALM-based data provide a reasonable basis for understanding limb regeneration. We agree that there are important remaining questions—such as which cell populations express Wnt10b and Fgf2 and how endogenous WNT10B and FGF2 signals induce Shh expression in normal regeneration—which should be investigated in future studies to deepen our understanding of limb regeneration.


      The following is the authors’ response to the original reviews.

      Recommendations for the authors:

      Reviewing Editor Comments:

      The authors should be commended for addressing this gap - how cues from the DV axis interact with the AP axis during limb regeneration. Overall, the concept presented in this manuscript is extremely interesting and could be of high value to the field. However, the manuscript in its current form is lacking a few important data and resolution to fully support their conclusions, and the following needs to be addressed before publication:

      (1) ISH data on Wnt10b and FGF2 from various regeneration time points are essential to derive the conclusion. Preferably multiplex ISH of Wnt10b/Fgf2/Shh or at least canonical ISH on serial sections to demonstrate their expression in dermis/epidermis and order of gene expression i.e. Shh is only expressed after expression of Wnt10b/FGF2. It would certainly help if this can also be shown in regular blastema.

      We are grateful for the constructive suggestion on assessing Wnt10b and Fgf2 expression during regular regeneration, and we agree that clarifying their expression patterns in regular blastemas is important for strengthening the conclusions of our study. Because we cannot currently ensure sufficient sensitivity with multiplex FISH in our laboratory—partly due to high background—, we conducted conventional ISH on serial sections of regular blastemas at several time points (Fig. S5A). However, the expression patterns of Wnt10b and Fgf2 were not clear. To complement the ISH results, we performed RT-qPCR on microdissected dorsal and ventral halves of regular blastemas at the MB stage (Fig. S5B). We found that Wnt10b and Fgf2 were expressed at significantly higher levels in the dorsal and ventral halves, respectively, compared to the opposite half. This dorsal/ventral biased expression of Wnt10b/Fgf2 is consistent with our RNA-seq data. We further quantified expression levels of Wnt10b, Fgf2, and Shh across stages (intact, EB, MB, LB, and ED) and found that Wnt10b and Fgf2 peaked at the MB stage, whereas Shh peaked at the LB stage—consistent with the editor’s request regarding the order of gene expression (Fig. S5C). This temporal offset in upregulation supports our model. These results are now included in the revised manuscript (Line 294‒306).

      To identify the cell types expressing Wnt10b or Fgf2, we analyzed published single-cell RNA-seq data (7 dpa blastema (MB), Li et al., 2021). As a result, Fgf2 expression was observed in the mesenchymal cluster, whereas Wnt10b expression was observed in both mesenchymal and epithelial clusters (Fig. S6). However, because only a small fraction of cells expressed Wnt10b, the principal cellular source of WNT10B protein remains unclear. The apparent low abundance likely contributes to the weak ISH signals and reflects current technical limitations. In addition, Wnt10b and Fgf2 expression did not follow Lmx1b expression (Fig. S6J, K), and Wnt10b and Fgf2 themselves were not exclusive (Fig. S6L). These results are now included in the revised manuscript (Line 307‒321). Together with the RT-qPCR data (Fig. S5B), these results suggest that Wnt10b and Fgf2 are not exclusively confined to purely dorsal or ventral cells at the single-cell level, even though they show dorsoventral bias when assessed in bulk tissue. These results suggest that Wnt10b/Fgf2 expression is not restricted to dorsal/ventral cells but mediated by dorsal/ventral cells, and co-existence of both signals should provide a permissive environment for Shh induction. Defining the precise spatial patterns of Wnt10b and Fgf2 in regular regeneration will therefore be an important goal for future work.  

      (2) Validation of the absence of gene expression via qRT PCR in the given sample will increase the rigor, as suggested by reviewers.

      We thank for this important suggestion and agree that validation by qRT-PCR increases the rigor of our study. Accordingly, we performed RT-qPCR on AntBL, PostBL, DorBL, and VentBL to corroborate the ISH results. The results are now included in Fig. 2. We also verified by RT-qPCR that Shh expression following electroporation and the quantitative results are now provided in Fig. 5.

      (3) Please increase n for experiments where necessary and mention n values in the figures.

      We thank for this helpful comment and agree on the importance of providing sufficient sample sizes. Accordingly, we increased the n for the relevant experiments and have indicated the n values in the corresponding figure legends.

      (4) Most comments by all three reviewers are constructive and largely focus on improving the tone and language of the manuscript, and I expect that the authors should take care of them.

      We thank the reviewers for their constructive feedback on the tone and language of the manuscript. We have carefully revised the text according to each comment, and we hope these modifications have improved both clarity and readability.

      In addition, in revising the manuscript we also refined the conceptual framework. Our new analysis of Wnt10b and Fgf2 expression during normal regeneration suggests that these genes are not expressed in a strictly dorsal- or ventral-specific manner at the single-cell level. When these observations are considered together with (i) the RNA-seq comparison of dorsally and ventrally induced ALM blastemas, (ii) RT-qPCR of microdissected dorsal and ventral halves of regenerating blastemas, and (iii) the functional electroporation experiments, our interpretation is that Wnt10b and Fgf2 act as dorsal- and ventral-mediated signals, respectively: their production is regulated by dorsal or ventral cells, and the presence of both signals is required to induce Shh expression. Given those, we now think our conclusion might be explained without using the confusing term, “positional cue”. Because the distinction between “positional cue” and “positional information” could be confusing as noted by the reviewers, we rewrote our manuscript without using “positional cue.

      Reviewer #1 (Recommendations for the authors):

      (1) Line 61: More explanation for what a double-half limb means is needed.

      We thank the reviewer for this suggestion. We have revised the manuscript (Line 73‒76). Specifically, we now explain that a double-dorsal limb, for example, is a chimeric limb generated by excising the ventral half and replacing it with a dorsal half from the contralateral limb while preserving the anteroposterior orientation.

      (2) Line 63-65: "Such blastemas form hypomorphic, spike-like structures or fail to regenerate entirely." This statement does not represent the breadth of work on the APDV axis in limb regeneration. The cited Bryant 1976 reference tested only double-posterior and double-anterior newt limbs, demonstrating the importance of disposition along the AP axis, not DV. Others have shown that the regeneration of double-half limbs depends upon the age of the animal and the length of time between the grafting of double-half limbs and amputation. Also, some double-dorsal or double-ventral limbs will regenerate complete AP axes with symmetrical DV duplications (Burton, Holder, and Jesani, 1986). Also, sometimes half dorsal stylopods regenerate half dorsal and half ventral, or regenerate only half ventral, suggesting there are no inductive cues across the DV axis as there are along the AP axis. Considering this is the basis of the study under question, more is needed to convince that the DV axis is necessary for the generation of the AP axis.

      We thank the reviewer for this detailed and constructive comment. We acknowledge that previous studies have reported a range of outcomes for double-half limbs. For example, Burton et al. (1986) described regeneration defects in double-dorsal (DD) and double-ventral (VV) limbs, although limb patterning did occur in some cases (Burton et al., 1986, Table 1). As the reviewer notes, regenerative outcomes depend on variables such as animal age and the interval between construction of the double-half limb and amputation, sometimes called the effect of healing time (Tank and Holder, 1978). Moreover, variability has been reported not only in DD/VV limbs but also in double-anterior (AA) and double-posterior (PP) limbs (e.g., Bryant, 1976; Bryant and Baca, 1978; Burton et al., 1986). In the revised manuscript, we have therefore modified the statement to avoid over-generalization and to emphasize that regeneration can be incomplete under these conditions (Line 76‒82). Importantly, in order to provide the additional evidence requested and to directly re-evaluate whether dorsal and ventral cells are required for limb patterning, we performed the ALM experiments shown in Fig. 1. The ALM system allows us to assess this question in a binary manner (regeneration vs. non-regeneration), thereby strengthening the rationale for our conclusions regarding the necessity of the APDV orientations. We also revised a sentence at the beginning of the Results section to emphasize this point (Line 139‒140).

      (3) Line 71: These findings suggest that specific signals from all four positional domains must be integrated for successful limb patterning, such that the absence of any one of them leads to failure." I was under the impression that half posterior limbs can grow all elements, but half anterior can only grow anterior elements.

      We thank the reviewer for this helpful clarification. As summarized by Stocum, half-limb experiments show that while some digit formation can occur, limb patterning remains incomplete in both anterior-half and posterior-half limbs in some cases (Stocum, 2017). We see this point as closely related to the broader question of whether proper limb patterning requires the integration of signals from all four positional domains. As noted in our response above, our ALM experiments in Fig. 1 were designed to test this point directly, and our data support the interpretation that cells from all four orientations are necessary for correct limb patterning.

      (4) Line 79-81: This is stated later in lines 98-105. I suggest expanding here or removing it here.

      We thank the reviewer for this suggestion. In the original version, lines 79–81 introduced our use of the terms “positional cue” and “positional information,” and this content partially overlapped with what later appeared in lines 98–105. In the revised manuscript, we have substantially rewritten this section (Line 82‒84), including the sentences corresponding to lines 79–81 in the original version, to remove the term “positional cue,” as explained in our response to the Editor’s comment (4); our revision reflects new analyses indicating that Wnt10b and Fgf2 appear not be strictly restricted to dorsal or ventral cell populations, and we now describe these factors as dorsal- or ventral-mediated signals that act across dorsoventral domains to induce Shh expression. Accordingly, we no longer maintain the original use of “positional cue” and “positional information.”

      (5) Line 92 - 93: "Similarly, an ALM blastema can be induced in a position-specific manner along the limb axes. In this case, the induced ALM blastema will lack cells from the opposite side." This sentence is difficult to follow. Isn't it the same thing stated in lines 88-90?

      We thank the reviewer for this comment. We revised the sentence to improve readability and to avoid redundancy with original Lines 88–90 (Line 104‒106).

      (6) Line 107: I think the appropriate reference is McCusker et al., 2014 (Position-specific induction of ectopic limbs in non-regenerating blastemas on axolotl forelimbs), although Vieira et al., 2019 can be included here. In addition, Ludolph et al 1990 should be cited.

      We thank the reviewer for this suggestion. We have added McCusker et al. (2014) and Ludolph et al. (1990) as references in the revised manuscript (Line 120‒121).

      (7) Line 107-109: A missing point is how the ventral information is established in the amniote limb. From what I remember, it is the expression of Engrailed 1, which inhibits the ventral expression of Wnt7a, and hence Lmx1b. This would suggest that there is no secreted ventral cue. This is a relatively large omission in the manuscript.

      We thank the reviewer for this comment. We agree that ventral fate in amniotes is specified by En1 in the ventral ectoderm, which represses Wnt7a and thereby prevents induction of Lmx1b; accordingly, a secreted ventral morphogen analogous to dorsal Wnt7a has not been established. We added this point to the revised Introduction (Line 61‒64).

      By contrast, in axolotl limb regeneration, our previous work on Lmx1b expression suggests that DV identities reflect the original positional identity rather than being re-specified during regeneration (Yamamoto et al., 2022). Within this framework, our original use of the term “ventral positional cue” does not imply a ventral patterning morphogen in the amniote sense; rather, it denotes downstream signals induced by cells bearing ventral identity that are required for the blastema to form a patterned limb. This interpretation is consistent with classic studies on double-half chimeras and ectopic contacts between opposite regions (Iten & Bryant, 1975; Bryant & Iten, 1976; Maden, 1980; Stocum, 1982) as well as with our ALM data (Fig. 1). For this reason, we intentionally used the term “positional cues” to refer to signals provided by cells bearing ventral identity, which can be considered separable from the DV patterning mechanism itself, in the original text. As explained in our response to the Editor’s comment (4), we describe these signals as “signals mediated by dorsal/ventral cells,” rather than “positional cues” in the revised manuscript.

      The necessity of dorsal- and ventral-mediated signals is supported by classic studies on the double-half experiment. In the non-regenerating cases, structural patterns along the anteroposterior axis appear to be lost even though both anterior and posterior cells should, in principle, be present in a blastema induced from a double-dorsal or double-ventral limbs. In limb development of amniotes, Wnt7a/Lmx1b or En-1 mutants show that limbs can exhibit anteroposterior patterning even when tissues are dorsalized or ventralized—that is, in the relative absence of ventral or dorsal cells, respectively (Riddle et al., 1995; Chen et al., 1998; Loomis et al., 1996). Taken together, axolotl limb regeneration, in which the presence of both dorsal and ventral cells plays a role in anteroposterior patterning, should differ from other model organisms. It is reasonable to predict the dorsal- and ventral-mediated signals in axolotl limb regeneration. We included this point in the revised manuscript (Line 82‒89). However, there is no evidence that these signals are secreted molecules. For this reason, we have carefully used the term “dorsal-/ventral-mediated signals” in the Introduction without implying secretion.

      (8) Introduction - In general, the argument is a bit misleading. It is written as if it is known that a ventral cue is necessary, but the evidence from other animal models is lacking, from what I know. I may be wrong, but further argument would strengthen the reasoning for the study.

      We thank the reviewer for this thoughtful comment. We agree that it should not read as if it is known that a ventral cue is necessary. In the revised Introduction, we have addressed this in several ways. First, as described in our response to comment (7), we now explicitly note that in amniote limb development ventral identity is specified by En1-mediated repression of Wnt7a, and that a secreted ventral morphogen equivalent to dorsal Wnt7a has not been established. Second, we removed the term “positional cue” and no longer present “ventral positional cue” as a defined entity. Instead, we use mechanistic phrasing such as “signals mediated by ventral cells” and “signals mediated by dorsal cells,” which does not assume that such signals are secreted morphogens or universally conserved. Third, we have reframed the role of dorsal- and ventral-mediated signals as a working hypothesis specific to axolotl limb regeneration, rather than as a general conclusion across model systems.

      (9) Line 129: Remove "As mentioned before".

      We thank the reviewer for this suggestion. We have removed the phrase “As mentioned before” in the revised manuscript (Line 143).

      (10) Figure 1: Are Lmx1, Fgf8, and Shh mutually exclusive? Multiplexed FISH would provide this information, and is a relatively important question considering the strong claims in the study.

      We thank the reviewer for raising this important point. As noted in our response to the editor’s comment, we cannot currently ensure sufficiently high detection sensitivity with multiplex FISH in our laboratory. However, based on previous reports (Nacu et al., 2016), Fgf8 and Shh should be mutually exclusive. In contrast, with respect to Lmx1b, our analysis suggests that its expression is not mutually exclusive with either Fgf8 or Shh, at least their expression domains. To confirm this, we analyzed the published scRNA-seq data and the results were added to the supplemental figure 6. Fgf8 and Shh were expressed in both Lmx1b-positive and Lmx1b-negative cells (Fig. S6H, I), but Fgf8 and Shh themselves were mutually exclusive (Fig. S6M). This point is now included in the revised manuscript (Line 314‒317).

      (11) Results section and Figure 2: More evidence is needed for the lack of Shh expression ISH in tissue sections. Demonstrating the absence of something needs some qPCR or other validation to make such a claim.

      We thank the reviewer for this suggestion. We performed qRT-PCR on ALM blastemas to complement the ISH data (Fig. 2).

      (12) Line 179: I think they are likely leucistic d/d animals and not wild-type animals based upon the images.

      We thank the reviewer for this observation. In the revised manuscript, we have corrected the description to “leucistic animals” (Line 194).

      (13) Line 183-186: I'm a bit confused about this interpretation. If Shh turns on in just a posterior blastema, wouldn't it turn on in a grafted posterior tissue into a dorsal or ventral region? Isn't this independent of environment, meaning Shh turns on if the cells are posterior, regardless of environment?

      Our interpretation is that only posterior-derived cells possess the competency to express Shh. In other words, whether a cell is capable of expressing Shh depends on its original positional identity (Iwata et al., 2020), but whether it actually expresses Shh depends on the environment in which the cell is placed. The results of Fig. 3E and G indicate that Shh activation is dependent on environment and that the posterior identity is not sufficient to activate Shh expression. We have revised the manuscript to emphasize this distinction more clearly (Line 198‒203).

      (14) Figure 4: Do the limbs have an elbow, or is it just a hand?

      We thank the reviewer for this thoughtful question. From the appearance, an elbow-like structure can occasionally be seen; however, we did not examine the skeletal pattern in detail because all regenerated limbs used for this analysis were sectioned for the purpose of symmetry evaluation, and we therefore cannot state this conclusively. While this is indeed an important point, analyzing proximodistal patterning would require a very large number of additional experiments, which falls outside the main focus of the present study. For this reason, and also to minimize animal use in accordance with ethical considerations, we did not pursue further experiments here. In response to this point, we have added a description of the skeletal morphology of ectopic limbs induced by BMP2+FGF2+FGF8 bead implantation (Fig. 6). In these experiments, multiple ectopic limbs were induced along the same host limb. In most cases, these ectopic limbs did not show fusion with the proximal host skeleton, similar to standard ALM-induced limbs, although in one case we observed fusion at the stylopod level. We now note this observation in the revised manuscript (Line 347‒354).

      We regard the relationship between APDV positional information and proximodistal patterning as an important subject for future investigation.

      (15) Line 203 - 237: I appreciate the symmetry score to estimate the DV axis. Are there landmarks that would better suggest a double-dorsal or double-ventral phenotype, like was done in the original double-half limb papers?

      We thank the reviewer for this thoughtful comment. In most cases, the limbs induced by the ALM exhibit abnormal and highly variable morphologies compared to normal limbs, making it difficult to apply consistent morphological landmarks as used in the original double-half limb studies. For this reason, we focused our analysis on “morphological symmetry” as a quantitative measure of DV axis patterning, and we have added this explanation to the manuscript (Line 232‒235). Additionally, we provided transverse sections along the proximodistal axis as supplemental figures (Figs. S2 and S4). In addition to reporting the symmetry score, we have explicitly stated in the text that symmetry was also assessed by visual inspection of these sections.

      (16) Line 245-247: The experiment was done using bulk sequencing, so both the epithelium and mesenchyme were included in the sample. The posterior (Shh) and anterior (Fgf8) patterning cues are mesenchymally expressed. In amniotes, the dorsal cue has been thought to be Wnt7a from the epithelium. Can ISH, FISH, or previous scRNAseq data be used to identify genes expressed in the mesenchyme versus epithelium? This is very important if the authors want to make the claim for defining "The molecular basis of the dorsal and ventral positional cues" as was stated by the authors.

      We thank the reviewer for highlighting this important point. As the reviewer notes, our bulk RNA-seq data do not distinguish between epithelial and mesenchymal expression domains. As noted in our response to the editor’s comment, we performed ISH and qPCR on regular blastemas. However, these approaches did not provide definitive information regarding the specific cell types expressing Wnt10b and Fgf2. To complement this, we re-analyzed publicly available single-cell RNA-seq data (from Li et al., 2021). As a results, Fgf2 was expressed mainly by the mesenchymal cells, and Wnt10b expression was observed in both mesenchymal and epithelial cells. These results are now included in the revised manuscript (Line 294‒321) and in supplemental figures (Fig. S6, S7).

      (17) Was engrailed 1, lmx1b, or Wnt7a differentially expressed along the DV axis, suggesting similar signaling between? Are these expressed in mesenchyme? Previous work suggests Wnt7a is expressed throughout the mesenchyme, but publicly available scRNAseq suggests that it is expressed in the epithelium.

      We thank the reviewer for this important comment. As noted, the reported expression patterns of DV-related genes are not consistent across studies, which likely reflects the technical difficulty of detecting these genes with high sensitivity. In our own experiments, expression of DV markers other than Lmx1b has been very weak or unclear by ISH. Whether these genes are expressed in the epithelium or mesenchyme also appears to vary depending on the detection method used. In our RNA-seq dataset, Wnt7a expression was detected at very low levels and showed no significant difference along the DV axis, while En1 expression was nearly absent. We have clarified these results in the revised manuscript (Line 437‒441). Our reanalysis of the published scRNA-seq likewise detected Wnt7a in only a very small fraction of cells. Accordingly, we consider it premature to reach a definitive conclusion—such as whether Wnt7a is broadly mesenchymal or restricted to epithelium—as suggested in prior reports. We also note that whether Wnt7a is epithelial or mesenchymal does not affect the conclusions or arguments of the present study. Although the roles of Wnt7a and En1 in axolotl DV patterning are certainly important, we feel that drawing a definitive conclusion on this issue lies beyond the scope of the present study, and we have therefore limited our description to a straightforward presentation of the data.

      (18) Line 247-249: The sentence suggests that all the ligands were tried. This should be included in the supplemental data.

      We thank the reviewer for this clarification. In fact, we tested only Wnt4, Wnt10b, Fgf2, Fgf7, and Tgfb2, and all of these results are presented in the figures. To avoid misunderstanding, we have revised the text to explicitly state that our analysis focused on these five genes (Line 272‒274).

      (19) Line 249: An n =3 seems low and qPCR would be a more sensitive means of measuring gene induction compared to ISH. The ISH would confirm the qPCR results. Figure 5C is also not the most convincing image of Shh induction without support from a secondary method.

      We have increased the sample size for these experiments (Line 277‒280). In addition, to complement the ISH results, we confirmed Shh induction by qPCR following electroporation of Wnt10b and Fgf2 (Fig. 5D, E). In addition, because Shh signal in the Wnt10b-electroporated VentBL images was particularly weak and difficult to discern, we replaced that panel with a representative example in which Shh signal is more clearly visible. These data are now included in the revised manuscript (Line 280‒282).

      (20) Line 253: It is confusing why Wnt10b, but not Wnt4 would work? As far as I know, both are canonical Wnt ligands. Was Wnt7a identified as expressed in the RNAseq, but not dorsally localized? Would electroporation of Wnt7a do the same thing as Wnt10b and hence have the same dorsalizing patterning mechanisms as amniotes?

      We thank the reviewer for raising this challenging but important question. Wnt10b was identified directly from our bulk RNA-seq analysis, as was Wnt4. The difference in the ability of Wnt10b and Wnt4 to induce Shh expression in VentBL may reflect differences in how these ligands activate downstream WNT signaling programs. WNT10B is a potent activator of the canonical WNT/β-catenin pathway (Bennett et al., 2005), although WNT10B has also been reported to trigger a β-catenin–independent pathway (Lin et al., 2021). By contrast, WNT4 can signal through both canonical and non-canonical (β-catenin–independent) pathways, and the balance between these outputs is known to depend on cellular context (Li et al., 2013; Li et al., 2019). Consistent with a requirement for canonical WNT signaling, we found that pharmacological activation of canonical WNT signaling with BIO (a GSK3 inhibitor) was also sufficient to induce Shh expression in VentBL. However, despite this, it is still unclear why Wnt10b, but not Wnt4, was able to induce Shh under our experimental conditions. One possible explanation is that different WNT ligands can engage the same receptors (e.g., Frizzled/LRP6) yet can drive distinct downstream transcriptional programs (This may depend on the state of the responding cells, as Voss et al. predicted), resulting in ligand-specific outputs (Voss et al., 2025). This point is now included in the revised discussion section (Line 402‒412). At present, we cannot distinguish between these possibilities experimentally, and we therefore refrain from making a stronger mechanistic claim.

      With respect to Wnt7a, we detected Wnt7a expression at very low levels, and without a clear dorsoventral bias, in our RNA-seq analysis of ALM blastemas (we describe this point in Line 437‒440). This is consistent with previous work suggesting that axolotl Wnt7a is not restricted to the dorsal region in regeneration. Because of this low and unbiased expression, and because our data already implicated Wnt10b as a dorsal-mediated signal that can act across dorsoventral domains to permit Shh induction, we did not prioritize Wnt7a electroporation in the present study. We therefore cannot conclude whether Wnt7a would behave similarly to Wnt10b in this context.

      Importantly, these uncertainties about ligand-specific mechanisms do not alter our main conclusion. Our data support the idea that a dorsal-mediated WNT signal (represented here by WNT10B and canonical WNT activation) and a ventral-mediated FGF signal (FGF2) must act together to permit Shh induction, and that the coexistence of these dorsal- and ventral-mediated signals is required for patterned limb formation in axolotl limb regeneration.

      (21) Is canonical Wnt signaling induced after electroporation of Wnt10b or Wnt4? qPCR of Lef1 and axin is the most common way of showing this.

      We thank the reviewer for this helpful suggestion. In addition to examining Shh expression, we also assessed canonical WNT signaling by qPCR analysis of Axin2 and Lef1 following Wnt10b electroporation. The data is now included in Fig. 5.

      (22) Line 255-256: qPCR was presented for Figure 5D, but ISH was used for everything else. Is there a technical reason that just qPCR was used for the bead experiments?

      We thank the reviewer for this helpful comment. In the original submission, our goal was to test whether treatment with commercial FGF2 protein or BIO could reproduce the results obtained by electroporation. In the revised manuscript, to avoid confusion between distinct experimental aims, we removed the FGF2–bead data from this section and instead used RT-qPCR to quantitatively corroborate Shh induction after electroporation (Fig. 5D–E). RT-qPCR provided a sensitive, whole-blastema readout and allowed a paired design (left limb: factor; right limb: GFP control) that increased statistical power while minimizing animal use. To address the reviewer’s point more directly, we additionally performed ISH for the BIO treatment and now include those results in Supplementary Figure 3 (Line 287‒288).

      (23) Line 261-263: The authors did not show where Wnt10B or Fgf2 is expressed in the limb as claimed. The RNAseq was bulk, so ISH of these genes is needed to make this claim. Where are Wnt10b and Fgf2 expressed in the amputated limb? Do they show a dorsal (Wnt10b) and ventral (Fgf2) expression pattern?

      We thank the reviewer for raising this important point. As noted in our response to the editor’s comment, we performed ISH on serial sections of regular blastemas at several time points (Fig. S5A). However, the expression patterns of Wnt10b and Fgf2 along the dorsoventral axis were not clear. To complement the ISH results, we performed RT-qPCR on microdissected dorsal and ventral halves of regular blastemas at the MB stage (Fig. S5B). We found that Wnt10b and Fgf2 were expressed at significantly higher levels in the dorsal and ventral halves, respectively, compared to the opposite half. This dorsal/ventral biased expression of Wnt10b/Fgf2 is consistent with our RNA-seq data. To identify the cell types expressing Wnt10b or Fgf2, we analyzed published single-cell RNA-seq data (7 dpa blastema (MB), Li et al., 2021). As a result, Fgf2 expression was observed in the mesenchymal cluster, whereas Wnt10b expression was observed in both mesenchymal and epithelial clusters (Fig. S6). However, because only a small fraction of cells expressed Wnt10b, the principal cellular source of WNT10B protein remains unclear. The apparent low abundance likely contributes to the weak ISH signals and reflects current technical limitations. In addition, Wnt10b and Fgf2 expression did not follow Lmx1b expression (Fig. S6J, K), and Wnt10b and Fgf2 themselves were not exclusive (Fig. S6L). Together with the RT-qPCR data (Fig. S5B), these results suggest that Wnt10b and Fgf2 are not exclusively confined to purely dorsal or ventral cells at the single-cell level, even though they show dorsoventral bias when assessed in bulk tissue, suggesting that Wnt10b/Fgf2 expression is not dorsal-/ventral-specific but mediated by dorsal/ventral cells. Defining the precise spatial patterns of Wnt10b and Fgf2 in regular regeneration will therefore be an important goal for future work. These points are now included in the revised manuscript (Line 485‒501).

      (24) Line 266-288: The formation of multiple limbs is impressive. Do these new limbs correspond to the PD location they are generated?

      We thank the reviewer for this interesting question. Interestingly, from our observations, there does appear to be a tendency for the induced limbs to vary in length depending on their PD location. The skeletal patterns of the induced multiple limbs are now included in Fig. 6. However, as noted earlier, the supernumerary limbs exhibit highly variable morphologies, and a rigorous analysis of PD correlation would require a large number of induced limbs. Since this lies outside the main focus of the present study, we have not pursued this point further in the manuscript.

      (25) Line 288: The minimal requirement for claiming the molecular basis for DV signaling was identified is to ISH or multiplexed FISH for Wnt10b and Fgf2 in amputated limb blastemas to show they are expressed in the mesenchyme or epithelium and are dorsally and ventrally expressed, respectively. In addition, the current understanding of DV patterning through Wnt7a, Lmx1b, and En1 shown not to be important in this model.

      We thank the reviewer for this comment and fully agree with the point raised. We would like to clarify that we are not claiming to have identified the molecular basis of DV patterning. As the reviewer notes, molecules such as Lmx1b, Wnt7a, and En1 are well identified in other animal models as key regulators of DV positional identity. There is no doubt that these molecules play central roles in DV patterning. However, in axolotl limb regeneration, clear DV-specific expression has not been demonstrated for these genes except for Lmx1b. Therefore, further studies will be required to elucidate the molecular basis of DV patterning in axolotls.

      Our focus here is more limited: we aim to identify the molecular basis for the mechanisms in which positional domain-mediated signals (FGF8, SHH, WNT10B, and FGF2) regulate the limb patterning process, rather than the molecular basis of DV patterning. In fact, our results on Wnt10b and Fgf2 suggest that these genes did not affect dorsoventral identities.

      We recognize that this distinction was not sufficiently clear in the original text, and we have revised the manuscript to describe DV patterning mechanisms in other animals and clarify that the dorsal- and ventral-mediated signals are distinct from DV patterning (Line 444‒450). At least, we avoid claiming that the molecular basis for DV signaling was identified.

      (26) Line 335: References are needed for this statement. From what I found, Wnt4 can be canonical or non-canonical.

      We thank the reviewer for this helpful comment. We have revised the manuscript (Line 404‒407). We added these citations at the relevant location and adjusted nearby wording to avoid implying pathway exclusivity, in alignment with our response to comment (20).

      (27) Line 337-338: The authors cannot claim "that canonical, but not non-canonical, WNT signaling contributes to Shh induction" as this was not thoroughly tested is based upon the negative result that Wnt4 electroporation did not induce Shh expression.

      We thank the reviewer for this important clarification. We agree that our data do not allow us to conclude that non-canonical WNT signaling in general does not contribute to Shh induction. Accordingly, we have removed the phrase “but not non-canonical” and revised the text to emphasize that, within the scope of our experiments, Shh induction was not observed following Wnt4 electroporation, whereas it was observed with Wnt10b.

      (28) Line 345: In order to claim "WNT10B via the canonical WNT pathway...appears to regulate Shh expression" needs at least qPCR to show WNT10B induces canonical signaling.

      We thank the reviewer for this comment. As noted in our response to comment (21), we also assessed canonical WNT signaling by qPCR analysis of Axin2 and Lef1 following Wnt10b electroporation (Line 282‒285).

      (29) Lines 361-372: A few studies have been performed on DV patterning of the mouse digit regeneration in regards to Lmx1b and En1. It may be good to discuss how the current study aligns with these findings.

      We appreciate the reviewer’s suggestion. As the reviewer refers, several studies have been performed on dorsoventral (DV) patterning in mouse digit tip regeneration in relation to Lmx1b and En1 (e.g., Johnson et al., 2022; Castilla-Ibeas et al., 2023). In the present study, however, our main conclusion is different in the scope of studies on mouse digit tip regeneration. We show that, in the axolotl, pre-existing dorsal and ventral identities (as reflected by dorsally derived and ventrally derived cells in the ALM blastema) are required together to induce Shh expression, and that this Shh induction in turn supports anteroposterior interaction at the limb level. This mechanism—dorsal-mediated and ventral-mediated signals acting in combination to permit Shh expression—does not have a clear direct counterpart in the mouse digit tip literature. Moreover, even with respect to Lmx1b, the two systems behave differently. In mouse digit tip regeneration, loss of Lmx1b during regeneration does not grossly affect DV morphology of the regenerate (Johnson et al., 2022). By contrast, in our axolotl ALM system, the presence or absence of Lmx1b-positive dorsal tissue correlates with the final dorsoventral organization of the induced limb-like structures (e.g., production of double-dorsal or double-ventral symmetric structures in the absence of appropriate dorsoventral contact). Thus, the role of dorsoventral identity in our model is directly tied to patterned limb outgrowth at the whole-limb scale, whereas in the mouse digit tip it has been reported primarily in the context of digit tip regrowth and bone regeneration competence, not robust DV repatterning (Johnson et al., 2022).

      For these reasons, we believe that an extended discussion of mouse digit tip regeneration would risk implying a mechanistic equivalence between axolotl limb regeneration and mouse digit tip regeneration that is not supported by current data. Because the regenerative contexts differ, and because Lmx1b does not appear to re-establish DV patterning in the mouse regenerates (Johnson et al., 2022), we have chosen not to include an explicit discussion of mouse digit tip regeneration in the main text.

      (30) Line 408-433: Although I appreciate generating a model, this section takes some liberties to tell a narrative that is not entirely supported by previous literature or this study. For example, lines 415-416 state "Wnt10b and Fgf2 are expressed at higher levels in dorsal and the ventral blastemal cells, respectively" which were not shown in the study or other studies.

      We thank the reviewer for this important comment. We agree that the original model based on RNA-seq data overstated the evidence. To address this point experimentally, we examined Wnt10b and Fgf2 expression in regular blastemas (Supplemental Figure 5 and 6). Accordingly, our model is now framed as an inductive mechanism for Shh expression—supported by results in ALM (WNT10B in VentBL; FGF2 in DorBL) and by DV-biased expression. Concretely, the sentence previously paraphrased as “Wnt10b and Fgf2 are expressed at higher levels in dorsal and ventral blastemal cells, respectively” has been replaced with wording that (i) avoids single-cell DV specificity and (ii) emphasizes dorsal-/ventral-mediated regulation and the requirement for both signals to allow Shh induction (Line 510‒511).

      Reviewer #2 (Recommendations for the authors):

      (1) Introduction:

      The authors' definitions of positional cues vs positional information are a little hard to follow, and do not appear to be completely accurate. From my understanding of what the authors explain, "positional information" is defined as a signal that generates positional identities in the regenerating tissue. This is a somewhat different definition than what I previously understood, which is the intrinsic (likely epigenetic) cellular identity associated with specific positional coordinates. On the other hand, the authors define "positional cues" as signals that help organize the cells according to the different axes, but don't actually generate positional identities in the regenerating cells. The authors provide two examples: Wnt7a as an example of positional information, and FGF8 as a positional cue. I think that coording to the authors definitions, FGF8 (and probobly Shh) are bone fide positional cues, since both signals work together to organize the regenerating limb cells - yet do not generate positional identities, because ectopic limbs formed from blastemas where these pathways have been activated do not regenerate (Nacu et al 2016). However, I am not sure Wnt7a constitutes an example of a "positional information" signal, since as far as I know, it has not been shown to generate stable dorsal limb identities (that remain after the signal has stopped) - at least yet. If it has, the authors should cite the paper that showed this. I think that some sort of diagram to help define these visually will be really helpful, especially to people who do not study regenerative patterning.

      We thank the reviewer for this thoughtful comment. We now agree with the reviewer that our use of “positional cue” and “positional information” may have been confusing. In the revision—and as noted in our response to the Editor’s comment (4)—we have removed the term “positional cue” and no longer attempt to contrast it with “positional information.” Instead, we adopt phrasing that reflects our data and hypothesis: during limb patterning, dorsal-mediated signals act on ventral cells and ventral-mediated signals act on dorsal cells to induce Shh expression. This wording avoids implying that these signals specify dorsoventral identity.

      Regarding WNT7A, we agree it has not been shown to generate a stable dorsal identity after signal withdrawal. In the revised Introduction we therefore describe WNT7A in amniote limb development as an extracellular regulator that induces Lmx1b in dorsal mesenchyme (with En1 repressing Wnt7a ventrally), rather than labeling it as “positional information” in a strict, identity-imprinting sense. We highlight this contrast because, in our axolotl experiments, WNT10B and FGF2 did not alter Lmx1b expression or dorsal–ventral limb characteristics when overexpressed, consistent with the idea that they act downstream of DV identity to enable Shh induction, not to establish DV identity.

      (2) Results:

      It would be helpful if the number of replicates per sample group were reported in the figure legends.

      We thank the reviewer for this suggestion. In accordance with the comment, we have added the number of replicates (n) for each sample group in the figure legends.

      Figure 2 shows ISH for A/P and D/V transcripts in different-positioned blastemas without tissue grafts. The images show interesting patterns, including the lack of Shh expression in all blastemas except in posterior-located blastemas, and localization of the dorsal transcript (Lmx1b) to the dorsal half of A or P located blastemas. My only concern about this data is that the expression patterns are described in only a small part of the ectopic blastema (how representative is it?) and the diagrams infer that these expression patterns are reflective of the entire blastema, which can't be determined by the limited field of view. It is okay if the expression patterns are not present in the entire blastema -in fact, that might be an important observation in terms of who is generating (and might be receiving) these signals.

      We thank the reviewer for this insightful comment. Because Fgf8 and Shh expression was detectable only in a limited subset of cells, the original submission included only high-magnification images. In response to the reviewer’s valid concern about representativeness, we have now added low-magnification overviews of the entire blastema as a supplemental figure (Fig. S1) and clarified in the figure legend that these expression patterns can be focal rather than pan-blastemal (Line 795‒796).

      In Figure 3, they look at all of these expression patterns in the grafted blastemas, showing that Shh expression is only visible when both D and V cells are present in the blastema. My only concern about this data is that the number of replicates is very low (some groups having only an N=3), and it is unclear how many sections the authors visualized for each replicate. This is especially important for the sample groups where they report no Shh expression -I agree that it is not observable in the single example sections they provide, but it is uncertain what is happening in other regions of the blastema.

      We thank the reviewer for this important comment. To increase the reliability of the results, we have increased the number of biological replicates in groups where n was previously low. For all samples, we collected serial sections spanning the entire blastema. For blastemas in which Shh expression was observed, we present representative sections showing the signal. For blastemas without detectable Shh expression, we selected a section from the central region that contains GFP-positive cells for the Figure. To make these points explicit, we have added the following clarification to the Fig. 3 legend (Line 811‒815).

      Figure 4: Shh overexpression in A/P/D/V blastemas - expression induces ectopic limbs in A/D/V locations. They analyzed the symmetry of these regenerates (assuming that Do and V located blastemas will exhibit D/V symmetry because they only contain cells from one side of that axis. I am a little concerned about how the symmetry assay is performed, since oblique sections through the digits could look asymmetric, while they are actually symmetric. It is also unclear how the angle of the boxes that the symmetry scores were based on was decided - I imagine that the score would change depending on the angle. It also appears that the authors picked different digits to perform this analysis on the different sample groups. I also admit that the logic of classification scheme that the authors used AI to perform their symmetry scoring analysis (both in Figures 4 and 5) is elusive to me. I think it would have been more informative if the authors leveraged the structural landmarks, like the localization of specific muscle groups. (If this experiment were performed in WT animals, the authors could have used pigment cell localization)... or generate more proximal sections to look at landmarks in the zeugopod.

      We thank the reviewer for these detailed comments regarding the symmetry analysis. Because reliance on a computed symmetry score alone could raise the concerns noted by the reviewer, we now provide transverse sections along the proximodistal axis as supplemental figures (Figs. S2 and S4). These include levels corresponding to the distal end of the zeugopod and the proximal end of the autopod. In addition to reporting the symmetry score, we have explicitly stated in the text that symmetry was also assessed by visual inspection of these sections.

      As also noted in our response to Reviewer #1 (comment 15), ALM-induced limbs frequently exhibit abnormal and highly variable morphologies, which makes it difficult to use consistent anatomical landmarks such as particular digits or muscle groups. For this reason, we focused our analysis on morphological symmetry rather than landmark-based metrics, and we emphasize this rationale in the revised text (Line 232‒235).

      Regarding the use of bounding boxes, this procedure was chosen to minimize the effects of curvature or fixation-induced distortion. For each section, the box angle was adjusted so that the outer contour (epidermal surface) was aligned symmetrically; this procedure was applied uniformly across all conditions to avoid bias. We analyzed multiple biological replicates in each group, which helps mitigate potential artifacts due to oblique sectioning. To further reduce bias, we increased the number of fields included in the analysis to n = 24 per group in the revised version.

      In addition, staining intensity varied among samples, such that a region identified as “muscle” in one sample could be assigned differently in another if classification were based solely on color. To avoid this problem, we used a machine-learning classifier trained separately for each sample, allowing us to group the same tissues consistently within that sample irrespective of intensity differences. In the context of ALM-induced limbs, where stable anatomical landmarks are not available, we consider this strategy the most appropriate. We have added this rationale to the revised manuscript for clarity (Line 239‒247).

      Figure 5: The number of replicates in sample groups is relatively low and is quite variable between groups (ranging between 3 and 7 replicates). Zoom in to visualize Shh expression is small relative to the blastema, and it is difficult to discern why the authors positioned the window where they did, and how they maintained consistency among their different sample groups. In the examples of positive Shh expression - the signal is low and hard to see. Validating these expression patterns using some sort of quantitative transcriptional assay (like qRTPCR) would increase the rigor of this experiment ... especially given that they will be able to analyze gene expression in the entire blastema as opposed to sections that might not capture localized expression.

      We thank the reviewer for this important comment. To increase the rigor of these experiments, we have increased the number of biological replicates in groups where n was previously low. In addition, because Shh signal in the Wnt10b-electroporated VentBL images was particularly weak and difficult to discern, we replaced that panel with a representative example in which Shh signal is more clearly visible. We also validated the Shh expression for Wnt10b–electroporated VentBL and Fgf2–electroporated DorBL by RT-qPCR, which assesses gene expression across the entire blastema. These results are now included in Fig. 5 and Line 280‒282. Finally, we clarified in the figure legend how the “window” for imaging was chosen: for samples with detectable Shh expression, the window was placed in the region where the signal was observed; for conditions without detectable Shh expression, the window was positioned in a comparable region containing GFP-positive cells (Line 836‒839). These revisions are included in the revised manuscript.

      Figure 6: They treat dorsal and ventral wounds with gelatin beads soaked in a combination of BMP2+FGF8 (nerve factors) and FGF2 proposed ventral factor). Remarkably, they observe ectopic limb expression in only dorsal wounds, further supporting the idea that FGF2 provides the "ventral" signal. They show examples of this impressive phenotype on limbs with multiple ectopic structures that formed along the Pr/Di axis. Including images of tubulin staining (as they have in Figures 1 and 2) to ensure that the blastemas (or final regenerates) are devoid of nerves. The authors' whole-mount skeletal staining which shows fusion of the ectopic humerus with the host humerus, is a phenotype associated with deep wounding, which could provide an opportunity for more cellular contribution from different limb axes.

      We thank the reviewer for these constructive comments. As noted in the prior study, when beads are used to induce blastemas without surgical nerve orientation, fine nerve ingrowth can still occur (Makanae et al., 2014), and the induced blastemas are not completely devoid of nerves. While it is still uncertain whether these recruited nerves are functional after blastema induction, it is an important point, and we added sentences about this in the revised manuscript (Line 341‒345).

      Regarding the skeletal phenotype, despite careful implantation to avoid injuring deep tissues, bead-induced ectopic limbs on the dorsal side occasionally displayed fusion of the stylopod with the host humerus—a phenotype associated with deep wounding, as the reviewer notes. This observation suggests that contributions from a broader cellular population cannot be excluded. However, because fusion was observed in only 1 of 16 induced limbs analyzed, and because ectopic limbs induced at the forearm (zeugopod) level did not exhibit such fusion (n=1/6 for stylopod-level inductions; n=0/10 for zeugopod-level inductions), we believe that our main conclusion remains valid. Because fusion is not a typical outcome, we now present representative non-fusion cases—including zeugopod-origin examples—in the figure (Fig. 6L1, L2), and we report the fusion incidence explicitly in the text (Line 350‒354). We also note in the revised manuscript that stylopod fusion can occur in a minority of cases (Line 347‒349).

      Figure 7 nicely summarizes their findings and model for patterning.

      We thank the reviewer for this positive comment.

      The table is cut off in the PDF, so it cannot be evaluated at this time.

      In our copy of the PDF, the table appears in full, so this may have been a formatting issue. We have carefully checked the file and ensured that the table is completely included in the revised submission.

      There is a supplemental figure that doesn't seem to be referenced in the text.

      The supplemental figure (Fig. S1 of the original manuscript) is referenced in the text, but it may have been overlooked. To improve clarity, we have expanded the description in the manuscript so that the supplemental figure is more clearly referenced (Line 285‒291).

      (3) Materials and Methods:

      No power analysis was performed to calculate sample group sizes. The authors have used these experimental techniques in the past and could have easily used past data to inform these calculations.

      We thank the reviewer for this important comment. We did not include a power analysis in the manuscript because this was the first time we compared Shh and other gene expression levels among ALM blastemas of different positional origins using RT-qPCR in our experimental system. As we did not have prior knowledge of the expected variability under these specific conditions, it was difficult to predetermine appropriate sample sizes.

      Reviewer #3 (Recommendations for the authors):

      General:

      Congratulations - I found this an elegant and easy-to-read study with significant implications for the field! If possible, I would urge you to consider adding some more characterisation of Wnt10b and Fgf2- which cell types are they expressed in? If you can link your mechanisms to normal limb regeneration too (i.e., regenerating blastema, not ALM), this would significantly elevate the interest in your study.

      We sincerely thank the reviewer for these encouraging comments. As also noted in our response to the editor’s comment, we have analyzed the expression patterns of Wnt10b and Fgf2 in regular blastemas (Line 294‒306). Although clear specific expression patterns along dorsoventral axis were not detected by ISH, likely due to technical limitations of sensitivity, RT-qPCR revealed significantly higher expression levels of Wnt10b in the dorsal half and Fgf2 in the ventral half of a regular blastema (Fig. S5). In addition, we analyzed published single-cell RNA-seq data (7 dpa blastema, Li et al., 2021) (Line 307‒321). As a result, Fgf2 expression was observed in the mesenchymal clusters, whereasWnt10b expression was observed in both mesenchymal and epithelial clusters (Fig. S6). However, because only a small fraction of cells expressed Wnt10b, the principal cellular source of WNT10B protein remains unclear. Therefore, defining the precise spatial patterns of Wnt10b and Fgf2 in regular regeneration will be an important goal for future work.

      Data availability:

      I assume that the RNA-sequencing data will be deposited at a public repository.

      RNA-seq FASTQ files have been deposited in the DNA Data Bank of Japan (DDBJ; https://www.ddbj.nig.ac.jp/) under BioProject accession PRJDB38065. We have added a Data availability section to the revised manuscript.

      References

      Castilla-Ibeas, A., Zdral, S., Oberg, K. C., & Ros, M. A. (2024). The limb dorsoventral axis: Lmx1b’s role in development, pathology, evolution, and regeneration. Developmental Dynamics, 253(9), 798–814. https://doi.org/10.1002/dvdy.695

      Johnson, G. L., Glasser, M. B., Charles, J. F., Duryea, J., & Lehoczky, J. A. (2022). En1 and Lmx1b do not recapitulate embryonic dorsal-ventral limb patterning functions during mouse digit tip regeneration. Cell Reports, 41(8), 111701. https://doi.org/10.1016/j.celrep.2022.111701

      Stocum, D. (2017). Mechanisms of urodele limb regeneration. Regeneration, 4. https://doi.org/10.1002/reg2.92

      Tank, P. W., & Holder, N. (1978). The effect of healing time on the proximodistal organization of double-half forelimb regenerates in the axolotl, Ambystoma mexicanum. Developmental Biology, 66(1), 72–85. https://doi.org/10.1016/0012-1606(78)90274-9

    1. Author response:

      Global answer about the ATP analogs (concerns the 3 reviewers)

      We use ATP-Vanadate essentially for detecting the FRET efficiency for the closed state. But these data are not included in our theoretical model. Thus, even if the comments of the reviewers on the observation of a non-negligible fraction of proteins in the open state in the presence of ATP-vanadate are justified, this has no consequence on our conclusions on the effect of curvature on BmrA on the conformational changes with ATP or AMP-PNP.

      We agree with the comments of the reviewers that the binding of vanadate is not irreversible, but the reported lifetime of the closed state is very long compared to our experimental conditions (see (Urbatsch et al. JBC (1995)) on PgP).

      Nevertheless, we will perform new experiments independent of ATP analogs using the E504A BmrA mutant. It has been shown structurally and enzymatically to bind and not hydrolyze ATP and to be 100% in a closed conformation at 5 mM ATP (A. Gobet et al., Nat. Commun. 16, 1745 (2025)). It will clear up all doubts about our experiments.

      We will also add new references:

      I. L. Urbatsch, B. Sankaran, J. Weber, A. E. Senior, J. Biol. Chem. 270, 19383 (1995)

      T. Baukrowitz, T.-C. Hwang, A. C. Nairn, D. C. Gadsby, Neuron 12, 473 (1994)

      A. Gobet et al., Nat. Commun. 16, 1745 (2025)

      Y. Liu, M. Liao, Sci. Adv. 11, eadv9721 (2025) (on the effect of vanadate and temperature on a plant ABC)

      Public Reviews:

      Reviewer #1 (Public review):

      (1) An important aspect of this paper is the difference in mechanism between inhibitors AMP-PNP (a substrate analog) and vanadate (together with ADP, forms a transition state analog inhibitor). The mechanisms and inhibitory constants/binding affinities of these inhibitors are not very well-supported in the current form of the manuscript, either through citations or through experiments. Related to this, the interpretation of the different curvature response of BmrA in the presence of vanadate vs AMPPNP is not very clear.

      See the global answer about ATP-analogs (above)

      (2) Overall, the energetic contribution of the membrane curvature is subtle (less than a kT), so while the principles seem generalizable among membrane proteins, whether these principles impact transport or cell physiology remains to be established.

      This is correct that the effect is limited to high curvature in the case of BmrA. Our theoretical model allows predictions for different protein parameters. The effect is particularly dependent on the protein size and on protein conicity, which can vary over a wide range. We show that larger proteins, such as piezo 1 are in principle expected to display a much stronger curvature dependence than BmrA. But testing our predictions on other proteins and on their physiological function is indeed an exciting perspective but beyond the objective of the current manuscript.

      Reviewer #2 (Public review):

      (1) Although this study may be considered as a purely biophysical investigation of the sensitivity of an ABC transporter to mechanical perturbation of the membrane, the impact would be strengthened if a physiological rationale for this mode of regulation were discussed. Many factors, including temperature, pH, ionic strength, or membrane potential, are likely to affect flux through the transport cycle to some extent, without justifying describing BmrA as a sensor for changes in any of these. Indeed, a much stronger dependence on temperature than on membrane curvature was measured. It is not clear what radii of curvature BmrA would normally be exposed to, and whether this range of curvatures corresponds to the range at which modulation of transport activity could occur. Similarly, it is not clear what biological condition would involve a substantial change to membrane curvature or tension that would necessitate altered BmrA activity.

      Reviewers 1 and 2 both stressed that we showed that activity and conformational changes are mechanosensitive, not that the function of the protein is to be a mechanosensor. This will be corrected.

      Regarding the physiological relevance of the mechanosensitivity of BmrA, we have addressed this point in the manuscript (bottom of page 10 and top of page 11). This discussion was positively appreciated by Reviewer #3. We stress that we have used BmrA as a model system, but considering our results and the theoretical model, we can predict the parameters that are relevant for future studies on the sensitivity of other transmembrane proteins to membrane mechanical properties. And, as stated by the reviewer, "mechanosensitivity of proteins is an understudied phenomenon".

      (2) The size distributions of vesicles were estimated by cryoEM. However, grid blotting leaves a very thin layer of vitreous ice that could sterically exclude large vesicles, leading to a systematic underestimation of the vesicle size distribution.

      We used Lacey carbon grids with large mesh size ranges for our cryoEM images, and we blot on the backside, precisely to measure the largest size range accessible to cryoEM. In our hands, this was not the case when using Quantifoil or C-Flat grids with uniform hole sizes and a large fraction of carbon where the vesicles adhere. With our grids, we are able to image vesicles from 20 to 200 nm diameter and the precision on the diameter is high, but the statistics might not be as good as with DLS or other diffusion-based methods. DLS is an indirect method (as compared to cryoEM) to measure vesicle size distribution, that may overestimate the fraction of large objects and underestimate the small ones. We will perform DLS experiments for comparison purpose.

      (3) The relative difference in ATP turnover rates for BmrA in small versus large vesicles is modest (~2-fold) and could arise from different success rates of functional reconstitution with the different protocols.

      The ATPase activity is sensitive to several parameters. We thus carefully characterized our reconstituted samples, including ATPase activity, yield of incorporation and orientation of proteins that are often reported. In addition, we showed by cryo-EM the unilamellarity of the proteoliposomes and their stability during the experiments, which were never reported. The ATPase activity of our samples reconstituted in liposomes at 20 ° and at 4°C are high, among the highest reported for BmrA, and less sensitive to errors as compared to the low activities in micelles of detergent.

      We would also like to stress that with our protocol, we have prepared the same batch of lipid/protein mixture that we have split it 2 for the reconstitution at 4°C and 20°C conversely. Both preparations contain the same amount of detergent. The only difference is that we include more BioBeads for the preparation at 4°C to account for the difference of absorption of the detergent on the beads at low temperature (D. Lévy, A. Bluzat, M. Seigneuret, J.L. Rigaud Biochim. Biophys. Acta. 179 (1990)), but we also showed that the proteins do not adsorb on the BioBeads (J.-L. Rigaud, B. Pitard, D. Levy, Biochim. Biophys. Acta 1231, 223 (1995)). In addition, the activity of the protein at 37°C is high and comparable to those reported in the literature (E. Steinfels et al., Biochemistry 43, 7491 (2004)., W. Mi et al., Nature 549, 233 (2017).), which speaks for a good functional reconstitution. Finally, our results are consistent between the smFRET where we have only one protein maximum per vesicle and the activity measurements where the amount of protein is higher.

      We also performed reconstitution from molar LPR= 1:13600 to 1:1700 and found the same activity per protein, confirming that the proteins are functional, independently of their surface fraction. We will add these data in the revision.

      Altogether, these data suggest that we correctly estimate the rate of functional reconstitution in our experiments.

      Nevertheless, we will design additional experiments to further compare the activity of the proteins before and after reconstitution.

      (4) The conformational state of the NBDs of BmrA was measured by smFRET imaging. Several aspects of these investigations could be improved or clarified. Firstly, the inclusion and exclusion criteria for individual molecules should be more quantitatively described in the methods. Secondly, errors were estimated by bootstrapping. Given the small differences in state occupancies between conditions, true replicates and statistical tests would better establish confidence in their significance. Thirdly, it is concerning that very few convincing dynamic transitions between states were observed. This may in part be due to fast photobleaching compared to the rate of isomerization, but this could be overcome by reducing the imaging frequency and illumination power. Alternatively, several labs have established the ability to exchange solution during imaging to thereby monitor the change in FRET distribution as a ligand is delivered or removed. Visualizing dynamic and reversible responses to ligands would greatly bolster confidence in the condition-dependent changes in FRET distributions. Such pre-steady state experiments would also allow direct comparison of the kinetics of isomerization from the inward-facing to the outward-facing conformation on delivery of ATP between small and large vesicles.

      (a) We will better detail the inclusion and exclusion criteria.

      (b) For the smFRET, we have performed N=3 true replicates. We will add statistical tests on our graphs.

      (c) We will detail more how we have optimized our illumination protocol, considering the signal to noise ratio and the photobleaching. Practically, we cannot add ATP to our sealed observation chamber on our TIRF system to detect dynamical changes on our immobilized liposomes. The experiment suggested by the reviewer would imply to build a flow chamber to exchange the medium around immobilized liposomes, compatible with TIRF microscopy. This is an excellent idea, which has been achieved only recently (S. N. Lefebvre, M. Nijland, I. Maslov, D. J. Slotboom, Nat. Commun. 16, 4448 (2025)). It will require a full new study to optimize both the flow chamber and the dyes to track the smFRET changes over long periods of time.

      Nevertheless, we would like to stress that our objective is not to study the dynamics of the conformational changes, and that we expect it to be slow for BmrA, even at 33°C.

      (5) A key observation is that BmrA was more prone to isomerize ATP- or AMP-PNP-dependently to the outward-facing conformations in large vesicles. Surprisingly, the same was not observed with vanadate-trapping, although the sensitivity of state occupancy to membrane curvature would be predicted to be greatest when state occupancies of both inward- and outward-facing states are close to 50%. It is argued that this was due to irreversibility of vanadate-trapping, but both vanadate and AMP-PNP should work fully reversibly on ABC transporters (see e.g. PMID: 7512348 for vanadate). Further, if trapping were fully irreversible, a quantitative shift to the outward-facing condition would be predicted.

      See the global answer about ATP-analogs (above)

      Reviewer #3 (Public review):

      (1) The authors say that the protein activity is irreversibly inhibited by orthovanadate, but 50% of the proteins are still in open conformation, while being accessible to the analogue (Table 2). It is unclear what this means in the context of activity vs. conformation.

      See the global answer about ATP-analogs (above)

      (2) The difference in the fraction of proteins in closed conformation is quite similar between LV and SV treated with AMP-PNP at 20 {degree sign}C (Figure 2B), and it is not clear if the difference is significant. The presence of a much higher FRET tail in the plots of smFRET experiment in SVs at 20 {degree sign}C or 33 {degree sign}C in the apo conformation of the protein (Figure 3A-B) is cause of some concern since one would not expect BmrA to access the closed states more frequently in the Apo conformation especially when incorporated in the SV. This is because the subtraction of the higher fraction of closed states in the Apo conformation contributes directly to enhancing the bias between the closed states in SV versus LV membrane bilayers.

      We have consistently observed, both at 20°C and at 33°C, a fraction of proteins with a high FRET signal in our measurements, higher in SV (about 15% and 17%) than in LV (about 10% and 6%). We have quantified the fraction of proteins with NBDs facing inside the liposomes (page 5), 20% in LV and 23.85% in SV. Considering the inverted curvature of the membrane, this orientation could favor the closed conformation, even in the absence of ATP, more for SV than LV. The fraction with inverted orientation could explain our higher fraction of high FRET signal in SV.

      Moreover, for part of it, it can be due to a fraction of proteins with a non-specific labeling that would produce a higher FRET signal. We will add data with Cys-less mutants showing that less than 4% are labeled.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #3 (Public review):

      To summarize: The authors' overfilling hypothesis depends crucially on the premise that the very quickly reverting paired-pulse depression seen after unusually short rest intervals of << 50 ms is caused by depletion of release sites whereas Dobrunz and Stevens (1997) concluded that the cause was some other mechanism that does not involve depletion on. The authors now include experiments where switching extracellular Ca2+ from 1.2 to 2.5 mM increases synaptic strength on average, but not by as much as at other synapse types. They contend that the result supports the depletion on hypothesis. I didn't agree because the model used to generate the hypothesis had no room for any increase at all, and because a more granular analysis revealed a mixed population with a subset where: (a) synaptic strength increased by as much as at standard synapses; and yet (b) the quickly reverting depression for the subset was the same as the overall population.

      The authors raise the possibility of additional experiments, and I do think this could clarify things if they pre-treat with EGTA as I recommended initially. They've already shown they can do this routinely, and it would allow them to elegantly distinguish between pv and pocc explanations for both the increases in synaptic strength and the decreases in the paired pulse ratio upon switching Ca2+ to 2.5 mM. Plus/minus EGTA pre-treatment trials could be interleaved and done blind with minimal additional effort.

      Showing reversibility would be a great addition too, because, in our experience, this does not always happen in whole-cell recordings in ex-vivo tissue even when electrical properties do not change. If the goal is to show that L2/3 synapses are less sensitive to changes in Ca2+ compared to other synapse types - which is interesting but a bit off point - then I would additionally include a positive control, done by the same person with the same equipment, at one of those other synapse types using the same kind of presynaptic stimulation (i.e. ChRs).

      Specific points (quotations are from the Authors' rebuttal)

      (1) Regarding the Author response image 1, I was instead suggesting a plot of PPR in 1.2 mM Ca2+ versus the relative increase in synaptic strength in 2.5 versus in 1.2 mM. This continues to seem relevant.

      Complying with your suggestion, we studied the effects of external [Ca<sup>2+</sup>] ([Ca<sup>2+</sup>]<sub>o</sub>) after pre-incubating the slice in aCSF containing 50 μM EGTA-AM, and added the results as Figure 3—figure supplement 3C-D. Elevation of ([Ca<sup>2+</sup>]<sub>o</sub>) from 1.3 to 2.5 mM produced no significant change in either baseline EPSC amplitude or PPR, supporting that the p<sub>v</sub> is already saturated at 1.3 mM [Ca<sup>2+</sup>]<sub>o</sub> and implying that the modest Ca<sup>2+</sup> dependence of baseline EPSCs and PPR in the absence of EGTA (Figure 3—figure supplement 3A-B) is mediated by the change in baseline vesicular occupancy of release sites (p<sub>occ</sub>) rather than fusion probability of docked vesicles (p<sub>v</sub>).

      We found some correlation of high Ca<sup>2+</sup>-induced relative increase in synaptic strength with the PPR at low Ca<sup>2+</sup> (Author response image 1-A). But this correlation was abolished by pre-incubating the slices in EGTA-AM too (Author response image 1-B). It should be noted that high PPR does not always mean low p<sub>v</sub>. For example, when the replenishment is equal between high and low baseline p<sub>occ</sub> synapses, the PPR would be higher at low p<sub>occ</sub> synapses than that at high p<sub>occ</sub> synapses, even if p<sub>v</sub> is close to unity. Therefore, high baseline release probability (Pr), whatever it is attributed to high p<sub>v</sub> or high p<sub>occ</sub>, can result in low PPR, considering that Pr = p<sub>occ</sub> x p<sub>v</sub>.

      As we have already mentioned in our previous letter, the relationship of PPR with refilling rate is complicated and can be bidirectional, whereas an increase in p<sub>v</sub> always results in a reduction of PPR. For example, PPR can be reduced by both a decrease and an increase in the refilling rate (Figure 2— figure supplement 1 and Lin et al., 2025). Therefore, the PPR analysis alone is insufficient to differentiate the contributions of p<sub>v</sub> and p<sub>occ</sub> Thanks to your suggestion, we could resolve this ambiguity by the EGTA-AM pre-incubation study (Figure 3—figure supplement 3C-D).

      Author response image 1.

      Plot of PPR at low [Ca<sup>2+</sup>]<sub>o</sub> (1.3 mM) as a function of the baseline EPSC at high [Ca<sup>2+</sup>]<sub>o</sub> (2.5 mM) normalized to that at low [Ca<sup>2+</sup>]<sub>o</sub> measured at recurrent excitatory synapses in L2/3 of the prelimbic cortex under the conditions without EGTA-AM (A) and after pre-incubating the slices in EGTA-AM (50 μM) (B)

      (2) "Could you explain in detail why two-fold increase implies pv < 0.2?"

      (a) start with power((2.5/(1 + (2.5/K1) + 1/2.97)),4) = 2<sup>*</sup>power((1.3/(1 + (1.3/K1) + 1/2.97)),4);

      (b) solve for K1 (this turns out to be 0.48);

      (c) then implement the premise that pv -> 1.0 when Ca2+ is high by calculating Max = power((C/(1 + (C/K1) + 1/2.97)),4) where C is [Ca] -> infinity.

      (d) pv when [Ca] = 1.3. mM must then be power((1.3/(1 + (1.3/K1) + 1/2.97)),4)/Max, which is <0.2. Note that modern updates of Dodge and Rahamimoff typically include a parameter that prevents pv from approaching 1.0; this is the gamma parameter in the versions from Neher group.

      Thank you very much for your kind explanation. This interpretation, however, based on the premise that pv is not saturated at low[Ca<sup>2+</sup>]<sub>o</sub>, and that Pr = p<sub>v</sub>. In the present study, however, we presented multiple convergent lines of evidence supporting that p<sub>v</sub> is already saturated at 1.3 mM [Ca<sup>2+</sup>]<sub>o</sub> as follows: (1) little effect of EGTA-AM on the baseline EPSCs (Figure 2—figure supplement 1); (2) high double failure rates (Figure 3—figure supplement 2); (3) little effect of high [Ca<sup>2+</sup>]<sub>o</sub> on baseline EPSC (Figure 3—figure supplement 3). Therefore, our results suggest that the classical Dodge-Rahamimoff fourth-power relationship can not be applied to estimate p<sub>v</sub> at the L2/3 recurrent excitatory synapses. 

      (3) "If so, we can not understand why depletion-dependent PPD should lead to PPF." When PPD is caused by depletion and pv < 0.2, the number of occupied release sites should not be decreased by more than one-filth at the second stimulus so, without facilitation, PPR should be > 0.8. The EGTA results then indicate there should be strong facilitation, driving PPR to something like 1.2 with conservative assumptions. And yet, a value of < 0.4 is measured, which is a large miss.

      As mentioned above, the framework used for inferring that p<sub>v</sub> < 0.2, the Dodge-Rahamimoff equation, is not applicable to our experimental system. Consequently, the subsequent deduction— that depletion-dependent PPD should logically lead to PPF—is based on a model that does not compatible with aforementioned multiple convergent lines of evidence, which supports high p<sub>v</sub> rather than the low p<sub>v</sub> facilitation model.

      (4) Despite the authors' suggestion to the contrary, I continue to think there is a substantial chance that Ca2+-channel inactivation is the mechanism underlying the very quickly reverting paired-pulse depression. However, this is only one example of a non-depletion mechanism among many, with the main point being that any non-depletion mechanism would undercut the reasoning for overfilling. And, this is what Dobrunz and Stevens claimed to show; that the mechanism - whatever it is - does not involve depletion. The most effective way to address this would be affirmative experiments showing that the quickly reverting depression is caused by depletion after all. Attempting to prove that Ca2+channel inactivation does not occur does not seem like a worthwhile strategy because it would not address the many other possibilities.

      We have systematically ruled out alternative possibilities that may underlie the strong PPD observed at our synapses and demonstrated that it arises from high p<sub>v</sub>-induced vesicle depletion through multiple independent lines of evidence. First, we excluded (1) AMPAR desensitization or saturation (Figure 1—figure supplement 5), (2) Ca<sup>2+</sup> channel inactivation (Figure 2—figure supplement 2), (3) channelrhodopsin inactivation (Figure 1—figure supplement 2), (4) artificial bouton stimulation (Figure 1—figure supplement 4), and (5) transient vesicle undocking (Figure 5; addressed in our previous rebuttal). Second, EGTA-AM experiments (Figure 2, Figure 2—figure supplement 1) revealed that release sites are tightly coupled to Ca<sup>2+</sup>  channels, and that EGTA further exacerbates PPD. Third, we validated high baseline p<sub>v</sub> through analysis of double failure rates (Figure 3—figure supplement 2). Fourth, the minimal increase in baseline EPSCs upon elevation of external [Ca<sup>2+</sup>] (Figure 3—figure supplement 3) further supports that baseline p<sub>v</sub> is already saturated at low [Ca<sup>2+</sup>]<sub>o</sub>. Additionally, to further validate our hypothesis, we performed the specific experiment suggested by the reviewer. We have now added EGTA pre-incubation experiments (Figure 3—figure supplement 3C-D) and have revised the manuscript. Specifically, when slices were pre-incubated with 50 μM EGTA-AM, elevation of extracellular [Ca<sup>2+</sup>] from 1.3 to 2.5 mM produced no significant change in either baseline EPSC amplitude or PPR, strongly supporting that the high [Ca<sup>2+</sup>]<sub>o</sub> effects in the absence of EGTA are primarily mediated by changes in p<sub>occ</sub> rather than p<sub>v</sub>

      (5) True that Kusick et al. observed morphological re-docking, but then vesicles would have to re-prime and Mahfooz et al. (2016) showed that re-priming would have to be slower than 110 ms (at least during heavy use at calyx of Held).

      As previously discussed, Kusick et al. (2020) demonstrated that the transient destabilization of the docked vesicle pool recovers very rapidly within 14 ms after stimulation. This implies that any posts stimulation undocking events are likely recovered before the 20 ms ISI used in our PPR experiments. Consequently, transient undocking/re-docking events are unlikely to significantly influence the PPR measured at this interval. Furthermore, regarding the slow re-priming kinetics (>100 ms) reported by Mahfooz et al. (2016) and Kusick et al., (2020), our 20 ms ISI effectively falls into a me window that avoids the potential confounds of both processes: it is long enough for the rapid morphological recovery (~14 ms) of docked vesicles to occur, yet too short for the slow re-priming process to make a substantial  contribution. Furthermore, Vevea et al. (2021) showed that post-stimulus undocking is facilitated in synaptotagmin-7 (Syt7) knockout synapses. In our study, however, Syt7 knockdown did not affect PPR at 20 ms ISI, suggesting that the undocking process described in Kusick et al. (2020) is not a major contributor to the PPD observed at 20 ms intervals in our experiments. Therefore, we conclude that the 20 ms ISI used in our experiments falls within a me window that is influenced neither by the rapid undocking (<14 ms) reported nor by the slow re-priming process (>100 ms).

    1. Author response:

      The following is the authors’ response to the current reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      The revised manuscript presents an interesting and technically competent set of experiments exploring the role of the infralimbic cortex (IL) in extinction learning. The inclusion of histological validation in the supplemental material improves the transparency and credibility of the results, and the overall presentation has been clarified. However, several key issues remain that limit the strength of the conclusions.

      We thank the Reviewer for their positive assessment of our revised manuscript. We discussed the issues raised by the Reviewer below.

      The behavioral effects reported are modest, as evident from the trial-by-trial data included in the supplemental figures. Although the authors interpret their findings as evidence that IL stimulation facilitates extinction only after prior inhibitory learning, this conclusion is not directly supported by their data. The experiments do not include a condition in which IL stimulation is delivered during extinction training alone, without prior inhibitory experience. Without this control, the claim that prior inhibitory memory is necessary for facilitation remains speculative.

      The manuscript provides evidence across five experiments (Figures 2-6) that IL stimulation fails to facilitate extinction training in the absence of prior inhibitory experience. We therefore remain confident that the data support our conclusion: prior inhibitory learning enables IL stimulation to facilitate subsequent inhibitory learning.

      The electrophysiological example provided shows that IL stimulation induces a sustained inhibition that outlasts the stimulation period. This prolonged suppression could potentially interfere with consolidation processes following tone presentation rather than facilitating them. The authors should consider and discuss this alternative interpretation in light of their behavioral data.

      The possibility that IL stimulation exerted its effects by interfering with consolidation processes is inconsistent with the literature. Disrupting consolidation processes in the IL impairs extinction learning (1), even when animals have prior inhibitory learning experience (2). Yet our experiments found that IL stimulation failed to interfere with initial extinction learning but instead facilitated subsequent learning. Furthermore, the electrophysiological example demonstrates that the inhibitory effect is transient: the cell returned to firing properties similar to those observed pre-stimulation, making it unlikely that inhibition persists during the consolidation window.

      It is unfortunate that several animals had to be excluded after histological verification, but the resulting mismatch between groups remains a concern. Without a power analysis indicating the number of subjects required to achieve reliable effects, it is difficult to determine whether the modest behavioral differences reflect genuine biological variability or insufficient statistical power. Additional animals may be needed to properly address this imbalance.

      As noted in the revised manuscript, we are confident about the reliability of the findings reported. The manuscript provides evidence across five experiments that IL stimulation fails to facilitate brief extinction in the absence of prior inhibitory experience, replicating previous findings (3, 4). The manuscript also replicates these prior studies by demonstrating that experience with either fear or appetitive extinction enables IL stimulation to facilitate subsequent fear extinction. Furthermore, the present experiments replicate the facilitative effects of IL stimulation following fear or appetitive backward conditioning.

      Overall, while the manuscript is improved in clarity and methodological detail, the behavioral effects remain weak, and the mechanistic interpretation requires stronger experimental support and consideration of alternative explanations.

      We respectfully disagree with the assertion that the reported results are weak. The manuscript replicates all main findings internally or reproduces findings from previously published studies. While alternative explanations cannot be entirely excluded, we are not aware of any competing account that predicts the pattern of results reported here.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, the authors examine the mechanisms by which stimulation of the infralimbic cortex (IL) facilitates the retention and retrieval of inhibitory memories. Previous work has shown that optogenetic stimulation of the IL suppresses freezing during extinction but does not improve extinction recall when extinction memory is probed one day later. When stimulation occurs during a second extinction session (following a prior stimulation-free extinction session), freezing is suppressed during the second extinction as well as during the tone test the following day. The current study was designed to further explore the facilitatory role of the IL in inhibitory learning and memory recall. The authors conducted a series of experiments to determine whether recruitment of IL extends to other forms of inhibitory learning (e.g., backward conditioning) and to inhibitory learning involving appetitive conditioning. Further, they assessed whether their effects could be explained by stimulus familiarity. The results of their experiments show that backward conditioning, another form of inhibitory learning, also enabled IL stimulation to enhance fear extinction. This phenomenon was not specific to aversive learning as backward appetitive conditioning similarly allowed IL stimulation to facilitate extinction of aversive memories. Finally, the authors ruled out the possibility that IL facilitated extinction merely because of prior experience with the stimulus (e.g., reducing the novelty of the stimulus). These findings significantly advance our understanding of the contribution of IL to inhibitory learning. Namely, they show that the IL is recruited during various forms of inhibitory learning and its involvement is independent of the motivational value associated with the unconditioned stimulus.

      We thank the Reviewer for their positive assessment.

      Strengths to highlight:

      (1) Transparency about the inclusion of both sexes and the representation of data from both sexes in figures

      We thank the Reviewer for their positive assessment.

      (2) Very clear representation of groups and experimental design for each figure

      We thank the Reviewer for their positive assessment.

      (3) The authors were very rigorous in determining the neurobehavioral basis for the effects of IL stimulation on extinction. They considered multiple interpretations and designed experiments to address these possible accounts of their data.

      We thank the Reviewer for their positive assessment.

      (4) The rationale for and the design of the experiments in this manuscript are clearly based on a wealth of knowledge about learning theory. The authors leveraged this expertise to narrow down how the IL encodes and retrieves inhibitory memories.

      We thank the Reviewer for their positive assessment.

      Reviewer #3 (Public review):

      Summary:

      This is a really nice manuscript with different lines of evidence to show that the IL encodes inhibitory memories that can then be manipulated by optogenetic stimulation of these neurons during extinction. The behavioral designs are excellent, with converging evidence using extinction/re-extinction, backwards/forwards aversive conditioning, and backwards appetitive/forwards aversive conditioning. Additional factors, such as nonassociative effects of the CS or US, also are considered, and the authors evaluate the inhibitory properties of the CS with tests of conditioned inhibition. The authors have addressed the prior reviews. I still think it is unfortunate that the groups were not properly balanced in some of the figures (as noted by the authors, they were matched appropriately in real time, but some animals had to be dropped after histology, which caused some balancing issues). I think the overall pattern of results is compelling enough that more subjects do not need to be added, but it would still be nice to see more acknowledgement and statistical analyses of how these pre-existing differences may have impacted test performance.

      We thank the Reviewer for their positive assessment of our revised manuscript. We discussed the comments regarding group balancing below.

      Strengths:

      The experimental designs are very rigorous with an unusual level of behavioral sophistication.

      We thank the Reviewer for their positive assessment

      Weaknesses:

      The various group differences in Figure 2 prior to any manipulation are still problematic. There was a reliable effect of subsequent group assignment in Figure 2 (p<0.05, described as "marginal" in multiple places). Then there are differences in extinction (nonsignificant at p=.07). The test difference between ReExt OFF/ON is identical to the difference at the end of extinction and the beginning of Forward 2, in terms of absolute size. I really don't think much can be made of the test result. The authors state in their response that this difference was not evident during the forward phase, but there clearly is a large ordinal difference on the first trial. I think it is appropriate to only focus on test differences when groups are appropriately matched, but when there are pre-existing differences (even when not statistically significant) then they really need to be incorporated into the statistical test somehow.

      We carefully considered the Reviewer's suggestion, but it is not possible to adjust the statistical analyses at test because these analyses do not directly compare the two ReExt groups. Any scaling of performance would require including the two Ext groups, which is not feasible since these groups did not receive initial extinction. Moreover, the analyses provide no conclusive evidence of pre-existing differences between the two ReExt groups: the difference was not significant during initial extinction and was absent during the Forward 2 stage. We acknowledge that closer performance between the two ReExt groups during initial extinction would have been preferable. However, we remain confident in the results obtained because they replicate previous experiments in which the two ReExt groups displayed identical performance during initial extinction.

      The same problem is evident in Figure 4B, but here the large differences in the Same groups are opposite to the test differences. It's hard to say how those large differences ultimately impacted the test results. I suppose it is good that the differences during Forward conditioning did not ultimately predict test differences, but this really should have been addressed with more subjects in these experiments. The authors explore the interactions appropriately but with n=6 in the various subgroups, it's not surprising that some of these effects were not detected statistically.

      As the Reviewer noted, the unexpected differences in Figure 4B are opposite in direction to the test differences. Importantly, Figure 4B replicates the main findings from Figure 3, which did not show these unexpected differences.

      It is useful to see the trial-by-trial test data now presented in the supplement. I think the discussion does a good job of addressing the issues of retrieval, but the ideas of Estes about session cues that the authors bring up in their response haven't really held up over the years (e.g., Robbins, 1990, who explicitly tested this; other demonstrations of within-session spontaneous recovery), for what it's worth.

      We thank the Reviewer for bringing our attention to Robbins’ work on session cues. We understand that the issue of retrieval is important but as we noted before, our manuscript and its conclusions do not claim to differentiate retrieval from additional learning.

      References

      (1) K. E. Nett, R. T. LaLumiere, Infralimbic cortex functioning across motivated behaviors: Can the differences be reconciled Neurosci Biobehav Rev 131, 704–721 (2021).

      (2) V. Laurent, R. F. Westbrook, Inactivation of the infralimbic but not the prelimbic cortex impairs consolidation and retrieval of fear extinction Learn Mem 16, 520–529 (2009).

      (3) N. W. Lingawi, R. F. Westbrook, V. Laurent, Extinction and Latent Inhibition Involve a Similar Form of Inhibitory Learning that is Stored in and Retrieved from the Infralimbic Cortex Cereb Cortex 27, 5547–5556 (2017).

      (4) N. W. Lingawi, N. M. Holmes, R. F. Westbrook, V. Laurent, The infralimbic cortex encodes inhibition irrespective of motivational significance Neurobiol Learn Mem 150, 64–74 (2018).


      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript reports a series of experiments designed to test whether optogenetic activation of infralimbic (IL) neurons facilitates extinction retrieval and whether this depends on animals' prior experience. In Experiment 1, rats underwent fear conditioning followed by either one or two extinction sessions, with IL stimulation given during the second extinction; stimulation facilitated extinction retrieval only in rats with prior extinction experience. Experiments 2 and 3 examined whether backward conditioning (CS presented after the US) could establish inhibitory properties that allowed IL stimulation to enhance extinction, and whether this effect was specific to the same stimulus or generalized to different stimuli. Experiments 5 - 7 extended this approach to appetitive learning: rats received backward or forward appetitive conditioning followed by extinction, and then fear conditioning, to determine whether IL stimulation could enhance extinction in contexts beyond aversive learning and across conditioning sequences. Across studies, the key claim is that IL activation facilitates extinction retrieval only when animals possess a prior inhibitory memory, and that this effect generalizes across aversive and appetitive paradigms.

      Strengths:

      (1) The design attempts to dissect the role of IL activity as a function of prior learning, which is conceptually valuable.

      We thank the Reviewer for their positive assessment.

      (2) The experimental design of probing different inhibitory learning approaches to probe how IL activation facilitates extinction learning was creative and innovative.

      We thank the Reviewer for their positive assessment.

      Weaknesses:

      (1) Non-specific manipulation.

      ChR2 was expressed in IL without distinction between glutamatergic and GABAergic populations. Without knowing the relative contribution of these cell types or the percentage of neurons affected, the circuit-level interpretation of the results is unclear.

      ChR2 was intentionally expressed in the infralimbic cortex (IL) without distinction between local neuronal populations for two reasons. First, the primary aim of this was to uncover some of the features characterizing the encoding of inhibitory memories in the IL, and this encoding likely engages interactions among various neuronal populations within the IL. Second, the hypotheses tested in the manuscript derived from findings that indiscriminately stimulated the IL using the GABA<sub>A</sub> receptor antagonist picrotoxin, which is best mimicked by the approach taken. We agree that it is also important to determine the respective contributions of distinct IL neuronal populations to inhibitory encoding; however, the global approach implemented in the present experiments represents a necessary initial step. These matters have been incorporated in the Discussion of the revised manuscript.

      (2) Extinction retrieval test conflates processes

      The retrieval test included 8 tones. Averaging across this many tone presentations conflate extinction retrieval/expression (early tones) with further extinction learning (later tones). A more appropriate analysis would focus on the first 2-4 tones to capture retrieval only. As currently presented, the data do not isolate extinction retrieval.

      It is unclear when retrieval of what has been learned across extinction ceases and additional extinction learning occurs. In fact, it is only the first stimulus presentation that unequivocally permits a distinction between retrieval and additional extinction learning, as the conditions for this additional learning have not been fulfilled at that presentation. However, confining evidence for retrieval to the first stimulus presentation introduces concerns that other factors could influence performance. For instance, processing of the stimulus present at the start of the session may differ from that present at the end of the previous session, thereby affecting what is retrieved. Such differences between the stimuli present at the start and end of an extinction session have been long recognized as a potential explanation for spontaneous recovery (Estes, 1955). More importantly, whether the test data presented confound retrieval and additional extinction learning or not, the interpretation remains the same with respect to the effects of a prior history of inhibitory learning on enabling the facilitative effects of IL stimulation. Finally, it is unclear how these facilitative effects could occur in the absence of the subjects retrieving the extinction memory formed under the stimulation. Nevertheless, the revised manuscript now provides the trial-by-trial performance (see Supplemental Figure 3) during the post-extinction retrieval tests and addresses this issue in the Discussion.

      (3) Under-sampling and poor group matching.

      Sample sizes appear small, which may explain why groups are not well matched in several figures (e.g., 2b, 3b, 6b, 6c) and why there are several instances of unexpected interactions (protocol, virus, and period). This baseline mismatch raises concerns about the reliability of group differences.

      Efforts were made to match group performance upon completion of each training stage and before IL stimulation. Unfortunately, these efforts were not completely successful due to exclusions following post-mortem analyses. This has been made explicit in the revised manuscript (Materials and Methods, Subjects section). However, we acknowledge that the unexpected interactions deserve further discussion, and this has been incorporated into the revised manuscript (see also comment from Reviewer 2). Although we cannot exclude the possibility that sample sizes may have contributed to some of these interactions, we remain confident about the reliability of the main findings reported, especially given their replication across the various protocols. Overall, the manuscript provides evidence that IL stimulation does not facilitate brief extinction in the absence of prior inhibitory experience in five different experiments, replicating previous findings (Lingawi et al., 2018; Lingawi et al., 2017). It also replicates these previous findings by showing that prior experience with either fear or appetitive extinction enables IL stimulation to facilitate subsequent fear extinction. Furthermore, the facilitative effects of such stimulation following fear or appetitive backward conditioning are replicated in the present manuscript. This is discussed in the Discussion of the revised manuscript.

      (4) Incomplete presentation of conditioning data

      Figure 3 only shows a single conditioning session despite five days of training. Without the full dataset, it is difficult to evaluate learning dynamics or whether groups were equivalent before testing.

      We apologize, as we incorrectly labeled the X axis for the backward conditioning data in Figures 3B, 4B, 4D and 5B. It should have indicated “Days” instead of “Trials”. This error has been corrected in the revised manuscript (see also second comment from Reviewer 2).

      (5) Interpretation stronger than evidence.

      The authors conclude that IL activation facilitates extinction retrieval only when an inhibitory memory has been formed. However, given the caveats above, the data are insufficient to support such a strong mechanistic claim. The results could reflect nonspecific facilitation or disruption of behavior by broad prefrontal activation. Moreover, there is compelling evidence that optogenetic activation of IL during fear extinction does facilitate subsequent extinction retrieval without prior extinction training (DoMonte et al 2015, Chen et al 2021), which the authors do not directly test in this study.

      As noted above, the interpretations of the main findings stand whether the test data confounds retrieval with additional extinction learning or not. The revised manuscript also clarifies the plotting of the data for the backward conditioning stages. We do agree that further discussion of the unexpected interactions is necessary, and this has been incorporated into the revised manuscript. However, the various replications of the core findings provide strong evidence for their reliability and the interpretations advanced in the original manuscript. The proposal that the results reflect non-specific facilitation or disruption of behavior seems highly unlikely. Indeed, the present experiments and previous findings (Lingawi et al., 2018; Lingawi et al., 2017) provide multiple demonstrations that IL stimulation fails to produce any facilitation in the absence of prior inhibitory experience with the target stimulus. Although these demonstrations appear inconsistent with previous studies (Do-Monte et al., 2015; Chen et al., 2021), this inconsistency is likely explained by the fact that these studies manipulated activity in specific IL neuronal populations. Previous work has already revealed differences between manipulations targeting discrete IL neuronal populations as opposed to general IL activity (Kim et al., 2016). Importantly, as previously noted, the present manuscript aimed to generally explore inhibitory encoding in the IL that is likely to engage several neuronal populations within the IL. Adequate statements on these matters have been included in the Discussion of the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, the authors examine the mechanisms by which stimulation of the infralimbic cortex (IL) facilitates the retention and retrieval of inhibitory memories. Previous work has shown that optogenetic stimulation of the IL suppresses freezing during extinction but does not improve extinction recall when extinction memory is probed one day later. When stimulation occurs during a second extinction session (following a prior stimulation-free extinction session), freezing is suppressed during the second extinction as well as during the tone test the following day. The current study was designed to further explore the facilitatory role of the IL in inhibitory learning and memory recall. The authors conducted a series of experiments to determine whether recruitment of IL extends to other forms of inhibitory learning (e.g., backward conditioning) and to inhibitory learning involving appetitive conditioning. Further, they assessed whether their effects could be explained by stimulus familiarity. The results of their experiments show that backward conditioning, another form of inhibitory learning, also enabled IL stimulation to enhance fear extinction. This phenomenon was not specific to aversive learning, as backward appetitive conditioning similarly allowed IL stimulation to facilitate extinction of aversive memories. Finally, the authors ruled out the possibility that IL facilitated extinction merely because of prior experience with the stimulus (e.g., reducing the novelty of the stimulus). These findings significantly advance our understanding of the contribution of IL to inhibitory learning. Namely, they show that the IL is recruited during various forms of inhibitory learning, and its involvement is independent of the motivational value associated with the unconditioned stimulus.

      Strengths:

      (1) Transparency about the inclusion of both sexes and the representation of data from both sexes in figures.

      We thank the Reviewer for their positive assessment.

      (2) Very clear representation of groups and experimental design for each figure.

      We thank the Reviewer for their positive assessment.

      (3) The authors were very rigorous in determining the neurobehavioral basis for the effects of IL stimulation on extinction. They considered multiple interpretations and designed experiments to address these possible accounts of their data.

      We thank the Reviewer for their positive assessment.

      (4) The rationale for and the design of the experiments in this manuscript are clearly based on a wealth of knowledge about learning theory. The authors leveraged this expertise to narrow down how the IL encodes and retrieves inhibitory memories.

      We thank the Reviewer for their positive assessment.

      Weaknesses:

      (1) In Experiment 1, although not statistically significant, it does appear as though the stimulation groups (OFF and ON) differ during Extinction 1. It seems like this may be due to a difference between these groups after the first forward conditioning. Could the authors have prevented this potential group difference in Extinction 1 by re-balancing group assignment after the first forward conditioning session to minimize the differences in fear acquisition (the authors do report a marginally significant effect between the groups that would undergo one vs. two extinction sessions in their freezing during the first conditioning session)?

      Efforts were made daily to match group performance across the training stages, but these efforts were ultimately hampered by the necessary exclusions following postmortem analyses. This has been made explicit in the revised manuscript (Materials and Methods, Subjects section). Regarding freezing during Extinction 1, as noted by the Reviewer, the difference, which was not statistically significant, was absent across trials during the subsequent forward fear conditioning stage. Likewise, the protocol difference observed during the initial forward fear conditioning was absent in subsequent stages. We are therefore confident that these initial differences (significant or not) did not impact the main findings at test. Importantly, these findings replicate previous work using identical protocols in which no differences were present during the training stages. These considerations have been addressed in the revised manuscript (see Results for Experiment 1).

      (2) Across all experiments (except for Experiment 1), the authors state that freezing during the initial conditioning increased across "days". The figures that correspond to this text, however, show that freezing changes across trials. In the methods, the authors report that backward conditioning occurred over 5 days. It would be helpful to understand how these data were analyzed and collated to create the final figures. Was the freezing averaged across the five days for each trial for analyses and figures?

      We apologize, as noted above, for having incorrectly labeled the X axis across the backward conditioning data sets in Figures 3B, 4B, 4D and 5B. It should have indicated “Days” instead of “Trials”. The data shown in these Figures use the average of all trials on a given day. This has been clarified in the methods section of the revised manuscript (Statistical Analyses section). The labeling errors on the Figures have been corrected.

      (3) In Experiment 3, the authors report a significant Protocol X Virus interaction. It would be useful if the authors could conduct post-hoc analyses to determine the source of this interaction. Inspection of Figure 4B suggests that freezing during the two different variants of backward conditioning differs between the virus groups. Did the authors expect to see a difference in backward conditioning depending on the stimulus used in the conditioning procedure (light vs. tone)? The authors don't really address this confounding interaction, but I do think a discussion is warranted.

      We agree with the Reviewer that further discussion of the Protocol x Virus interaction that emerged during the backward conditioning and forward conditioning stages of Experiment 3 is warranted. This discussion has been provided in the revised manuscript (see Results section). Briefly, during both stages, follow-up analyses did not reveal any differences (main effects or interactions) between the two groups trained with the light stimulus (Diff-EYFP and Diff-ChR2). By contrast, the ChR2 group trained with the tone (Back-ChR2) froze more overall than the EYFP group (Back-EYFP), but there were no other significant differences between the two groups. Based on these analyses, the Protocol x Virus interaction appears to be driven by greater freezing in the ChR2 group trained with the tone rather than a difference in the backward conditioning performance based on stimulus identity. Consistent with this, the statistical analyses did not reveal a main effect of Protocol during either the backward conditioning stage or the stimulus trials during the forward conditioning stage. Nevertheless, during this latter stage, a main effect of Protocol emerged during baseline performance, but once again, this seems to be driven by the Back-ChR2 group. Critically, it is unclear how greater stimulus freezing in the Back-ChR2 group during forward conditioning would lead to lower freezing during the post-extinction retrieval test.

      We note that an unexpected Protocol x Period interaction was found during appetitive backward conditioning in Experiment 5. For consistency, we conducted additional analyses to determine the source of this interaction (see Results section). As previously noted, performance during appetitive backward conditioning is noisy and cannot be taken as a failure to generate inhibitory learning. It is therefore unlikely that this interaction implied a difference in such learning.

      (4) In this same experiment, the authors state that freezing decreased during extinction; however, freezing in the Diff-EYFP group at the start of extinction (first bin of trials) doesn't look appreciably different than their freezing at the end of the session. Did this group actually extinguish their fear? Freezing on the tone test day also does not look too different from freezing during the last block of extinction trials.

      We confirm that overall, there was a significant decline in freezing across the extinction session shown in Figure 4B. The Reviewer is correct to point out that this decline was modest (if not negligible) in the Diff-EYFP group, which was receiving its first inhibitory training with the target tone stimulus. It is worth noting that across all experiments, most groups that did not receive infralimbic stimulation displayed a modest decline in freezing during the extinction session since it was relatively brief, involving only 6 or 8 tone alone presentations. This was intentional, as we aimed for the brief extinction session to generate minimal inhibitory learning and thereby to detect any facilitatory effect of infralimbic stimulation. This has been clarified and explained in the revised version of the manuscript (see Results section, description of Experiment 1).

      (5) The Discussion explored the outcomes of the experiments in detail, but it would be useful for the authors to discuss the implications of their findings for our understanding of circuits in which the IL is embedded that are involved in inhibitory learning and memory. It would also be useful for the authors to acknowledge in the Discussion that although they did not have the statistical power to detect sex differences, future work is needed to explore whether IL functions similarly in both sexes.

      In line with the Reviewer’s suggestion (see also Reviewer 3), the Discussion section has been substantially altered in the revised manuscript. Among other things, it does mention that future studies will need to examine the role of additional brain regions in the effects reported and it acknowledges the need to further explore sex differences and IL functions.

      Reviewer #3 (Public review):

      Summary:

      This is a really nice manuscript with different lines of evidence to show that the IL encodes inhibitory memories that can then be manipulated by optogenetic stimulation of these neurons during extinction. The behavioral designs are excellent, with converging evidence using extinction/re-extinction, backwards/forwards aversive conditioning, and backwards appetitive/forwards aversive conditioning. Additional factors, such as nonassociative effects of the CS or US, are also considered, and the authors evaluate the inhibitory properties of the CS with tests of conditioned inhibition.

      Strengths:

      The experimental designs are very rigorous with an unusual level of behavioral sophistication.

      We thank the Reviewer for their positive assessment

      Weaknesses:

      (1) More justification for parametric choices (number of days of backwards vs forwards conditioning) could be provided.

      All experimental parameters were based on previously published experiments showing the capacity of the backward conditioning protocols to generate inhibitory learning and the forward conditioning protocols to produce excitatory learning. Although this was mentioned in the methods section, we acknowledge that further explanation was required to justify the need for multiple days of backward training. This has been provided in the revised manuscript (see Results section and description of the backward parameters.

      (2) The current discussion could be condensed and could focus on broader implications for the literature.

      The discussion has been severely condensed and broader implications have been discussed with respect to the existing literature looking at the neural circuitry underlying inhibitory learning.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Re-analyze extinction retrieval, focusing only on the first 2-4 tones to capture extinction expression.

      This recommendation corresponds to the second public comment made by the Reviewer, and we have replied to this comment.

      (2) Directly test whether activation of IL during fear extinction is insufficient to facilitate extinction retrieval without prior extinction training.

      The manuscript provides five separate demonstrations that the optogenetic approach to stimulate IL activity did not facilitate the initial brief extinction session. This reproduces what had been found with indiscriminate pharmacological stimulation in our previous research (Lingawi et al., 2018; Lingawi et al., 2017). We appreciate that other work that stimulated specific IL neuronal populations has observed facilitation of extinction but, the present manuscript focuses on the role of all IL neuronal populations in encoding inhibitory memories. The Reviewer’s request would imply contrasting the role of various neuronal populations, which is beyond the scope of this manuscript. Nevertheless, we have modified our discussion to indicate that future research should establish which IL neuronal population(s) contribute to the effects reported here.

      (3) Show the percentage of neurons that exhibit excitatory or inhibitory responses in IL after non-specific optogenetic activation to better understand how this manipulation is affecting IL circuitry.

      All electrophysiological recordings (n = 10 cells) are presented in Figure 1C. ChR2 excitation was substantial and overwhelming. Based on the physiological and morphological characteristics of the recorded cells, one was non-pyramidal and was excited by LED light delivery. The remaining 9 cells were pyramidal. One did not respond to LED delivery, but we cannot exclude the possibility that this was due to a lack of ChR2 expression in the somatic compartment. Another cell showed a mild reduction in activity following LED stimulation, while the remaining 7 cells displayed clear excitation upon LED stimulation. We have modified our manuscript to reflect these observations. We did not include percentages since only 10 recordings are shown.

      (4) Present data from all five conditioning sessions, not just one, to allow evaluation of learning history.

      This recommendation corresponds to the fourth public comment made by the Reviewer, and we have replied to this comment.

      (5) Address the issue of small and poorly matched groups, particularly in Figures 2b, 3b, 6b, and 6c.

      This recommendation corresponds to the third public comment made by the Reviewer, and we have replied to this comment.

      (6) Temper the conclusions to reflect the limitations of sampling, group matching, and the lack of specificity in the manipulation.

      We have modified our Discussion to address potential issues related to sampling and group matching. However, we are unsure how the lack of specificity of the IL stimulation has any impact on the interpretations made, since no statement is made about neuronal specificity. That said, as noted above, “we have modified our discussion to indicate that future research should establish which IL neuronal population(s) contribute to the effects reported here”.

      Reviewer #2 (Recommendations for the authors):

      Nothing additional to include beyond what is written for public view.

      Reviewer #3 (Recommendations for the authors):

      This is a really nice manuscript with different lines of evidence to show that the IL encodes inhibitory memories that can then be manipulated by optogenetic stimulation of these neurons during extinction. The behavioral designs are excellent, with converging evidence using extinction/re-extinction, backwards/forwards aversive conditioning, and backwards appetitive/forwards aversive conditioning. Additional factors, such as nonassociative effects of the CS or US, are also considered, and the authors evaluate the inhibitory properties of the CS with tests of conditioned inhibition. I only have a couple of comments that the authors may want to consider.

      We thank the Reviewer for their positive assessment.

      First, in Figure 2, it is unfortunate that there is a general effect of the LED assignment before the LED experience (p=.07 during that first extinction session). This is in the same direction as the difference during the test, so it is not clear that the test difference really reflects differences due to Extinction 2 treatment or to preexisting differences based on group assignments.

      The Reviewer’s comment is identical to the first public comment of Reviewer 2, which has been addressed.

      Second, it is notable that the backwards fear conditioning phase was conducted over 5 days, but the forward conditioning phase was conducted over one day. The rationale for these differences should be presented. There is an old idea going back to Konorski that backwards conditioning may lead to excitation initially, and it is only after more extensive trials that inhibitory conditioning occurs (a finding supported by Heth, 1976). Some discussion of the potential biphasic nature of backwards conditioning would be useful, especially for people who want to run this type of experiment but with only a single session of backwards conditioning.

      In line with the Reviewer’s suggestion, the revised manuscript (see results section) provide an explanation for conducting backward conditioning across multiple days.

      Third, as written, each paragraph of the discussion is mostly a recapitulation of the findings from each experiment. This could be condensed significantly, and it would be nice to see more integration with the current literature and how these results challenge or suggest nuance in current thinking about IL function.

      We have significantly condensed the recapitulation of our findings in the Discussion of the revised manuscript. The Discussion now dedicates space to address comments from the other Reviewers and integrate the present findings with the current literature.

      References

      Chen, Y.-H., Wu, J.-L., Hu, N.-Y., Zhuang, J.-P., Li, W.-P., Zhang, S.-R., Li, X.-W., Yang, J.-M., & Gao, T.-M. (2021). Distinct projections from the infralimbic cortex exert opposing effects in modulating anxiety and fear. J Clin Invest, 131(14), e145692. https://doi.org/10.1172/JCI145692

      Do-Monte, F. H., Manzano-Nieves, G., Quiñones-Laracuente, K., Ramos-Medina, L., & Quirk, G. J. (2015). Revisiting the role of infralimbic cortex in fear extinction with optogenetics. J Neurosci, 35(8), 3607-3615. https://doi.org/10.1523/JNEUROSCI.3137-14.2015

      Estes, W. K. (1955). Statistical theory of spontaneous recovery and regression. Psychol Rev, 62(3), 145-154. https://doi.org/10.1037/h0048509

      Kim, H.-S., Cho, H.-Y., Augustine, G. J., & Han, J.-H. (2016). Selective Control of Fear Expression by Optogenetic Manipulation of Infralimbic Cortex after Extinction. Neuropsychopharmacology, 41(5), 1261-1273. https://doi.org/10.1038/npp.2015.276

      Lingawi, N. W., Holmes, N. M., Westbrook, R. F., & Laurent, V. (2018). The infralimbic cortex encodes inhibition irrespective of motivational significance. Neurobiol Learn Mem, 150, 64-74. https://doi.org/10.1016/j.nlm.2018.03.001

      Lingawi, N. W., Westbrook, R. F., & Laurent, V. (2017). Extinction and Latent Inhibition Involve a Similar Form of Inhibitory Learning that is Stored in and Retrieved from the Infralimbic Cortex. Cereb Cortex, 27(12), 5547-5556.

      https://doi.org/10.1093/cercor/bhw322.

    1. Author response:

      The following is the authors’ response to the current reviews.

      Reviewer #4 (Public review):

      Summary:

      The authors demonstrate a computational rational design approach for developing RNA aptamers with improved binding to the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. They demonstrate the ability of their approach to improve binding affinity using a previously identified RNA aptamer, RBD-PB6-Ta, which binds to the RBD. They also computationally estimate the binding energies of various RNA aptamers with the RBD and compare against RBD binding energies for a few neutralizing antibodies from the literature. Finally, experimental binding affinities are estimated by electrophoretic mobility shift assays (EMSA) for various RNA aptamers and a single commercially available neutralizing antibody to support the conclusions from computational studies on binding. The authors conclude that their computational framework, CAAMO, can provide reliable structure predictions and effectively support rational design of improved affinity for RNA aptamers towards target proteins. Additionally, they claim that their approach achieved design of high affinity RNA aptamer variants that bind to the RBD as well or better than a commercially available neutralizing antibody.

      Strengths:

      The thorough computational approaches employed in the study provide solid evidence of the value of their approach for computational design of high affinity RNA aptamers. The theoretical analysis using Free Energy Perturbation (FEP) to estimate relative binding energies supports the claimed improvement of affinity for RNA aptamers and provides valuable insight into the binding model for the tested RNA aptamers in comparison to previously studied neutralizing antibodies. The multimodal structure prediction in the early stages of the presented CAAMO framework, combined with the demonstrated outcome of improved affinity using the structural predictions as a starting point for rational design, provide moderate confidence in the structure predictions.

      We thank the reviewer for this accurate summary and for recognizing the strength of our integrated computational–experimental workflow in improving aptamer affinity.

      Weaknesses:

      The experimental characterization of RBD affinities for the antibody and RNA aptamers in this study present serious concerns regarding the methods used and the data presented in the manuscript, which call into question the major conclusions regarding affinity towards the RBD for their aptamers compared to antibodies. The claim that structural predictions from CAAMO are reasonable is rational, but this claim would be significantly strengthened by experimental validation of the structure (i.e. by chemical footprinting or solving the RBD-aptamer complex structure).

      The conclusions in this work are somewhat supported by the data, but there are significant issues with experimental methods that limit the strength of the study's conclusions.

      (1) The EMSA experiments have a number of flaws that limit their interpretability. The uncropped electrophoresis images, which should include molecular size markers and/or positive and negative controls for bound and unbound complex components to support interpretation of mobility shifts, are not presented. In fact, a spliced image can be seen for Figure 4E, which limits interpretation without the full uncropped image.

      Thank you for your valuable comments and careful review.

      In response to your suggestion, we will provide all uncropped electrophoresis raw images corresponding to the results in the main figures and supplementary figures (Figure 2F, 3D, 3E, 4E, S9A and S10 of the original manuscript) in the revised version. Regarding the spliced image in Figure 4E, the uncropped raw gel image clearly shows that the two C23U samples were run on an adjacent lane of the same gel due to the total number of samples exceeding the well capacity of a single lane. All samples were electrophoresed and signal-detected under identical experimental conditions in one single experiment, ensuring the validity of direct signal intensity comparison across all samples. These complete uncropped raw images will be supplemented in the revised manuscript as Figure S12 (also see Author response image 1).

      Author response image 1.

      Uncropped electrophoresis images corresponding to Figures 2F, 3D, 3E, 4E, S9A and S10 of the original manuscript.

      Additionally, he volumes of EMSA mixtures are not presented when a mass is stated (i.e. for the methods used to create Figure 3D), which leaves the reader without the critical parameter, molar concentration, and therefore leaves in question the claim that the tested antibody is high affinity under the tested conditions.

      Thank you for your valuable comment on this oversight.

      For the EMSA assay in Figure 3D, the reaction mixture (10 μL total volume) contained 3 μg of RBD protein and 3 μg of antibody (40592-R001), either individually or in combination, with incubation at room temperature for 20 minutes. Based on the molecular weights (35 kDa for RBD and 150 kDa for the IgG antibody), the corresponding molar concentrations in the mixture were calculated as 8.57 μM for RBD and 2 μM for the antibody. To ensure consistency, clarity and provide the critical molar concentration parameter, we will revise the legend of Figure 3D, replacing the mass values with the calculated molar concentrations as you suggested in the revised manuscript.

      Additionally, protein should be visualized in all gels as a control to ensure that lack of shifts is not due to absence/aggregation/degradation of the RBD protein. In the case of Figure 3E, for example, it can be seen that there are degradation products included in the RBD-only lane, introducing a reasonable doubt that the lack of a shift in RNA tests (i.e. Figure 2F) is conclusively due to a lack of binding.

      We sincerely appreciate your careful evaluation of our work, which helps us further clarify the experimental details and data reliability.

      First, we would like to clarify the nature of the gel electrophoresis in Figure 3E: the RBD protein was separated by native-PAGE rather than denaturing SDS-PAGE. The RBD protein used in all experiments was purchased from HUABIO (Cat. No. HA210064) with guaranteed quality, and its integrity and purity were independently verified in our laboratory via denaturing SDS-PAGE (see Author response image 2), which showed a single, intact band without any degradation products. The ladder-like bands observed in the RBD-only lane of the native-PAGE gel are not a result of protein degradation. Instead, they arise from two well-characterized properties of recombinant SARS-CoV-2 Spike RBD protein expressed in human cells: intrinsic conformational heterogeneity (the RBD domain exists in multiple dynamic conformations due to its structural flexibility) (Cai et al., Science, 2020; Wrapp et al., Science, 2020) and heterogeneity in N-glycosylation modification (variable glycosylation patterns at the conserved N-glycosylation sites of RBD) (Casalino et al., ACS Cent. Sci., 2020; Ives et al., eLife, 2024), both of which could cause distinct migration bands in native-PAGE under non-denaturing conditions.

      Second, to ensure the reliability of the RNA-binding results, the EMSA experiments for determining the binding affinity (K<sub>d</sub>) of RBD to Ta, Tc and Ta variants were performed with three independent biological replicates (the original manuscript includes all replicate data in Figure 2F and S9). Consistent results were obtained across all replicates, which effectively rules out false-negative outcomes caused by accidental absence or loss of functional RBD protein in the reaction system. In addition, our gel images (Figure 2F and S9 in the original manuscript) and uncropped raw images of all EMSA gels (see Author response image 1) show no significant signal accumulation in the sample wells, confirming the absence of RBD protein aggregation in the binding reactions—an issue that would otherwise interfere with RNA-protein interaction and band shift detection.

      New results for RBD analysis by denaturing SDS-PAGE, along with the associated discussion, will be added to the revised manuscript as Figure S10 (also see Author response image 2).

      Author response image 2.

      SDS-PAGE analysis of the SARS-CoV-2 Spike RBD protein, neutralizing antibody (40592-R001) and BSA reference. This gel validates the high purity and structural integrity of the commercially sourced RBD protein and neutralizing antibody used in this study.

      References

      Cai, Y. et al. Distinct conformational states of SARS-CoV-2 spike proteins. Science 369, 1586-1592 (2020).

      Casalino, L. et al. Beyond shielding: the roles of glycans in the SARS-CoV-2 spike protein. ACS Cent. Sci. 6, 1722-1734 (2020).

      Ives, C.M. et al. Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern. eLife 13, RP95708 (2024).

      Wrapp, D. et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367, 1260-1263 (2020).

      Finally, there is no control for nonspecific binding, such as BSA or another non-target protein, which fails to eliminate the possibility of nonspecific interactions between their designed aptamers and proteins in general. A nonspecific binding control should be included in all EMSA experiments.

      Thank you for this constructive comment.

      Following your recommendation, we are currently supplementing the EMSA assays with BSA as a non-target protein control to rigorously exclude potential non-specific binding between our designed aptamers (Ta and Ta variants) and exogenous proteins. These additional experiments are designed to directly assess whether the aptamers exhibit unintended interactions with unrelated proteins and to further validate the protein specificity of the RBD–aptamer interaction observed in our study.

      The resulting nonspecific binding control data will be formally incorporated into the revised manuscript as Figure S11, and the corresponding Results and Discussion sections will be updated accordingly to reflect this critical validation once the experiments are completed.

      (2) The evidence supporting claims of better binding to RBD by the aptamer compared to the commercial antibody is flawed at best. The commercial antibody product page indicates an affinity in low nanomolar range, whereas the fitted values they found for the aptamers in their study are orders of magnitude higher at tens of micromolar. Moreover, the methods section is lacking in the details required to appropriately interpret the competitive binding experiments. With a relatively short 20-minute equilibration time, the order of when the aptamer is added versus the antibody makes a difference in which is apparently bound. The issue with this becomes apparent with the lack of internal consistency in the presented results, namely in comparing Fig 3E (which shows no interference of Ta binding with 5uM antibody) and Fig 5D (which shows interference of Ta binding with 0.67-1.67uM antibody). The discrepancy between these figures calls into question the methods used, and it necessitates more details regarding experimental methods used in this manuscript.

      Thank you for your insightful comments, which have helped us refine the rigor of our study. We address each of your concerns in detail below:

      First, we agree with your observation that the commercial neutralizing antibody (Sino Biological, Cat# 40592-R001) is reported to bind Spike RBD with low nanomolar affinity on its product page. However, this discrepancy in affinity values (nanomolar vs. micromolar) stems from the use of distinct analytical methods. The product page affinity was determined via the Octet RED System, a technique analogous to Surface Plasmon Resonance (SPR) that offers high sensitivity for kinetic and affinity measurements. In contrast, our study employed EMSA, a method primarily optimized for semi-quantitative assessment of binding interactions. The inherent differences in sensitivity and principle between these two techniques—with Octet RED System enabling real-time monitoring of biomolecular interactions and EMSA relying on gel separation—account for the observed variation in affinity values.

      Second, regarding the competitive binding experiments, we appreciate your note on the critical role of reagent addition order and equilibration time. To eliminate potential biases from sequential addition, we clarify that Cy3-labeled RNAs, RBD proteins, and the neutralizing antibody were added simultaneously to the reaction system. We will revise the Methods section in the revised manuscript to provide a detailed protocol for the EMSA experiments, to ensure full reproducibility and appropriate interpretation of the results.

      Third, we acknowledge and apologize for a critical error in the figure legends of Figure 3E: the concentrations reported (5 μM aptamer and antibody 40592-R001) refer to stock solutions, not the final concentrations in the EMSA reaction mixture. The correct final concentrations are 0.5 μM for aptamer Ta, and 0.5 μM for the antibody. This correction resolves the apparent inconsistency between Figure 3E and Figure 5D, as the final antibody concentration in Figure 3E is now consistent with the concentration range used in Figure 5D. We will update the figure legends for Figure 3E and revise the Methods section to explicitly distinguish between stock and final reaction concentrations, ensuring clarity and internal consistency of the results.

      We sincerely thank you for highlighting these issues, which will prompt important revisions to improve the clarity, accuracy, and rigor of our manuscript.

      (3) The utility of the approach for increasing affinity of RNA aptamers for their targets is well supported through computational and experimental techniques demonstrating relative improvements in binding affinity for their G34C variant compared to the starting Ta aptamer. While the EMSA experiments do have significant flaws, the observations of relative relationships in equilibrium binding affinities among the tested aptamer variants can be interpreted with reasonable confidence, given that they were all performed in a consistent manner.

      We sincerely appreciate your valuable concerns and constructive feedback, which have greatly facilitated the improvement of our manuscript. Regarding the flaws of the EMSA experiments you pointed out, we have provided a detailed response to clarify the related issues and supplemented necessary experimental details to enhance the rigor and reproducibility of our work (see corresponding response above). It is worth noting that EMSA remains a classic and widely used technique for studying biomolecular interactions, and its reliability in qualitative and semi-quantitative analysis of binding events has been well recognized in the field. Furthermore, we fully agree with and are grateful for your view that, since all tested aptamer variants were analyzed using a consistent experimental protocol, the observations on the relative relationships of their equilibrium binding affinities can be interpreted with reasonable confidence. This recognition reinforces the validity of the relative affinity improvements we observed for the G34C variant compared to the parental Ta aptamer, which is a key finding of our study.

      (4) The claim that the structure of the RBD-Aptamer complex predicted by the CAAMO pipeline is reliable is tenuous. The success of their rational design approach based on the structure predicted by several ensemble approaches supports the interpretation of the predicted structure as reasonable, however, no experimental validation is undertaken to assess the accuracy of the structure. This is not a main focus of the manuscript, given the applied nature of the study to identify Ta variants with improved binding affinity, however the structural accuracy claim is not strongly supported without experimental validation (i.e. chemical footprinting methods).

      We thank the reviewer for this comment and agree that experimental validation would be required to establish the structural accuracy of the predicted RBD–aptamer complex. We note, however, that the primary aim of this study is not structural determination, but the development of a general computational framework for aptamer affinity maturation. In most practical applications, experimentally resolved structures of aptamer–protein complexes are unavailable. Accordingly, CAAMO is designed to operate under such conditions, using computationally generated binding models as working hypotheses to guide rational optimization rather than as definitive structural descriptions. In this context, the predicted structure is evaluated by its utility for affinity improvement, rather than by direct structural validation. We will revise the manuscript accordingly to further clarify this scope.

      (5) Throughout the manuscript, the phrasing of "all tested antibodies" was used, despite there being only one tested antibody in experimental methods and three distinct antibodies in computational methods. While this concern is focused on specific language, the major conclusion that their designed aptamers are as good or better than neutralizing antibodies in general is weakened by only testing only three antibodies through computational binding measurements and a fourth single antibody for experimental testing. The contact residue mapping furthermore lacks clarity in the number of structures that were used, with a vague description of structures from the PDB including no accession numbers provided nor how many distinct antibodies were included for contact residue mapping.

      We thank the reviewer for this important comment regarding language precision, experimental scope, and clarity of the antibody dataset used in this study. We agree that the phrase “all tested antibodies” was imprecise and could lead to overgeneralization. We will carefully revise the manuscript to use more accurate and explicit wording throughout, clearly distinguishing between experimentally tested antibodies, computationally analyzed antibodies, and antibody structures used for large-scale contact analysis.

      Specifically, the experimental comparison in this study was performed using one commercially available SARS-CoV-2 neutralizing antibody, whereas free energy–based computational analyses were conducted on three representative neutralizing antibodies with available structural data. We will revise the manuscript to explicitly state these distinctions and avoid general statements referring to neutralizing antibodies as a class.

      Importantly, the residue-level contact frequency analysis was not based solely on these individual antibodies. Instead, this analysis leveraged a comprehensive set of experimentally resolved SARS-CoV-2 RBD–antibody complex structures curated from the Coronavirus Antibody Database (CoV-AbDab), a publicly available and actively maintained resource developed by the Oxford Protein Informatics Group. CoV-AbDab aggregates all published coronavirus-binding antibodies with associated PDB structures and provides a systematic and unbiased structural foundation for antibody–RBD interaction analysis. All available high-resolution RBD–antibody complex structures indexed in CoV-AbDab at the time of analysis were included to compute contact residue frequencies across the structural ensemble. We will explicitly state this data source, clarify the number and nature of structures used, and add the appropriate citation (Raybould et al., Bioinformatics, 2021, doi: 10.1093/bioinformatics/btaa739).

      Finally, we will revise the conclusions to avoid claims that extend beyond the scope of the data. The comparison between aptamers and antibodies is now framed in terms of representative antibodies and consensus interaction patterns derived from a large structural ensemble, rather than as a general statement about all neutralizing antibodies. These revisions will improve the clarity, rigor, and reproducibility of the manuscript, while preserving the core conclusion that the CAAMO framework enables effective structure-guided affinity maturation of RNA aptamers.

      Overall, the manuscript by Yang et al presents a valuable tool for rational design of improved RNA aptamer binding affinity toward target proteins, which the authors call CAAMO. Notably, the method is not intended for de novo design, but rather as a tool for improving aptamers that have been selected for binding affinity by other methods such as SELEX. While there are significant issues in the conclusions made from experiments in this manuscript, the relative relationships of observed affinities within this study provide solid evidence that the CAAMO framework provides a valuable tool for researchers seeking to use rational design approaches for RNA aptamer affinity maturation.


      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this study, the authors attempt to devise general rules for aptamer design based on structure and sequence features. The main system they are testing is an aptamer targeting a viral sequence.

      Strengths:

      The method combines a series of well-established protocols, including docking, MD, and a lot of system-specific knowledge, to design several new versions of the Ta aptamer with improved binding affinity.

      We thank the reviewer for this accurate summary and for recognizing the strength of our integrated computational–experimental workflow in improving aptamer affinity.

      Weaknesses:

      The approach requires a lot of existing knowledge and, importantly, an already known aptamer, which presumably was found with SELEX. In addition, although the aptamer may have a stronger binding affinity, it is not clear if any of it has any additional useful properties such as stability, etc.

      Thanks for these critical comments.

      (1) On the reliance on a known aptamer: We agree that our CAAMO framework is designed as a post-SELEX optimization platform rather than a tool for de novo discovery. Its primary utility lies in rationally enhancing the affinity of existing aptamers that may not yet be sequence-optimal, thereby complementing experimental technologies such as SELEX. The following has been added to “Introduction” of the revised manuscript. (Page 5, line 108 in the revised manuscript)

      ‘Rather than serving as a de novo aptamer discovery tool, CAAMO is designed as a post-SELEX optimization platform that rationally improves the binding capability of existing aptamers.’

      (2) On stability and developability: We also appreciate the reviewer’s important reminder that affinity alone is not sufficient for therapeutic development. We acknowledge that the present study has focused mainly on affinity optimization, and properties such as nuclease resistance, structural stability, and overall developability were not evaluated. The following has been added to “Discussion and conclusion” of the revised manuscript. (Page 25, line 595 in the revised manuscript)

      ‘While the present study primarily focused on affinity optimization, we acknowledge that other key developability traits—such as nuclease resistance, structural and thermodynamic stability, and in vivo persistence—are equally critical for advancing aptamers toward therapeutic applications. These properties were not evaluated here but will be systematically addressed in future iterations of the CAAMO framework to enable comprehensive optimization of aptamer candidates.’

      Reviewer #2 (Public review):

      Summary:

      This manuscript proposes a workflow for discovering and optimizing RNA aptamers, with application in the optimization of a SARS-CoV-2 RBD. The authors took a previously identified RNA aptamer, computationally docked it into one specific RBD structure, and searched for variants with higher predicted affinity. The variants were subsequently tested for RBD binding using gel retardation assays and competition with antibodies, and one was found to be a stronger binder by about three-fold than the founding aptamer.

      Overall, this would be an interesting study if it were performed with truly high-affinity aptamers, and specificity was shown for RBD or several RBD variants.

      Strengths:

      The computational workflow appears to mostly correctly find stronger binders, though not de novo binders.

      We thank the reviewer for the clear summary and for acknowledging that our workflow effectively prioritizes stronger binders.

      Weaknesses:

      (1) Antibody competition assays are reported with RBD at 40 µM, aptamer at 5 µM, and a titration of antibody between 0 and 1.2 µg. This approach does not make sense. The antibody concentration should be reported in µM. An estimation of the concentration is 0-8 pmol (from 0-1.2 µg), but that's not a concentration, so it is unknown whether enough antibody molecules were present to saturate all RBD molecules, let alone whether they could have displaced all aptamers.

      Thanks for your insightful comment. We have calculated that 0–1.2 µg antibody corresponds to a final concentration range of 0–1.6 µM (see Author response image 1). In practice, 1.2 µg was the maximum amount of commercial antibody that could be added under the conditions of our assay. In the revised manuscript, all antibody amounts previously reported in µg have been converted to their corresponding molar concentrations in Fig. 1F and Fig. 5D. In addition, the exact antibody concentrations used in the EMSA assays are now explicitly stated in the Materials and Methods section under “EMSA experiments.” The following has been added to “EMSA experiments” of the revised manuscript. (Page 30 in the revised manuscript)

      ‘For competitive binding experiments, 40 μM of RBP proteins, 5 μM of annealed Cy3-labelled RNAs and increasing concentrations of SARS-CoV-2 neutralizing antibody 40592-R001 (0–1.67 μM) were mixed in the EMSA buffer and incubated at room temperature for 20 min.’

      Author response image 1.

      Estimation of antibody concentration. Assuming a molecular weight of 150 kDa, dissolving 1.2 µg of antibody in a 5 µL reaction volume results in a final concentration of 1.6 µM.

      As shown in Figure 5D, the purpose of the antibody–aptamer competition assay was not to achieve full saturation but rather to compare the relative competitive binding of the optimized aptamer (Ta<sup>G34C</sup>) versus the parental aptamer (Ta). Molecular interactions at this scale represent a dynamic equilibrium of binding and dissociation. While the antibody concentration may not have been sufficient to saturate all available RBD molecules, the experimental results clearly reveal the competitive binding behavior that distinguishes the two aptamers. Specifically, two consistent trends emerged:

      (1) Across all antibody concentrations, the free RNA band for Ta was stronger than that of Ta<sup>G34C</sup>, while the RBD–RNA complex band of the latter was significantly stronger, indicating that Ta<sup>G34C</sup> bound more strongly to RBD.

      (2) For Ta, increasing antibody concentration progressively reduced the RBD–RNA complex band, consistent with antibody displacing the aptamer. In contrast, for Ta<sup>G34C</sup>, the RBD–RNA complex band remained largely unchanged across all tested antibody concentrations, suggesting that the antibody was insufficient to displace Ta<sup>G34C</sup> from the complex.

      Together, these observations support the conclusion that Ta<sup>G34C</sup> exhibits markedly stronger binding to RBD than the parental Ta aptamer, in line with the predictions and objectives of our CAAMO optimization framework.

      (2) These are not by any means high-affinity aptamers. The starting sequence has an estimated (not measured, since the titration is incomplete) K<sub>d</sub> of 110 µM. That's really the same as non-specific binding for an interaction between an RNA and a protein. This makes the title of the manuscript misleading. No high-affinity aptamer is presented in this study. If the docking truly presented a bound conformation of an aptamer to a protein, a sub-micromolar K<sub>d</sub> would be expected, based on the number of interactions that they make.

      In fact, our starting sequence (Ta) is a high-affinity aptamer, and then the optimized sequences (such as Ta<sup>G34C</sup>) with enhanced affinity are undoubtedly also high-affinity aptamers. See descriptions below:

      (1) Origin and prior characterization of Ta. The starting aptamer Ta (referred to as RBD-PB6-Ta in the original publication by Valero et al., PNAS 2021, doi:10.1073/pnas.2112942118) was selected through multiple positive rounds of SELEX against SARS-CoV-2 RBD, together with counter-selection steps to eliminate non-specific binders. In that study, Ta was reported to bind RBD with an IC₅₀ of ~200 nM as measured by biolayer interferometry (BLI), supporting its high affinity and specificity. The following has been added to “Introduction” of the revised manuscript. (Page 4 in the revised manuscript)

      ‘This aptamer was originally identified through SELEX and subsequently validated using surface plasmon resonance (SPR) and biolayer interferometry (BLI), which confirmed its high affinity (sub-nanomolar) and high specificity toward the RBD. Therefore, Ta provides a well-characterized and biologically relevant starting point for structure-based optimization.’

      (2) Methodological differences between EMSA and BLI measurements. We acknowledge that the discrepancy between our obtained binding affinity (K<sub>d</sub> = 110 µM) and the previously reported one (IC<sub>50</sub> ~ 200 nM) for the same Ta sequence arises primarily from methodological and experimental differences between EMSA and BLI. Namely, different experimental measurement methods can yield varied binding affinity values. While EMSA may have relatively low measurement precision, its relatively simple procedures were the primary reason for its selection in this study. Particularly, our framework (CAAMO) is designed not as a tool for absolute affinity determination, but as a post-SELEX optimization platform that prioritizes relative changes in binding affinity under a consistent experimental setup. Thus, the central aim of our work is to demonstrate that CAAMO can reliably identify variants, such as Ta<sup>G34C</sup>, that bind more strongly than the parental sequence under identical assay conditions. The following has been added to “Discussion and conclusion” of the revised manuscript. (Page 24 in the revised manuscript)

      ‘Although the absolute K<sub>d</sub> values determined by EMSA cannot be directly compared with surface-based methods such as SPR or BLI, the relative affinity trends remain highly consistent. While EMSA provides semi-quantitative affinity estimates, the close agreement between experimental EMSA trends and FEP-calculated ΔΔG values supports the robustness of the relative affinity changes reported here. In future studies, additional orthogonal biophysical techniques (e.g., filter-binding, SPR, or BLI) will be employed to further validate and refine the protein–aptamer interaction models.’

      (3) Evidence of specific binding in our assays. We emphasize that the binding observed in our EMSA experiments reflects genuine aptamer–protein interactions. As shown in Figure 2G, a control RNA (Tc) exhibited no detectable binding to RBD, whereas Ta produced a clear binding curve, confirming that the interaction is specific rather than non-specific.

      (3) The binding energies estimated from calculations and those obtained from the gel-shift experiments are vastly different, as calculated from the K<sub>d</sub> measurements, making them useless for comparison, except for estimating relative affinities.

      Author Reply: We thank the reviewer for raising this important point. CAAMO was developed as a post-SELEX optimization tool with the explicit goal of predicting relative affinity changes (ΔΔG) rather than absolute binding free energies (ΔG). Empirically, CAAMO correctly predicted the direction of affinity change for 5 out of 6 designed variants (e.g., ΔΔG < 0 indicates enhanced binding free energy relative to WT); such predictive power for relative ranking is highly valuable for prioritizing candidates for experimental testing. Our prior work on RNA–protein interactions likewise supports the reliability of relative affinity predictions (see: Nat Commun 2023, doi:10.1038/s41467-023-39410-8). The following has been added to “Discussion and conclusion” of the revised manuscript. (Page 24 in the revised manuscript)

      ‘While EMSA provides semi-quantitative affinity estimates, the close agreement between experimental EMSA trends and FEP-calculated ΔΔG values supports the robustness of the relative affinity changes reported here.’

      Recommendations for the Authors:

      Reviewer #1 (Recommendations for the authors)

      (1) Overall, the paper is well-written and, in the opinion of this reviewer, could remain as it is.

      We thank the reviewer for the positive evaluation and supportive comments regarding our manuscript. We are grateful for the endorsement of its quality and suitability for publication.

      Reviewer #2 (Recommendations for the authors)

      (1) All molecules present in experiments need to be reported with their final concentrations (not µg).

      We thank the reviewer for raising this important point. In the revised manuscript, all antibody amounts previously reported in µg have been converted to their corresponding molar concentrations in Fig. 1F and Fig. 5D. In addition, the exact antibody concentrations used in the EMSA assays are now explicitly stated in the Materials and Methods section under “EMSA experiments.” The following has been added to “EMSA experiments” of the revised manuscript. (Page 30 in the revised manuscript)

      ‘For competitive binding experiments, 40 μM of RBP proteins, 5 μM of annealed Cy3-labelled RNAs and increasing concentrations of SARS-CoV-2 neutralizing antibody 40592-R001 (0–1.67 μM) were mixed in the EMSA buffer and incubated at room temperature for 20 min.’

      (2) An independent K<sub>d</sub> measurement, for example, using a filter binding assay, would greatly strengthen the results.

      We thank the reviewer for this constructive suggestion and agree that an orthogonal biophysical measurement (e.g., a filter-binding assay, SPR or BLI) would further strengthen confidence in the reported dissociation constants. Unfortunately, all available SARS-CoV-2 RBD protein used in this study has been fully consumed and, due to current supply limitations, we were unable to perform new orthogonal binding experiments for the revised manuscript. We regret this limitation and have documented it in the Discussion as an item for future work.

      Importantly, although we could not perform a new filter-binding experiment at this stage, we have multiple independent lines of evidence that support the reliability of the EMSA-derived affinity trends reported in the manuscript:

      (1) Rigorous EMSA design and reproducibility. All EMSA binding curves reported in the manuscript (e.g., Figs. 2F–G, 4E–F, 5A and Fig. S9) are derived from three independent biological replicates and include standard deviations; the measured binding curves show good reproducibility across replicates.

      (2) Appropriate positive and negative controls. Our gel assays include clear internal controls. The literature-reported strong binder Ta forms a distinct aptamer–RBD complex band under our conditions, whereas the negative-control aptamer Tc shows no detectable binding under identical conditions (see Fig. 2F). These controls demonstrate that the EMSA system discriminates specific from non-binding sequences with high sensitivity.

      (3) Orthogonal computational validation (FEP) that agrees with experiment. The central strength of the CAAMO framework is the integration of rigorous physics-based calculations with experiments. We performed FEP calculations for the selected single-nucleotide mutations and computed ΔΔG values for each mutant. The direction and rank order of binding changes predicted by FEP are in good agreement with the EMSA measurements: five of six FEP-predicted improved mutants (Ta<sup>G34C</sup>, Ta<sup>G34U</sup>, Ta<sup>G34A</sup>, Ta<sup>C23A</sup>, Ta<sup>C23U</sup>) were experimentally confirmed to have stronger apparent affinity than wild-type Ta (see Fig. 4D–F, Table S2), yielding a success rate of 83%. The concordance between an independent, rigorous computational method and our experimental measurements provides strong mutual validation.

      (4) Independent competitive binding experiments. We additionally performed competitive EMSA assays against a commercial neutralizing monoclonal antibody (40592-R001). These competition experiments show that Ta<sup>G34C</sup>–RBD complexes are resistant to antibody displacement under conditions that partially displace the wild-type Ta–RBD complex (see Fig. 5D). This result provides an independent, functionally relevant line of evidence that Ta<sup>G34C</sup> binds RBD with substantially higher affinity and specificity than WT Ta under our assay conditions.

      Given these multiple, independent lines of validation (rigorous EMSA replicates and controls, FEP agreement, and antibody competition assays), we are confident that the relative affinity improvements reported in the manuscript are robust, even though the absolute K<sub>d</sub> values measured by EMSA are not directly comparable to surface-based methods (EMSA typically reports larger apparent K<sub>d</sub> values than SPR/BLI due to methodological differences). The following has been added to “Discussion and conclusion” of the revised manuscript. (Page 24 in the revised manuscript)

      ‘Although the absolute K<sub>d</sub> values determined by EMSA cannot be directly compared with surface-based methods such as SPR or BLI, the relative affinity trends remain highly consistent. While EMSA provides semi-quantitative affinity estimates, the close agreement between experimental EMSA trends and FEP-calculated ΔΔG values supports the robustness of the relative affinity changes reported here. In future studies, additional orthogonal biophysical techniques (e.g., filter-binding, SPR, or BLI) will be employed to further validate and refine the protein–aptamer interaction models.’

      (3) The project would really benefit from a different aptamer-target system. Starting with a 100 µM aptamer is really not adequate.

      We thank the reviewer for this important suggestion and for highlighting the value of testing the CAAMO framework in additional aptamer–target systems.

      First, we wish to clarify the rationale for selecting the Ta–RBD system as the proof-of-concept. The Ta aptamer is not an arbitrary or weak binder: it was originally identified by independent SELEX experiments and subsequently validated by rigorous biophysical assays (SPR and BLI) (see: Proc. Natl. Acad. Sci. 2021, doi: 10.1073/pnas.2112942118). That study confirmed that Ta exhibits high-affinity and high-specificity binding to the SARS-CoV-2 RBD, which is why it serves as a well-characterized and biologically relevant system for method validation and optimization. We have added a brief clarification to the “Introduction” to emphasize these points. The following has been added to “Introduction” of the revised manuscript. (Page 4 in the revised manuscript)

      ‘This aptamer was originally identified through SELEX and subsequently validated using surface plasmon resonance (SPR) and biolayer interferometry (BLI), which confirmed its high affinity and high specificity toward the RBD. Therefore, Ta provides a well-characterized and biologically relevant starting point for structure-based optimization.’

      Second, we agree that apparent discrepancies in absolute K<sub>d</sub> values can arise from different experimental platforms. Surface-based methods (SPR/BLI) and gel-shift assays (EMSA) have distinct measurement principles; EMSA yields semi-quantitative, solution-phase, apparent K<sub>d</sub> values that are not directly comparable in absolute magnitude to surface-based measurements. Crucially, however, our study focuses on relative affinity change. EMSA is well suited for parallel, comparative measurements across multiple variants when all samples are assayed under identical conditions, and thus provides a reliable readout for ranking and validating designed mutations. We have added a short statement in the “Discussion and conclusion”. The following has been added to “Discussion and conclusion” of the revised manuscript. (Page 24 in the revised manuscript)

      ‘Although the absolute K<sub>d</sub> values determined by EMSA cannot be directly compared with surface-based methods such as SPR or BLI, the relative affinity trends remain highly consistent. While EMSA provides semi-quantitative affinity estimates, the close agreement between experimental EMSA trends and FEP-calculated ΔΔG values supports the robustness of the relative affinity changes reported here. In future studies, additional orthogonal biophysical techniques (e.g., filter-binding, SPR, or BLI) will be employed to further validate and refine the protein–aptamer interaction models.’

      Third, and importantly, CAAMO is inherently generalizable. In addition to the Ta–RBD application presented here, we have already begun applying CAAMO to other aptamer–target systems. In particular, we have successfully deployed the framework in preliminary optimization studies of RNA aptamers targeting the epidermal growth factor receptor (EGFR) (see: Gastroenterology 2021, doi: 10.1053/j.gastro.2021.05.055) (see Author response image 2). These preliminary results support the transferability of the CAAMO pipeline beyond the SARS-CoV-2 RBD system. We have added a short statement in the “Discussion and conclusion”. The following has been added to “Discussion and conclusion” of the revised manuscript. (Page 259 in the revised manuscript)

      ‘In addition to the Ta–RBD system, the CAAMO framework itself is inherently generalizable. More work is currently underway to apply CAAMO to optimize aptamers targeting other therapeutically relevant proteins, such as the epidermal growth factor receptor (EGFR) [45], in order to further explore its potential for broader aptamer engineering.’

      Author response image 2.

      Overview of the predicted binding model of the EGFR–aptamer complex generated using the CAAMO framework.

      (4) Several RBD variants should be tested, as well as other proteins, for specificity. At such weak affinities, it is likely that these are non-specific binders.

      We thank the reviewer for this important concern. Below we clarify the basis for selecting Ta and its engineered variants, summarize the experimental controls that address specificity, and present the extensive in silico variant analysis we performed to assess sensitivity and breadth of binding.

      (1) Origin and validation of Ta. As noted in our response to “Comment (3)”, the Ta aptamer was not chosen arbitrarily. Ta was identified by independent SELEX with both positive and negative selection and subsequently validated using surface-based biophysical assays (SPR and BLI), which reported low-nanomolar affinity and high specificity for the SARS-CoV-2 RBD. Thus, Ta is a well-characterized, experimentally validated starting lead for method development and optimization.

      (2) Experimental specificity controls. We appreciate the concern that weak apparent affinities can reflect non-specific binding. As noted in our response to “Comment (2)”, we applied multiple experimental controls that argue against non-specificity: (i) a literature-reported weak binder (Tc) was used as a negative control and produced no detectable complex under identical EMSA conditions (see Figs. 2F–G), demonstrating the assay’s ability to discriminate non-binders from specific binders; (ii) competitive EMSA assays with a commercial neutralizing monoclonal antibody (40592-R001) show that both Ta and Ta<sup>G34C</sup> engage the same or overlapping RBD site as the antibody, and that Ta<sup>G34C</sup> is substantially more resistant to antibody displacement than WT Ta (see Figs. 3D–E, 5D). Together, these wet-lab controls support that the observed aptamer-RBD bands reflect specific interactions rather than general, non-specific adsorption.

      (3) Variant and specificity analysis by rigorous FEP calculations. To address the reviewer’s request to evaluate variant sensitivity, we performed extensive free energy perturbation combined with Hamiltonian replica-exchange molecular dynamics (FEP/HREX) for improved convergence efficiency and increased simulation time to estimate relative binding free energy changes (ΔΔG) of both WT Ta and the optimized Ta<sup>G34C</sup> against a panel of RBD variants. Results are provided in Tables S4 and S5. Representative findings include: For WT Ta versus early lineages, FEP reproduces the experimentally observed trends: Alpha (B.1.1.7; N501Y) yields ΔΔG<sub>FEP</sub> = −0.42 ± 0.07 kcal/mol (ΔΔG<sub>exp</sub> = −0.24), while Beta (B.1.351; K417N/E484K/N501Y) gives ΔΔG<sub>FEP</sub> = 0.64 ± 0.25 kcal/mol (ΔΔG<sub>exp</sub> = 0.36) (see Table S4). The agreement between the computational and experimental results supports the fidelity of our computational model for variant assessment. For the engineered Ta<sup>G34C</sup>, calculations across a broad panel of variants indicate that Ta<sup>G34C</sup> retains or improves binding (ΔΔG < 0) for the majority of tested variants, including Alpha, Beta, Gamma and many Omicron sublineages. Notable examples: BA.1 (ΔΔG = −3.00 ± 0.52 kcal/mol), BA.2 (ΔΔG = −2.54 ± 0.60 kcal/mol), BA.2.75 (ΔΔG = −5.03 ± 0.81 kcal/mol), XBB (ΔΔG = −3.13 ± 0.73 kcal/mol) and XBB.1.5 (ΔΔG = −2.28 ± 0.96 kcal/mol). A minority of other Omicron sublineages (e.g., BA.4 and BA.5) show modest positive ΔΔG values (2.11 ± 0.67 and 2.27 ± 0.68 kcal/mol, respectively), indicating a predicted reduction in affinity for those specific backgrounds. Overall, these data indicate that the designed Ta<sup>G34C</sup> aptamer can maintain its binding ability with most SARS-CoV-2 variants, showing potential for broad-spectrum antiviral activity (see Table S5). The following has been added to “Results” of the revised manuscript. (Page 22 in the revised manuscript)

      ‘2.6 Binding performance of Ta and Ta<sup>G34C</sup> against SARS-CoV-2 RBD variants

      To further evaluate the binding performance and specificity of the designed aptamer Ta<sup>G34C</sup> toward various SARS-CoV-2 variants [39], we conducted extensive free energy perturbation combined with Hamiltonian replica-exchange molecular dynamics (FEP/HREX) [40–42] for both the wild-type aptamer Ta and the optimized Ta<sup>G34C</sup> against a series of RBD mutants. The representative variants include the early Alpha (B.1.1.7) and Beta (B.1.351) lineages, as well as a panel of Omicron sublineages (BA.1–BA.5, BA.2.75, BQ.1, XBB, XBB.1.5, EG.5.1, HK.3, JN.1, and KP.3) carrying multiple mutations within the RBD region (residues 333–527). For each variant, mutations within 5 Å of the bound aptamer were included in the FEP to accurately estimate the relative binding free energy change (ΔΔG).

      For the wild-type Ta aptamer, the FEP-predicted binding affinities toward the Alpha and Beta RBD variants were consistent with the previous experimental results, further validating the reliability of our model (see Table S4). Specifically, Ta maintained comparable or slightly enhanced binding to the Alpha variant and showed only marginally reduced affinity for the Beta variant.

      In contrast, the optimized aptamer Ta<sup>G34C</sup> exhibited markedly improved and broad-spectrum binding capability toward most tested variants (see Table S5). For early variants such as Alpha, Beta, and Gamma, Ta<sup>G34C</sup> maintained enhanced affinities (ΔΔG < 0). Notably, for multiple Omicron sublineages—including BA.1, BA.2, BA.2.12.1, BA.2.75, XBB, XBB.1.5, XBB.1.16, XBB.1.9, XBB.2.3, EG.5.1, XBB.1.5.70, HK.3, BA.2.86, JN.1 and JN.1.11.1—the calculated binding free energy changes ranged from −1.89 to −7.58 kcal/mol relative to the wild-type RBD, indicating substantially stronger interactions despite the accumulation of multiple mutations at the aptamer–RBD interface. Only in a few other Omicron sublineages, such as BA.4, BA.5, and KP.3, a slight reduction in binding affinity was observed (ΔΔG > 0).

      These computational findings demonstrate that the Ta<sup>G34C</sup> aptamer not only preserves high affinity for the RBD but also exhibits improved tolerance to the extensive mutational landscape of SARS-CoV-2. Collectively, our results suggest that Ta<sup>G34C</sup> holds promise as a high-affinity and potentially cross-variant aptamer candidate for targeting diverse SARS-CoV-2 spike protein variants, showing potential for broad-spectrum antiviral activity.’

      The following has been added to “Materials and Methods” of the revised manuscript. (Page 29 in the revised manuscript)

      ‘4.7 FEP/HREX

      To evaluate the binding sensitivity of the optimized aptamer Ta<sup>G34C</sup> toward SARS-CoV-2 RBD variants, we employed free energy perturbation combined with Hamiltonian replica-exchange molecular dynamics (FEP/HREX) simulations for enhanced sampling efficiency and improved convergence. The relative binding free energy changes (ΔΔG) upon RBD mutations were estimated as:

      ΔΔ𝐺 = Δ𝐺<sub>bound</sub> − Δ𝐺<sub>free</sub>

      where ΔG<sub>bound</sub> and ΔG<sub>free</sub> represent the RBD mutations-induced free energy changes in the complexed and unbound states, respectively. All simulations were performed using GROMACS 2021.5 with the Amber ff14SB force field. For each mutation, dual-topology structures were generated in a pmx-like manner, and 32 λ-windows (0.0, 0.01, 0.02, 0.03, 0.06, 0.09, 0.12, 0.16, 0.20, 0.24, 0.28, 0.32, 0.36, 0.40, 0.44, 0.48, 0.52, 0.56, 0.60, 0.64, 0.68, 0.72, 0.76, 0.80, 0.84, 0.88, 0.91, 0.94, 0.97, 0.98, 0.99, 1.0) were distributed uniformly between 0.0 and 1.0. To ensure sufficient sampling, each window was simulated for 5 ns, with five independent replicas initiated from distinct velocity seeds. Replica exchange between adjacent λ states was attempted every 1 ps to enhance phase-space overlap and sampling convergence. The van der Waals and electrostatic transformations were performed simultaneously, employing a soft-core potential (α = 0.3) to avoid singularities. For each RBD variant system, this setup resulted in an accumulated simulation time of approximately 1600 ns (5 ns × 32 windows × 5 replicas × 2 states). The Gromacs bar analysis tool was used to estimate the binding free energy changes.’

      Tables S4 and S5 have been added to Supplementary Information of the revised manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The temporal regulation of neuronal specification and its molecular mechanisms are important problems in developmental neurobiology. This study focuses on Kenyon cells (KCs), which form the mushroom body in Drosophila melanogaster, in order to address this issue. Building on previous findings, the authors examine the role of the transcription factor Eip93F in the development of late-born KCs. The authors revealed that Eip93F controls the activity of flies at night through the expression of the calcium channel Ca-α1T. Thus, the study clarifies the molecular machinery that controls temporal neuronal specification and animal behavior.

      Strengths:

      The convincing results are based on state-of-the-art molecular genetics, imaging, and behavioral analysis.

      Weaknesses:

      Temporal mechanisms of neuronal specification are found in many nervous systems. However, the relationship between the temporal mechanisms identified in this study and those in other systems remains unclear.

      We have discussed the temporal mechanisms between different nervous systems at the beginning of the Discussion section.

      Reviewer #2 (Public review):

      Summary:

      Understanding the mechanisms of neural specification is a central question in neurobiology. In Drosophila, the mushroom body (MB), which is the associative learning region in the brain, consists of three major cell types: γ, α'/β', and α/β kenyon cells. These classes can be further subdivided into seven subtypes, together comprising ~2000 KCs per hemi-brain. Remarkably, all of these neurons are derived from just four neuroblasts in each hemisphere. Therefore, a lot of endeavors are put into understanding how the neuron is specified in the fly MB.

      Over the past decade, studies have revealed that MB neuroblasts employ a temporal patterning mechanism, producing distinct neuronal types at different developmental stages. Temporal identity is conveyed through transcription factor expression in KCs. High levels of Chinmo, a BTB-zinc finger transcription factor, promote γ-cell fate (Zhu et al., Cell, 2006). Reduced Chinmo levels trigger expression of mamo, a zinc finger transcription factor that specifies α'/β' identity (Liu et al., eLife, 2019). However, the specification of α/β neurons remains poorly understood. Some evidence suggests that microRNAs regulate the transition from α'/β' to α/β fate (Wu et al., Dev Cell, 2012; Kucherenko et al., EMBO J, 2012). One hypothesis even proposes that α/β represents a "default" state of MB neurons, which could explain the difficulty in identifying dedicated regulators.

      The study by Chung et al. challenges this hypothesis. By leveraging previously published RNA-seq datasets (Shih et al., G3, 2019), they systematically screened BAC transgenic lines to selectively label MB subtypes. Using these tools, they analyzed the consequences of manipulating E93 expression and found that E93 is required for α/β specification. Furthermore, loss of E93 impairs MB-dependent behaviors, highlighting its functional importance.

      Strengths:

      The authors conducted a thorough analysis of E93 manipulation phenotypes using LexA tools generated from the Janelia Farm and Bloomington collections. They demonstrated that E93 knockdown reduces expression of Ca-α1T, a calcium channel gene identified as an α/β marker. Supporting this conclusion, one LexA line driven by a DNA fragment near EcR (R44E04) showed consistent results. Conversely, overexpression of E93 in γ and α'/β' Kenyon cells led to downregulation of their respective subtype markers.

      Another notable strength is the authors' effort to dissect the genetic epistasis between E93 and previously known regulators. Through MARCM and reporter analyses, they showed that Chinmo and Mamo suppress E93, while E93 itself suppresses Mamo. This work establishes a compelling molecular model for the regulatory network underlying MB cell-type specification.

      Weaknesses:

      The interpretation of E93's role in neuronal specification requires caution. Typically, two criteria are used to establish whether a gene directs neuronal identity:

      (1) gene manipulation shifts the neuronal transcriptome from one subtype to another, and

      (2) gene manipulation alters axonal projection patterns.

      The results presented here only partially satisfy the first criterion. Although markers are affected, it remains possible that the reporter lines and subtype markers used are direct transcriptional targets of E93 in α/β neurons, rather than reflecting broader fate changes. Future studies using single-cell transcriptomics would provide a more comprehensive assessment of neuronal identity following E93 perturbation.

      We do plan conduct multi-omics experiments to provide a more comprehensive assessment of neuronal identity upon loss-of-function of E93. However, omics results take time to be conducted and analyzed, so the result will be summarized in a future manuscript.

      With respect to the second criterion, the evidence is also incomplete. While reporter patterns were altered, the overall morphology of the α/β lobes appeared largely intact after E93 knockdown. Overexpression of E93 in γ neurons produced a small subset of cells with α/β-like projections, but this effect warrants deeper characterization before firm conclusions can be drawn. While the results might be an intrinsic nature of KC types in flies, the interpretation of the reader of the data should be more careful, and the authors should also mention this in their main text.

      We have toned down our description on the effect of E93 (especially in the loss-offunction) in specifying the α/β-specific cell identity and discussed whether unidentified regulators would work together with E93 in α/β neural fate specification.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Changes in nighttime activity in flies upon knocking down Ca_α1T and Eip93F are interesting (Fig. 2C). However, examining the morphological changes in the mushroom body under these conditions would be essential.

      We did not find the morphological change of mushroom body lobes by examining with the Fas2 staining (shown in Figure S8D).

      (2) Temporal mechanisms of neuronal specification have been identified in various nervous systems, including the embryonic central nervous system (CNS), the optic lobe of Drosophila, and the nervous systems of other organisms. The Discussion section should address the relationship between the temporal mechanisms identified in this study and those identified in other systems.

      We have discussed the temporal mechanisms between different nervous systems at the beginning of the Discussion section.

      (3) Eip93F is an Ecdysone-induced protein. In the Discussion section, the authors should discuss the relationship between the ecdysone signal and the roles of Eip93F.

      We have added the discussion on the relationship between the ecdysone signal and the roles of Eip93F.

      Reviewer #2 (Recommendations for the authors):

      (1) The behavioral effect of Ca-α1T knockdown is pretty interesting. But how the downregulation of Ca-α1T in the mushroom body can affect locomotion is puzzling. Even though the mushroom body is known to suppress locomotion (Matin et al., Learn Mem, 1998), the real results are opposite. Can authors give further explanation in the discussion? Also, the behavioral experiments are hard to interpret, given that Figure 2C(1) and Figure 2C(3) as a control, also vary a lot. Since the behavioral experiments don't affect the main conclusion of the paper, I would suggest removing that part or adding more explanation in the discussion.

      First, we have discussed the puzzling part on the MB influence in locomotion between the previous study using tetanus toxin light chain (TeNT-Ln) and our Ca-α1T knockdown result. It is possible that the different effect is derived from TeNT-Ln’s function in MB axons and Ca-α1T’s function in MB dendrites. Secondly, we have re-conducted the behavioral results using a new α/β driver (13F02-AD/70F05-DBD) to replace our initial behavioral results (using c739-GAL4, which would cause the abnormal wing when drives E93 RNAi expression; see S8C(2) Fig). Current results (now in Fig 2I) are more consistent in control groups.

      (2) In the manuscript, the authors use "subtype" to describe γKC, α'/β'KC and α/βKC in the fly MB. However, in most of the literature, people use "main types" to summarize these three types, and "subtype" is mostly about the difference in γd, γm, α'/β'ap, α'/β'm, α/βp, α/βs and α/βc KC (Shih et al., G3, 2019). Replacing "subtypes" with "main types" will help to increase the clarity.

      We have replaced "KC subtypes" with "main KC types" or just “KC types”.

      (3) The authors have identified a lot of new markers for the KC cell types, and some of them are used in this manuscript. It will be helpful if they can have a figure to summarize the markers they used in this study and what cell types they labeled.

      We have summarized expression patterns of these markers in Supplemental table 1.

      (4) In the method, the authors mentioned that only females were selected for analysis of Ca-α1T-GFSTF. Could the authors explain the reasons in more detail?

      Since homozygous Ca-α1T-GFSTF female flies and hemizygous Ca-α1T-GFSTF male are a bit sick and hard to collect, we therefore used heterozygous Ca-α1T-GFSTF female in our experiments. I have added this description in the Materials and Methods section.

      (5) Figure S1: The legend of magenta fluorescence is missing. Please add which protein is shown in magenta.

      We have added the legend of magenta fluorescence, which is Trio.

      (6) The detailed genotypes of Figure 2C and Figure S7 are missing in Supplementary Table 1. Please include that, so that readers can know the genetic background.

      We have added genotypes of Figure 2I (previously Figure 2C) and Figure S8 (previously as Figure S7) in Supplementary Table 2.

      (7) Figure 2D-G: It will be helpful if the authors can outline the lobe (γ, α'/β', and α/β) in the figure, which will help readers to understand the images.

      We have outlined α, α', β, β' and γ lobes in Figure 2C-F (previously as Figure 2D-G).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      This is a rigorous data-driven modeling study, extending the authors' previous model of spinal locomotor central pattern generator (CPG) circuits developed for the mouse spinal cord and adapted here to the rat to explore potential circuit-level changes underlying altered speeddependent gaits, due to asymmetric (lateral) thoracic spinal hemisection and symmetric midline contusion. The model reproduces key features of the rat speed-dependent gait-related experimental data before injury and after recovery from these two different thoracic spinal cord injuries and suggests injury-specific mechanisms of circuit reorganization underlying functional recovery. There is much interest in the mechanisms of locomotor behavior recovery after spinal cord injury, and data-driven behaviorally relevant circuit modeling is an important approach. This study represents an important advance in the authors' previous experimental and modeling work on locomotor circuitry and in the motor control field.

      Strengths:

      (1) The authors use an advanced computational model of spinal locomotor circuitry to investigate potential reorganization of neural connectivity underlying locomotor control following recovery from symmetrical midline thoracic contusion and asymmetrical (lateral) hemisection injuries, based on an extensive dataset for the rat model of spinal cord injury.

      (2) The rat dataset used is from an in vivo experimental paradigm involving challenging animals to perform overground locomotion across the full range of speeds before and after the two distinct spinal cord injury models, enabling the authors to more completely reveal injury-specific deficits in speed-dependent interlimb coordination and locomotor gaits.

      (3) The model reproduces the rat gait-related experimental data before injury and after recovery from these two different thoracic spinal cord injuries, which exhibit roughly comparable functional recovery, and suggests injury-specific, compensatory mechanisms of circuit reorganization underlying recovery.

      (4) The model simulations suggest that recovery after lateral hemisection mechanistically involves partial functional restoration of descending drive and long propriospinal pathways. In contrast, recovery following midline contusion relies on reorganization of sublesional lumbar circuitry combined with altered descending control of cervical networks.

      (5) These observations suggest that symmetrical (contusion) and asymmetrical (lateral hemisection) injuries induce distinct types of plasticity in different spinal cord regions, suggesting that injury symmetry partly dictates the location and type of neural plasticity supporting recovery.

      (6) The authors suggest that therapeutic strategies may be more effective by targeting specific circuits according to injury symmetry.

      Weaknesses:

      The recovery mechanisms implemented in the model involve circuit connectivity/connection weights adjustment based on assumptions about the structures involved and compensatory responses to the injury. As the authors acknowledge, other factors affecting locomotor patterns and compensation, such as somatosensory afferent feedback, neurochemical modulator influences, and limb/body biomechanics, are not considered in the model.

      We appreciate the positive review and critical comments. We added a dedicate limitation and future direction section (see response recommendations below). Further, we also performed a sensitivity analysis: while the model still relies on a set of hypothesized connectivity changes, this analysis quantifies how robust our conclusions are to these parameter choices and indicates which pathways most strongly affect the recovered locomotor pattern.

      Reviewer #1 (Recommendations for the authors):

      The authors have used an advanced model of rodent spinal locomotor CPG circuits, adapted to the rat spinal cord, which remarkably reproduces the key features of the rat speed-dependent gait-related experimental data before injury and after recovery from the two different thoracic spinal cord injuries studied. Importantly, they have exploited the extensive dataset for the in vivo rat spinal cord injury model involving overground locomotion across the full range of speeds before and after the two distinct spinal cord injuries, enabling the authors to more completely reveal injury-specific deficits in speed-dependent interlimb coordination and locomotor gaits. The paper is well-written and well-illustrated.

      (1) My only general suggestion is that the authors include a section that succinctly summarizes the limitations of the modeling and points to elaborations of the model and experimental data required for future studies. Some important caveats are dispersed throughout the Discussion, but a more consolidated section would be useful.

      We added a dedicated Limitations and future directions section (page XX) that consolidates shortcomings and broadly outlines potential next steps in terms of modeling and experimental data. Specifically, we highlight the issue of lack of afferent feedback connections in the model, lack of consideration of biomechanic mechanisms, and restriction of the model to beneficial plasticity. To resolve these issues, we need neuromechancial models (integration of the neural circuits with a model of the musculoskeletal system), experimental data validating our predictions and data to constrain future models to be able to distinguish between beneficial and maladaptive plasticity.

      (2) Please correct the Figure 11 legend title to indicate recovery after contusion (not hemisection). 

      Done. Thanks for noticing.

      Reviewer #2 (Public review):

      Summary:

      In this paper, the authors present a detailed computational model and experimental data concerning overground locomotion in rats before and after recovery from spinal cord injury. They are able to manually tune the parameters of this physiologically based, detailed model to reproduce many aspects of the observed animals locomotion in the naive case and in two distinct injury cases.

      Strengths:

      The strengths are that the model is driven to closely match clean experimental data, and the model itself has detailed correspondence to proposed anatomical reality. As such, this makes the model more readily applicable to future experimental work. It can make useful suggestions. The model reproduces a large number of conditions across frequencies, and with the model structure changed by injury and recovery. The model is extensive and is driven by known structures, with links to genetic identities, and has been extensively validated across multiple experiments and manipulations over the years. It models a system of critical importance to the field, and the tight coupling to experimental data is a real strength.

      Weaknesses:

      A downside is that, scientifically, here, the only question tackled is one of sufficiency. By manually tuning parameters in a manner that aligns with the field's understanding from experimental work, the detailed model can accurately reproduce the experimental findings. One of the benefits of computational models is that the counterfactual can be tested to provide evidence against alternative hypotheses. That isn't really done here. I'm fairly certain that there are competing theories regarding what happens during recovery from a hemi-section injury and a contusion injury. The model could be used to make predictions for some alternative hypotheses, supporting or rejecting theories of recovery. This may be part of future plans. Here, the focus is on showing that the model is capable of reproducing the experimental results at all, for any set of parameters, however tuned.

      We agree with the reviewer that the present study focuses on sufficiency, and we now explicitly acknowledge this in the revised limitations section. We also added sensitivity analysis (for details see response to reviewer 3) that provides an initial assessment of robustness to the assumed connectivity changes. We note that the model reproduces a broad set of experimentally observed features across the full range of locomotor frequencies (including loss and emergence of specific gaits, reduced maximum stepping frequency, and altered variability of interlimb phase differences) using only a small set of hypothesized circuit reorganizations that have been experimentally observed but previously only correlated with recovery. Our results therefore suggest that this limited set of changes is indeed sufficient to account for the complex pattern of recovered locomotor behavior.

      Finally, although exploring alternative solutions is of interest, we believe such efforts will be most informative once afferent feedback is incorporated, which we see as the logical next step in our studies.

      Reviewer #2 (Recommendations for the authors):

      The paper could be strengthened with some more scientific interpretation and future directions. What are some novel predictions that can be made with the model, now that it has shown sufficiency here, that could guide future experimental work? Does it contradict in any way theories of CPG structure or neuronal plastic recovery?

      The sensitivity analysis that we performed in response to reviewer 3’s suggestion expanded our interpretation/conclusions by showing that, although injury symmetry (contusion vs. lateral hemisection) influences which pathways reorganize, recovered locomotion across injury type depends most strongly on restored activation of lumbar rhythm-generating and strengths of lumbar commissural circuits.

      Interestingly, this sensitivity analysis also showed that variations of strengths of long propriospinal pathways (ascending, descending, spared, injured-and-recovered) have a much smaller, almost negligible effect, when compared to variations of drive to lumbar rhythm generators or lumbar commissural interneuron connection weights in the same range (see Fig 13, 13-supplement 1 and 2). This is in accordance with our initial model suggestions that after contusion LPN connections weight had to be lowered to values substantially lower than what was expected by the severity of the injury. Which is also corroborated by our anatomical findings that in parallel to recovery from contusion, the number of synaptic connections by LAPNs to the cervical enlargement were reduced, and that silencing of LPNs post-contusion improves locomotion. These surprising findings have been extensively discussed in the discussion section.

      Together, these findings suggest that experimental characterization of reorganization of the lumbar circuitry with a specific focus on commissural interneurons and inputs to the lumbar circuitry that could restore activation of sublesional lumbar rhythm generators is a crucial next step for understanding post-injury plasticity and recovery of locomotor function. This is now clearly discussed.

      Finally, we note that a key contribution of this work is that the model demonstrates a plausible mechanistic link between specific circuit reorganizations and recovered locomotor function, a relationship previously supported mainly by correlative evidence.

      Reviewer #3 (Public review):

      Summary:

      This study describes a computational model of the rat spinal locomotor circuit and how it could be reconfigured after lateral hemisection or contusion injuries to replicate gaits observed experimentally.

      The model suggests the emergence of detour circuits after lateral hemisection, whereas after a midline contusion, the model suggests plasticity of left-right and sensory inputs below the injury.

      Strengths:

      The model accurately models many known connections within and between forelimb and hindlimb spinal locomotor circuits.

      The simulation results mirror closely gait parameters observed experimentally. Many gait parameters were studied, as well as variability in these parameters in intact versus injured conditions.

      Weaknesses:

      The study could provide some sense of the relative importance of the various modified connectivities after injury in setting the changes in gait seen after the two types of injuries.

      We performed a local sensitivity analysis of the hemisection and contusion models to identify which connectivity changes most strongly influence post-injury locomotor behavior. Key parameters (descending drive to sublesional rhythm generators and the strength of selected commissural and propriospinal pathways) were perturbed within 80–125% of their baseline values, and for each perturbation we quantified changes in model output using the Earth Mover’s Distance between baseline and perturbed simulations in a 7-dimensional space (six interlimb phase differences plus locomotor frequency). We then trained a surrogate model and computed Sobol first- and total-order sensitivity indices, which quantify how much each parameter and its interactions contribute to variability in this distance measure. This analysis showed that, across both injuries, variations in drive to sublesional lumbar rhythm generators and in lumbar V0/V3 commissural connectivity have the largest impact on recovered gait expression, whereas other pathways had comparatively minor effects within the tested range.

      The sensitivity analysis further refined our conclusions by showing that, although injury symmetry (contusion vs. lateral hemisection) influences which pathways reorganize, effective recovery in both cases depends on re-engaging lumbar rhythm-generating and commissural circuits, highlighting these networks as key therapeutic targets.

      Overall, the authors achieved their aims, and the model provides solid support for the changes in connectivity after the two types of injuries were modelled. This work emphasizes specific changes in connectivity after lateral hemisection or after contusion that could be investigated experimentally. The model is available for public use and could serve as a tool to analyze the relative importance of various highlighted or previously undiscovered changes in connectivity that may underlie the recovery of locomotor function in spinalized rats.

      Reviewer #3 (Recommendations for the authors):

      (1) It would be useful to study the sensitivity of the injured models to small changes in the connectivity changes to determine which ones play a greater role in the gait after injury.

      See response above on the added sensitivity analysis.

      (2) Was there any tissue analysis from the original experiments with the contusion experiments, as contusion experiments can be variable, so it would be good to know the level of variability in the injuries?

      Unfortunately, we were unable to complete tissue analysis of the injury epicenters for these animals because the tissue was not handled appropriately for histology. However, in the past, comparable animals with T10 12.5g-cm contusion injuries delivered by the NYU (MASCIS) Impactor had variability of up to ~30% of the mean (spared white matter, e.g. see Smith et al., 2006). It is also worth noting that spared white matter at the epicenter, at least in our hands, is generally well-correlated with BBB overground locomotor scale scores.

      (3) There is more variability in phase difference in rats than model in the lateral hemisection. Is there any way to figure out which of the connectivity changes is most responsible for that variability? 

      We agree that the variability of phase differences after lateral hemisection is larger in rats than in the model. One possible contributor to this discrepancy is the strength of spared long propriospinal neuron (LPN) pathways, which we kept fixed at pre-injury levels in the model. As an exploratory analysis, we varied the weights of these spared LPN connections and quantified the circular standard deviation of the phase differences (Author response image 1). Decreasing spared LPN weights increased the variability of all phase differences. This suggests that plasticity of spared LPNs (potentially reducing their effective connectivity and partly compensating for the asymmetry introduced by the lesion) could contribute to the higher variability seen in vivo. However, because these results remain speculative, we chose to include them in this response only and not in the main manuscript.

      Author response image 1.

      Variability of phase differences as a function of spared long propriospinal neuron connection weights (hemisection model).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Monziani and Ulitsky present a large and exhaustive study on the lncRNA EPB41L4A-AS1 using a variety of genomic methods. They uncover a rather complex picture of an RNA transcript that appears to act via diverse pathways to regulate the expression of large numbers of genes, including many snoRNAs. The activity of EPB41L4A-AS1 seems to be intimately linked with the protein SUB1, via both direct physical interactions and direct/indirect of SUB1 mRNA expression.

      The study is characterised by thoughtful, innovative, integrative genomic analysis. It is shown that EPB41L4A-AS1 interacts with SUB1 protein and that this may lead to extensive changes in SUB1's other RNA partners. Disruption of EPB41L4A-AS1 leads to widespread changes in non-polyA RNA expression, as well as local cis changes. At the clinical level, it is possible that EPB41L4A-AS1 plays disease-relevant roles, although these seem to be somewhat contradictory with evidence supporting both oncogenic and tumour suppressive activities.

      A couple of issues could be better addressed here. Firstly, the copy number of EPB41L4A-AS1 is an important missing piece of the puzzle. It is apparently highly expressed in the FISH experiments. To get an understanding of how EPB41L4A-AS1 regulates SUB1, an abundant protein, we need to know the relative stoichiometry of these two factors. Secondly, while many of the experiments use two independent Gapmers for EPB41L4A-AS1 knockdown, the RNA-sequencing experiments apparently use just one, with one negative control (?). Evidence is emerging that Gapmers produce extensive off-target gene expression effects in cells, potentially exceeding the amount of on-target changes arising through the intended target gene. Therefore, it is important to estimate this through the use of multiple targeting and non-targeting ASOs, if one is to get a true picture of EPB41L4A-AS1 target genes. In this Reviewer's opinion, this casts some doubt over the interpretation of RNA-seq experiments until that work is done. Nonetheless, the Authors have designed thorough experiments, including overexpression rescue constructs, to quite confidently assess the role of EPB41L4A-AS1 in snoRNA expression.

      It is possible that EPB41L4A-AS1 plays roles in cancer, either as an oncogene or a tumour suppressor. However, it will in the future be important to extend these observations to a greater variety of cell contexts.

      This work is valuable in providing an extensive and thorough analysis of the global mechanisms of an important regulatory lncRNA and highlights the complexity of such mechanisms via cis and trans regulation and extensive protein interactions.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Monziani et al. identified long noncoding RNAs (lncRNAs) that act in cis and are coregulated with their target genes located in close genomic proximity. The authors mined the GeneHancer database, and this analysis led to the identification of four lncRNA-target pairs. The authors decided to focus on lncRNA EPB41L4A-AS1.

      They thoroughly characterised this lncRNA, demonstrating that it is located in the cytoplasm and the nuclei, and that its expression is altered in response to different stimuli. Furthermore, the authors showed that EPB41L4A-AS1 regulates EPB41L4A transcription, leading to a mild reduction in EPB41L4A protein levels. This was not recapitulated with siRNA-mediated depletion of EPB41L4AAS1. RNA-seq in EPB41L4A-AS1-depleted cells with single LNA revealed 2364 DEGs linked to pathways including the cell cycle, cell adhesion, and inflammatory response. To understand the mechanism of action of EPB41L4A-AS1, the authors mined the ENCODE eCLIP data and identified SUB1 as an lncRNA interactor. The authors also found that the loss of EPB41L4A-AS1 and SUB1 leads to the accumulation of snoRNAs, and that SUB1 localisation changes upon the loss of EPB41L4A-AS1. Finally, the authors showed that EPB41L4A-AS1 deficiency did not change the steady-state levels of SNORA13 nor RNA modification driven by this RNA. The phenotype associated with the loss of EPB41L4A-AS1 is linked to increased invasion and EMT gene signature.

      Overall, this is an interesting and nicely done study on the versatile role of EPB41L4A-AS1 and the multifaceted interplay between SUB1 and this lncRNA, but some conclusions and claims need to be supported with additional experiments. My primary concerns are using a single LNA gapmer for critical experiments, increased invasion, and nucleolar distribution of SUB1- in EPB41L4A-AS1-depleted cells. These experiments need to be validated with orthogonal methods.

      Strengths:

      The authors used complementary tools to dissect the complex role of lncRNA EPB41L4A-AS1 in regulating EPB41L4A, which is highly commendable. There are few papers in the literature on lncRNAs at this standard. They employed LNA gapmers, siRNAs, CRISPRi/a, and exogenous overexpression of EPB41L4A-AS1 to demonstrate that the transcription of EPB41L4A-AS1 acts in cis to promote the expression of EPB41L4A by ensuring spatial proximity between the TAD boundary and the EPB41L4A promoter. At the same time, this lncRNA binds to SUB1 and regulates snoRNA expression and nucleolar biology. Overall, the manuscript is easy to read, and the figures are well presented. The methods are sound, and the expected standards are met.

      Weaknesses:

      The authors should clarify how many lncRNA-target pairs were included in the initial computational screen for cis-acting lncRNAs and why MCF7 was chosen as the cell line of choice. Most of the data uses a single LNA gapmer targeting EPB41L4A-AS1 lncRNA (eg, Fig. 2c, 3B, and RNA-seq), and the critical experiments should be using at least 2 LNA gapmers. The specificity of SUB1 CUT&RUN is lacking, as well as direct binding of SUB1 to lncRNA EPB41L4A-AS1, which should be confirmed by CLIP qPCR in MCF7 cells. Finally, the role of EPB41L4A-AS1 in SUB1 distribution (Figure 5) and cell invasion (Figure 8) needs to be complemented with additional experiments, which should finally demonstrate the role of this lncRNA in nucleolus and cancer-associated pathways. The use of MCF7 as a single cancer cell line is not ideal.

      Reviewer #3 (Public review):

      Summary:

      In this paper, the authors made some interesting observations that EPB41L4A-AS1 lncRNA can regulate the transcription of both the nearby coding gene and genes on other chromosomes. They started by computationally examining lncRNA-gene pairs by analyzing co-expression, chromatin features of enhancers, TF binding, HiC connectome, and eQTLs. They then zoomed in on four pairs of lncRNA-gene pairs and used LNA antisense oligonucleotides to knock down these lncRNAs. This revealed EPB41L4A-AS1 as the only one that can regulate the expression of its cis-gene target EPB41L4A. By RNA-FISH, the authors found this lncRNA to be located in all three parts of a cell: chromatin, nucleoplasm, and cytoplasm. RNA-seq after LNA knockdown of EPB41L4A-AS1 showed that this increased >1100 genes and decreased >1250 genes, including both nearby genes and genes on other chromosomes. They later found that EPB41L4A-AS1 may interact with SUB1 protein (an RNA-binding protein) to impact the target genes of SUB1. EPB41L4A-AS1 knockdown reduced the mRNA level of SUB1 and altered the nuclear location of SUB1. Later, the authors observed that EPB41L4A-AS1 knockdown caused an increase of snRNAs and snoRNAs, likely via disrupted SUB1 function. In the last part of the paper, the authors conducted rescue experiments that suggested that the full-length, intron- and SNORA13-containing EPB41L4A-AS1 is required to partially rescue snoRNA expression. They also conducted SLAM-Seq and showed that the increased abundance of snoRNAs is primarily due to their hosts' increased transcription and stability. They end with data showing that EPB41L4A-AS1 knockdown reduced MCF7 cell proliferation but increased its migration, suggesting a link to breast cancer progression and/or metastasis.

      Strengths:

      Overall, the paper is well-written, and the results are presented with good technical rigor and appropriate interpretation. The observation that a complex lncRNA EPB41L4A-AS1 regulates both cis and trans target genes, if fully proven, is interesting and important.

      Weaknesses:

      The paper is a bit disjointed as it started from cis and trans gene regulation, but later it switched to a partially relevant topic of snoRNA metabolism via SUB1. The paper did not follow up on the interesting observation that there are many potential trans target genes affected by EPB41L4A-AS1 knockdown and there was limited study of the mechanisms as to how these trans genes (including SUB1 or NPM1 genes themselves) are affected by EPB41L4A-AS1 knockdown. There are discrepancies in the results upon EPB41L4A-AS1 knockdown by LNA versus by CRISPR activation, or by plasmid overexpression of this lncRNA.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Copy number:

      Perhaps I missed it, but it seems that no attempt is made to estimate the number of copies of EPB41L4A-AS1 transcripts per cell. This should be possible given RNAseq and FISH. At least an order of magnitude estimate. This is important for shedding light on the later observations that EPB41L4A-AS1 may interact with SUB1 protein and regulate the expression of thousands of mRNAs.

      We thank the reviewer for the insightful suggestion. We agree that an estimate of EPB41L4A-AS1 copy number might further strengthen the hypotheses presented in the manuscript. Therefore, we analyzed the smFISH images and calculated the copy number per cell of this lncRNA, as well as that of GAPDH as a comparison.

      Because segmenting MCF-7 cells proved to be difficult due to the extent of the cell-cell contacts they establish, we imaged multiple (n = 14) fields of view, extracted the number of EPB41L4A-AS1/GAPDH molecules in each field and divided them by the number of cells (as assessed by DAPI staining, 589 cells in total). We detected an average of 33.37 ± 3.95 EPB41L4A-AS1 molecules per cell, in contrast to 418.27 ± 61.79 GAPDH molecules. As a comparison, within the same qPCR experiment the average of the Ct values of these two RNAs is about  22.3 and 17.5, the FPKMs in the polyA+ RNA-seq are ~ 2479.4 and 35.6, and the FPKMs in the rRNA-depleted RNA-seq are ~ 3549.9 and 19.3, respectively. Thus, our estimates of the EPB41L4A-AS1 copy number in MCF-7 cells fits well into these observations.

      The question whether an average of ~35 molecules per cell is sufficient to affect the expression of thousands of genes is somewhat more difficult to ascertain. As discussed below, it is unlikely that all the genes dysregulated following the KD of EPB41L4A-AS1 are all direct targets of this lncRNA, and indeed SUB1 depletion affects an order of magnitude fewer genes. It has been shown that lncRNAs can affect the behavior of interacting RNAs and proteins in a substoichiometric fashion (Unfried & Ulitsky, 2022), but whether this applies to EPB41L4A-AS1 remains to be addressed in future studies. Nonetheless, this copy number appears to be sufficient for a trans-acting functions for this lncRNA, on top of its cis-regulatory role in regulating EPB41L4A. We added this information in the text as follows:

      “Using single-molecule fluorescence in-situ hybridization (smFISH) and subcellular fractionation we found that EPB41L4A-AS1 is expressed at an average of 33.37 ± 3.95 molecule per cell, and displays both nuclear and cytoplasmic localization in MCF-7 cells (Fig. 1D), with a minor fraction associated with chromatin as well (Fig. 1E).”

      We have updated the methods section as well:

      “To visualize the subcellular localization of EPB41L4A-AS1 in vivo, we performed single-molecule fluorescence in situ hybridization (smFISH) using HCR™ amplifiers. Probe sets (n = 30 unique probes) targeting EPB41L4A-AS1 and GAPDH (positive control) were designed and ordered from Molecular Instruments. We followed the Multiplexed HCR v3.0 protocol with minor modifications. MCF-7 cells were plated in 8-well chambers (Ibidi) and cultured O/N as described above. The next day, cells were fixed with cold 4% PFA in 1X PBS for 10 minutes at RT and then permeabilized O/N in 70% ethanol at -20°C. Following permeabilization, cells were washed twice with 2X SSC buffer and incubated at 37°C for 30 minutes in hybridization buffer (HB). The HB was then replaced with a probe solution containing 1.2 pmol of EPB41L4A-AS1 probes and 0.6 pmol of GAPDH probes in HB. The slides were incubated O/N at 37°C. To remove excess probes, the slides were washed four times with probe wash buffer at 37°C for 5 minutes each, followed by two washes with 5X SSCT at RT for 5 minutes. The samples were then pre-amplified in amplification buffer for 30 minutes at RT and subsequently incubated O/N in the dark at RT in amplification buffer supplemented with 18 pmol of the appropriate hairpins. Finally, excess hairpins were removed by washing the slides five times in 5X SSCT at RT. The slides were mounted with ProLong™ Glass Antifade Mountant (Invitrogen), cured O/N in the dark at RT, and imaged using a Nikon CSU-W1 spinning disk confocal microscope. In order to estimate the RNA copy number, we imaged multiple distinct fields, extracted the number of EPB41L4A-AS1/GAPDH molecules in each field using the “Find Maxima” tool in ImageJ/Fiji, and divided them by the number of cells (as assessed by DAPI staining).”

      (2) Gapmer results:

      Again, it is quite unclear how many and which Gapmer is used in the genomics experiments, particularly the RNA-seq. In our recent experiments, we find very extensive off-target mRNA changes arising from Gapmer treatment. For this reason, it is advisable to use both multiple control and multiple targeting Gapmers, so as to identify truly target-dependent expression changes. While I acknowledge and commend the latter rescue experiments, and experiments using multiple Gapmers, I'd like to get clarification about how many and which Gapmers were used for RNAseq, and the authors' opinion on the need for additional work here.

      We agree with the Reviewer that GapmeRs are prone to off-target and unwanted effects (Lai et al., 2020; Lee & Mendell, 2020; Maranon & Wilusz, 2020). Early in our experiments, we found out that LNA1 triggers a non-specific CDKN1A/p21 activation (Fig. S5A-C), and thus, we have initially performed some experiments such as RNA-seq with only LNA2.

      Nonetheless, other experiments were performed using both GapmeRs, such as multiple RT-qPCRs, UMI-4C, SUB1 and NPM1 imaging, and the in vitro assays, among others, and consistent results were obtained with both LNAs.

      To accommodate the request by this and the other reviewers, we have now performed another round of polyA+ RNA-seq following EPB41L4A-AS1 knockdown using LNA1 or LNA2, as well as the previously used and an additional control GapmeR. The FPKMs of the control samples are highly-correlated both within replicates and between GapmeRs (Fig. S6A). More importantly, the fold-changes to control are highly correlated between the two on-target GapmeRs LNA1 and LNA2, regardless of the GapmeR used for normalization (Fig. S6B), thus showing that the bulk of the response is shared and likely the direct result of the reduction in the levels of EPB41L4A-AS1. Notably, key targets NPM1 and MTREX (see discussion, Fig. S12A-C and comments to Reviewer 3) were found to be downregulated by both LNAs (Fig. S6C).

      However, we acknowledge that some of the dysregulated genes are observed only when using one GapmeR and not the other, likely due to a combination of indirect, secondary and non-specific effects, and as such it is difficult to infer the direct response. Supporting this, LNA2 yielded a total of 1,069 DEGs (617 up and 452 down) and LNA1 2,493 DEGs (1,328 up and 1,287 down), with the latter triggering a stronger response most likely as a result of the previously mentioned CDKN1A/p21 induction. Overall, 45.1% of the upregulated genes following LNA2 transfection were shared with LNA1, in contrast to only the 24.3% of the downregulated ones.

      We have now included these results in the Results section (see below) and in Supplementary Figure (Fig. S6).

      “Most of the consequences of the depletion of EPB41L4A-AS1 are thus not directly explained by changes in EPB41L4A levels. An additional trans-acting function for EPB41L4A-AS1 would therefore be consistent with its high expression levels compared to most lncRNAs detected in MCF-7 (Fig. S5G). To strengthen these findings, we have transfected MCF-7 cells with LNA1 and a second control GapmeR (NT2), as well as the previous one (NT1) and LNA2, and sequenced the polyadenylated RNA fraction as before. Notably, the expression levels (in FPKMs) of the replicates of both control samples are highly correlated with each other (Fig. S6A), and the global transcriptomic changes triggered by the two EPB41L4A-AS1-targeting LNAs are largely concordant (Fig. S6B and S6C). Because of this concordance and the cleaner (i.e., no CDKN1A upregulation) readout in LNA2-transfected cells, we focused mainly on these cells for subsequent analyses.”

      (3) Figure 1E:

      Can the authors comment on the unusual (for a protein-coding mRNA) localisation of EPB41L4A, with a high degree of chromatin enrichment?

      We acknowledge that mRNAs from protein-coding genes displaying nuclear and chromatin localizations are quite unusual. The nuclear and chromatin localization of some mRNAs are often due to their low expression, length, time that it takes to be transcribed, repetitive elements and strong secondary structures (Bahar Halpern et al., 2015; Didiot et al., 2018; Lubelsky & Ulitsky, 2018; Ly et al., 2022).

      We now briefly mention this in the text:

      “In contrast, both EPB41L4A and SNORA13 were mostly found in the chromatin fraction (Fig. 1E), the former possibly due to the length of its pre-mRNA (>250 kb), which would require substantial time to transcribe (Bahar Halpern et al., 2015; Didiot et al., 2018; Lubelsky & Ulitsky, 2018; Ly et al., 2022).”

      Supporting our results, analysis of the ENCODE MCF-7 RNA-seq data of the cytoplasmic, nuclear and total cell fractions indeed shows a nuclear enrichment of the EPB41L4A mRNA (Author response image 1), in line with what we observed in Fig. 1E by RT-qPCR. 

      Author response image 1.

      The EPB41L4A transcript is nuclear-enriched in the MCF-7 ENCODE subcellular RNA-seq dataset. Scatterplot of gene length versus cytoplasm/nucleus ratio (as computed by DESeq2) in MCF-7 cells. Each dot represents an unique gene, color-coded reflecting if their DESeq2 adjusted p-value < 0.05 and absolute log<sub>2</sub>FC > .41 (33% enrichment or depletion).GAPDH and MALAT1 are shown as representative cytoplasmic and nuclear transcripts, respectively. Data from ENCODE.

      (4) Annotation and termini of EPB41L4A-AS1:

      The latest Gencode v47 annotations imply an overlap of the sense and antisense, different from that shown in Figure 1C. The 3' UTR of EPB41L4A is shown to extensively overlap EPB41L4A-AS1. This could shed light on the apparent regulation of the former by the latter that is relevant for this paper. I'd suggest that the authors update their figure of the EPB41L4A-AS1 locus organisation with much more detail, particularly evidence for the true polyA site of both genes. What is more, the authors might consider performing RACE experiments for both RNAs in their cells to definitely establish whether these transcripts contain complementary sequence that could cause their Watson-Crick hybridisation, or whether their two genes might interfere with each other via some kind of polymerase collision.

      We thank the reviewer for pointing this out. Also in previous GENCODE annotations, multiple isoforms were reported with some overlapping the 3’ UTR of EPB41L4A. In the EPB41L4A-AS1 locus image (Fig. 1C), we report at the bottom the different transcripts isoforms currently annotated, and a schematics of the one that is clearly the most abundant in MCF-7 cells based on RNA-seq read coverage. This is supported by both the polyA(+) and ribo(-) RNA-seq data, which are strand-specific, as shown in the figure.

      We now also examined the ENCODE/CSHL MCF-7 RNA-seq data from whole cell, cytoplasm and nucleus fractions, as well as 3P-seq data (Jan et al., 2011) (unpublished data from human cell lines), reported in Author response image 2. All these data support the predominant use of the proximal polyA site in human cell lines. This shorter isoform does not overlap EPB41L4A.

      Author response image 2.

      Most EPB41L4A-AS1 transcripts end before the 3’ end of EPB41L4A. UCSC genome browser view showing tracks from 3P-seq data in different cell lines and neural crest (top, with numbers representing the read counts, i.e. how many times that 3’ end has been detected), and stranded ENCODE subcellular RNA-seq (bottom).

      Based on these data, the large majority of cellular transcripts of EPB41L4A-AS1 terminate at the earlier polyA site and don’t overlap with EPB41L4A. There is a small fraction that appears to be restricted to the nucleus that terminates later at the annotated isoform. 3' RACE experiments are not expected to provide substantially different information beyond what is already available.

      (5) Figure 3C:

      There is an apparent correlation between log2FC upon EPB41L4A-AS1 knockdown, and the number of clip sites for SUB1. However, I expect that the clip signal correlates strongly with the mRNA expression level, and that log2FC may also correlate with the same. Therefore, the authors would be advised to more exhaustively check that there really is a genuine relationship between log2FC and clip sites, after removing any possible confounders of overall expression level.

      As the reviewer suggested, there is a correlation between the baseline expression level and the strength of SUB1 binding in the eCLIP data. To address this issue, we built expression-matched controls for each group of SUB1 interactors and checked the fold-changes following EPB41L4A-AS1 KD, similarly to what we have done in Fig. 3C. The results are presented, and are now part of Supplementary Figure 7 (Fig. S7C). 

      Based on this analysis, while there is a tendency of increased expression with increased SUB1 binding, when controlling for expression levels the effect of down-regulation of SUB1-bound RNAs upon lncRNA knockdown remains, suggesting that it is not merely a confounding effect. We have updated the text as follows:

      “We hypothesized that loss of EPB41L4A-AS1 might affect SUB1, either via the reduction in its expression or by affecting its functions. We stratified SUB1 eCLIP targets into confidence intervals, based on the number, strength and confidence of the reported binding sites. Indeed, eCLIP targets of SUB1 (from HepG2 cells profiled by ENCODE) were significantly downregulated following EPB41L4A-AS1 KD in MCF-7, with more confident targets experiencing stronger downregulation (Fig. 3C). Importantly, this still holds true when controlling for gene expression levels (Fig. S7C), suggesting that this negative trend is not due to differences in their baseline expression.”

      (6) The relation to cancer seems somewhat contradictory, maybe I'm missing something. Could the authors more clearly state which evidence is consistent with either an Oncogene or a Tumour Suppressive function, and discuss this briefly in the Discussion? It is not a problem if the data are contradictory, however, it should be discussed more clearly.

      We acknowledge this apparent contradiction. Cancer cells are characterized by a multitude of hallmarks depending on the cancer type and stage, including high proliferation rates and enhanced invasive capabilities. The notion that cells with reduced EPB41L4A-AS1 levels exhibit lower proliferation, yet increased invasion is compatible with a function as an oncogene. Cells undergoing EMT may reduce or even completely halt proliferation/cell division, until they revert back to an epithelial state (Brabletz et al., 2018; Dongre & Weinberg, 2019). Notably, downregulated genes following EPB41L4A-AS1 KD are enriched in GO terms related to cell proliferation and cell cycle progression (Fig. 2I), whereas those upregulated are enriched for terms linked to EMT processes. Thus, while we cannot rule out a potential function as tumor suppressor gene, our data fit better the notion that EPB41L4A-AS1 promotes invasion, and thus, primarily functions as an oncogene. We now address this in point in the discussion:

      “The notion that cells with reduced EPB41L4A-AS1 levels exhibit lower proliferation (Fig. 8C), yet increased invasion (Fig. 8A and 8B) is compatible with a function as an oncogene by promoting EMT (Fig. 8D and 8E). Cells undergoing this process may reduce or even completely halt proliferation/cell division, until they revert back to an epithelial state (Brabletz et al., 2018; Dongre & Weinberg, 2019). Notably, downregulated genes following EPB41L4A-AS1 KD are enriched in GO terms related to cell proliferation and cell cycle progression (Fig. 2I), whereas those upregulated for terms linked to EMT processes. Thus, while we cannot rule out a potential function as tumor suppressor gene, our data better fits the idea that this lncRNA promotes invasion, and thus, primarily functions as an oncogene.”

      Reviewer #2 (Recommendations for the authors):

      Below are major and minor points to be addressed. We hope the authors find them useful.

      (1) Figure 1:

      Where are LNA gapmers located within the EPB41L4A-AS1 gene? Are they targeting exons or introns of the EPB41L4A-AS1? Please clarify or include in the figure.

      We now report the location of the two GapmeRs in Fig. 1C. LNA1 targets the intronic region between SNORA13 and exon 2, and LNA2 the terminal part of exon 1.

      (2) Figure 2B:

      Why is a single LNA gapmer used for EPB41L4A Western? In addition, are the qPCR data in Figure 2B the same as in Figure 1B? Please clarify.

      The Western Blot was performed after transfecting the cells with either LNA1 or LNA2. We now have replaced Fig. 2C with the full Western Blot image, in order to show both LNAs. With respect to the qPCRs in Fig. 1B and 2B, they represent the results from two independent experiments.

      (3) Figure 2F:

      2364 DEGs for a single LNA is a lot of deregulated genes in RNA-seq data. How do the authors explain such a big number in DEGs? Is that because this LNA was intronic? Additional LNA gapmer would minimise the "real" lncRNA target and any potential off-target effect.

      We agree with the Reviewer that GapmeRs are prone to off-target and unwanted effects (Lai et al.,2020; Lee & Mendell, 2020; Maranon & Wilusz, 2020). Early in our experiments, we found out that LNA1 triggers a non-specific CDKN1A/p21 activation (Fig. S5A-C), and thus, we have initially performed some experiments such as RNA-seq with only LNA2.

      Nonetheless, other experiments were performed using both GapmeRs, such as multiple RT-qPCRs, UMI-4C, SUB1 and NPM1 imaging, and the in vitro assays, among others, and consistent results were obtained with both LNAs.

      To accommodate the request by this and the other reviewers, we have now performed another round of polyA+ RNA-seq following EPB41L4A-AS1 knockdown using LNA1 or LNA2, as well as the previously used and an additional control GapmeR. The FPKMs of the control samples are highly-correlated both within replicates and between GapmeRs (Fig. S6A). More importantly, the fold-changes to control are highly correlated between the two on-target GapmeRs LNA1 and LNA2, regardless of the GapmeR used for normalization (Fig. S6B), thus showing that despite significant GapmeR-specific effects, the bulk of the response is shared and likely the direct result of the reduction in the levels of EPB41L4A-AS1. Notably, key targets NPM1 and MTREX (see discussion, Fig. S12A-C and comments to Reviewer 3) were found to be downregulated by both LNAs (Fig. S6C).

      However, we acknowledge that some of the dysregulated genes are observed only when using one GapmeR and not the other, likely due to a combination of indirect, secondary and non-specific effects, and as such it is difficult to infer the direct response. Supporting this, LNA2 yielded a total of 1,069 DEGs (617 up and 452 down) and LNA1 2,493 DEGs (1,328 up and 1,287 down), with the latter triggering a stronger response most likely as a result of the previously mentioned CDKN1A/p21 induction. Overall, 45.1% of the upregulated genes following LNA2 transfection were shared with LNA1, in contrast to only the 24.3% of the downregulated ones.

      We have now included these results in the Results section (see below) and in Supplementary Figure (Fig. S6).

      “Most of the consequences of the depletion of EPB41L4A-AS1 are thus not directly explained by changes in EPB41L4A levels. An additional trans-acting function for EPB41L4A-AS1 would therefore be consistent with its high expression levels compared to most lncRNAs detected in MCF-7 (Fig. S5G). To strengthen these findings, we have transfected MCF-7 cells with LNA1 and a second control GapmeR (NT2), as well as the previous one (NT1) and LNA2, and sequenced the polyadenylated RNA fraction as before. Notably, the expression levels (in FPKMs) of the replicates of both control samples are highly correlated with each other (Fig. S6A), and the global transcriptomic changes triggered by the two EPB41L4A-AS1-targeting LNAs are largely concordant (Fig. S6B and S6C). Because of this concordance and the cleaner (i.e., no CDKN1A upregulation) readout in LNA2-transfected cells, we focused mainly on these cells for subsequent analyses.”

      (4) Figure 3B: Does downregulation of SUB1 and NPM1 reflect at the protein level with both LNA gapmers? The authors should show a heatmap and metagene profile for SUB1 CUT & RUN. How did the author know that SUB1 binding is specific, since CUT & RUN was not performed in SUB1-depleted cells?

      As requested by both Reviewer #2 and #3, we have performed WB for SUB1, NPM1 and FBL following EPB41L4A-AS1 KD with two targeting (LNA1 and LNA2) and the previous control GapmeRs. Interestingly, we did not detect any significant downregulation of either proteins (Author response image 3), although this might be the result of the high variability observed in the control samples. Moreover, the short timeframe in which the experiments have been conducted━that is, transient transfections for 3 days━might not be sufficient time for the existing proteins to be degraded, and thus, the downregulation is more evident at the RNA (Fig. 3B and Supplementary Figure 6C) rather than protein level.

      Author response image 3.

      EPB41L4A-AS1 KD has only marginal effects on the levels of nucleolar proteins. (A) Western Blots for the indicated proteins after the transfection for 3 days of the control and targeting GapmeRs. (B) Quantification of the protein levels from (A).  All experiments were performed in n=3 biological replicates, with the error bars in the barplots representing the standard deviation. ns - P>0.05; * - P<0.05; ** - P<0.01; *** - P<0.001 (two-sided Student’s t-test).

      Following the suggestion by the Reviewer, we now show both the SUB1 CUT&RUN metagene profile (previously available as Fig. 3F) and the heatmap (now Fig. 3G) around the TSS of all genes, stratified by their expression level. Both graphs are reported.

      We show that the antibody signal is responsive to SUB1 depletion via siRNAs in both WB (Fig. S8F) and IF (Fig. 5E) experiments. As mentioned below, this and the absence of non-specific signals makes us confident in the CUT&RUN data. Performing CUT&RUN in SUB1 depleted cells would be difficult to interpret as perturbations are typically not complete, and so the remaining protein can still bind the same regions. Since there isn’t a clear way to add spike-ins to CUT&RUN experiments, it is very difficult to show specificity of binding by CUT&RUN in siRNA-knockdown cells.

      (5) Figure 3D: The MW for the depicted proteins are lacking. Why is there no SUB1 protein in the input? Please clarify. Since the authors used siRNA to deplete SUB1, it would be good to know if the antibody is specific in their CUT & RUN (see above)

      We apologize for the lack of the MW in Fig. 3D. As shown in Fig. S8F, SUB1 is ~18 kDa and the antibody signal is responsive to SUB1 depletion via siRNAs in both WB (Fig. S8F) and IF (Fig. 5E) experiments. Thus, given its 1) established specificity in those two settings and 2) the lack of generalized signal at most open chromatin regions, which is typical of nonspecific CUT&RUN experiments, we are confident in the specificity of the CUT&RUN results.

      We now mention the MW of SUB1 in Fig. 3D as well and we provide in Author response image 4 the full SUB1 WB picture, enhancing the contrast to highlight the bands. We agree that the SUB1 band in the input is weak, likely reflecting the low abundance in that fraction and the detection difficulty due to its low MW (see Fig. S8F).

      Author response image 4.

      Western blot for SUB1 following RIP using either a SUB1 or IgG antibody. IN - input, SN - supernatant/unbound, B - bound.

      (6) Supplementary Figure 6C:

      The validation of lncRNA EPB41L4A-AS1 binding to SUB1 should be confirmed by CLIP qPCR, since native RIP can lead to reassociation of RNA-protein interactions (PMID: 15388877). Additionally, the eclip data presented in Figure 3a were from a different cell line and not MCF7.

      We acknowledge that the SUB1 eCLIP data was generated in a different cell line, as we mentioned in the text:

      “Indeed, eCLIP targets of SUB1 (from HepG2 cells profiled by ENCODE) were significantly downregulated following EPB41L4A-AS1 KD in MCF-7, with more confident targets experiencing stronger downregulation (Fig. 3C). Importantly, this still holds true when controlling for gene expression levels (Fig. S7C), suggesting that this negative trend is not due to differences in their baseline expression. To obtain SUB1-associated transcripts in MCF-7 cells; we performed a native RNA immunoprecipitation followed by sequencing of polyA+ RNAs (RIP-seq) (Fig. 3D, S7D and S7E).”

      Because of this, we resorted to native RIP, in order to get binding information in our experimental system. As we show independent evidence for binding using both eCLIP and RIP, and the substantial challenge in establishing the CLIP method, which has not been successfully used in our group, we respectfully argue that further validations are out of scope of this study. We nonetheless agree that several genes which are nominally significantly enriched in our RIP data are likely not direct targets of SUB1, especially given that it is difficult to assign the perfect threshold that discriminates between bound and unbound RNAs.

      We now additionally mention this at the beginning of the paragraph as well:

      “In order to identify potential factors that might be associated with EPB41L4A-AS1, we inspected protein-RNA binding data from the ENCODE eCLIP dataset(Van Nostrand et al., 2020). The exons of the EPB41L4A-AS1 lncRNA were densely and strongly bound by SUB1 (also known as PC4) in both HepG2 and K562 cells (Fig. 3A).”

      (7) Figure 3G:

      Can the authors distinguish whether loss of EPB41L4A-AS1 affects SUB1 chromatin binding or its activity as RBP? Please discuss.

      Distinguishing between altered SUB1 chromatin and RNA binding is challenging, as this protein likely does not interact directly with chromatin and exhibits rather promiscuous RNA binding properties (Ray et al., 2023). In particular, SUB1 (also known as PC4) interacts with and regulates the activity of all three RNA polymerases, and was reported to be involved in transcription initiation and elongation, response to DNA damage, chromatin condensation (Conesa & Acker, 2010; Das et al., 2006; Garavís & Calvo, 2017; Hou et al., 2022) and telomere maintenance (Dubois et al., 2025; Salgado et al., 2024).

      Based on our data, genes whose promoters are occupied by SUB1 display marginal, yet highly significant changes in their steady-state expression levels upon lncRNA perturbations. We also show that upon EPB41L4A-AS1 KD, SUB1 acquires a stronger nucleolar localization (Fig. 5A), which likely affects its RNA interactome as well. However, further elucidating these activities would require performing RIP-seq and CUT&RUN in lncRNA-depleted cells, which we argue is out of the scope of the current study. We note that  KD of SUB1 with siRNAs have milder effects than that of EPB41L4A-AS1 (Fig. S8G), suggesting that additional players and effects shape the observed changes. Therefore, it is highly likely that the loss of this lncRNA affects both SUB1 chromatin binding profile and RNA binding activity, with the latter likely resulting in the increased snoRNAs abundance.

      (8) Figure 4: Can the authors show that a specific class of snorna is affected upon depletion of SUB1 and EPB41L4A-AS1? Can they further classify the effect of their depletion on H/ACA box snoRNAs, C/D box snoRNAs, and scaRNAs?

      Such potential distinct effect on the different classes of snoRNAs was considered, and the results are available in Fig. S8B and S8H (boxplots, after EPB41L4A-AS1 and SUB1 depletion), as well as Fig. 4F and S9F (scatterplots between EPB41L4A-AS1 and SUB1 depletion, and EPB41L4A-AS1 and GAS5 depletion, respectively). We see no preferential effect on one group of snoRNAs or the other.

      (9) Figure 5: From the representative images, it looks to me that LNA 2 targeting EPB41L4A-AS1 has a bigger effect on nucleolar staining of SUB1. To claim that EPB41L4A-AS1 depletion "shifts SUB1 to a stronger nucleolar distribution", the authors need to perform IF staining for SUB1 and Fibrillarin, a known nucleolar marker. Also, how does this data fit with their qPCR data shown in Figure 3B? It is instrumental for the authors to demonstrate by IF or Western blotting that SUB1 levels decrease in one fraction and increase specifically in the nucleolus. They could perform Western blot for SUB1 and Fibrillarin in EPB41L4A-AS1-depleted cells and isolate cytoplasmic, nuclear, and nucleolar fractions.This experiment will strengthen their finding. The scale bar is missing for all the images in Figure 5. The authors should also show magnified images of a single representative cell at 100x.

      We apologize for the confusion regarding the scale bars. As mentioned here and elsewhere, the scale bars are present in the top-left image of each panel only, in order to avoid overcrowding the panel. All the images are already at 100X, with the exception of Fig. 5E (IF for SUB1 upon siSUB1 transfection) which is 60X in order to better show the lack of signal. We however acknowledge that the images are sometimes confusing, due to the PNG features once imported into the document. In any case, in the submission we have also provided the original images in high-quality PDF and .ai formats.  The suggested experiment would require establishing a nucleolar fractionation protocol which we currently don’t have available and we argue that it is out of scope of the current study.

      (10) Additionally, is rRNA synthesis affected in SUB1- and EPB41L4A-AS1-depleted cells? The authors could quantify newly synthesised rRNA levels in the nucleoli, which would also strengthen their findings about the role of this lncRNA in nucleolar biology.

      We acknowledge that there are many aspects of the role of EPB41L4A-AS1 in nucleolar biology that remain to be explored, as well as in nucleolar biology itself, but given the extensive experimental data we already provide in this and other subjects, we respectfully suggest that this experiment is out of scope of the current work. We note that a recent study has shown that SUB1 is required for Pol I-mediated rDNA transcription in the nucleolus (Kaypee et al., 2025). In the presence of nucleolar SUB1, rDNA transcription proceeds as expected, but when SUB1 is depleted or its nucleolar localization is affected—by either sodium butyrate treatment or inhibition of KAT5-mediated phosphorylation at its lysine 35 (K35)—the levels of the 47S pre-rRNA are significantly reduced. In our settings, SUB1 enriches into the nucleolus following EPB41L4A-AS1 KD; thus, we might expect to see a slightly increased rDNA transcription or no effect at all, given that SUB1 localizes in the nucleolus in baseline conditions as well. We now mention this novel role of SUB1 both in the results and discussion.

      “SUB1 interacts with all three RNA polymerases and was reported to be involved in transcription initiation and elongation, response to DNA damage, chromatin condensation(Conesa & Acker, 2010; Das et al., 2006; Garavís & Calvo, 2017; Hou et al., 2022), telomere maintenance(Dubois et al., 2025; Salgado et al., 2024) and rDNA transcription(Kaypee et al., 2025). SUB1 normally localizes throughout the nucleus in various cell lines, yet staining experiments show a moderate enrichment for the nucleolus (source: Human Protein Atlas; https://www.proteinatlas.org/ENSG00000113387-SUB1/subcellular)(Kaypee et al., 2025).”

      “Several features of the response to EPB41L4A-AS1 resemble nucleolar stress, including altered distribution of NPM1(Potapova et al., 2023; Yang et al., 2016). SUB1 was shown to be involved in many nuclear processes, including transcription(Conesa & Acker, 2010), DNA damage response(Mortusewicz et al., 2008; Yu et al., 2016), telomere maintenance(Dubois et al., 2025), and nucleolar processes including rRNA biogenesis(Kaypee et al., 2025; Tafforeau et al., 2013). Our results suggest a complex and multi-faceted relationship between EPB41L4A-AS1 and SUB1, as SUB1 mRNA levels are reduced by the transient (72 hours) KD of the lncRNA (Fig. 3B), the distribution of the protein in the nucleus is altered (Fig. 5A and 5C), while the protein itself is the most prominent binder of the mature EPB41L4A-AS1 in ENCODE eCLIP data (Fig. 3A). The most striking connection between EPB41L4A-AS1 and SUB1 is the similar phenotype triggered by their loss (Fig. 4). We note that a recent study has shown that SUB1 is required for Pol I-mediated rDNA transcription in the nucleolus(Kaypee et al., 2025). In the presence of nucleolar SUB1, rDNA transcription proceeds as expected, but when SUB1 is depleted or its nucleolar localization is affected—by either sodium butyrate treatment or inhibition of KAT5-mediated phosphorylation at its lysine 35 (K35)—the levels of the 47S pre-rRNA are significantly reduced. In our settings, SUB1 enriches into the nucleolus following EPB41L4A-AS1 KD; thus, we might expect to see a slightly increased rDNA transcription or no effect at all, given that SUB1 localizes in the nucleolus in baseline conditions as well. It is however difficult to determine which of the connections between these two genes is the most functionally relevant and which may be indirect and/or feedback interactions. For example, it is possible that EPB41L4A-AS1 primarily acts as a transcriptional regulator of SUB1 mRNA, or that its RNA product is required for proper stability and/or localization of the SUB1 protein, or that EPB41L4A-AS1 acts as a scaffold for the formation of protein-protein interactions of SUB1.”

      (11) Figure 8: The scratch assay alone cannot be used as a measure of increased invasion, and this phenotype must be confirmed with a transwell invasion or migration assay. Thus, I highly recommend that the authors conduct this experiment using the Boyden chamber. Do the authors see upregulation of N-cadherin, Vimentin, and downregulation of E-cadherin in their RNA-seq?

      We agree with the reviewer that those phenotypes are complex and normally require multiple in vitro, as well as in vivo assays to be thoroughly characterized. However, we respectfully consider those as out of scope of the current work, which is more focused on RNA biology and the molecular characterization and functions of EPB41L4A-AS1.

      Nevertheless, in Fig. 8D we show that the canonical EMT signature (taken from MSigDB) is upregulated in cells with reduced expression of EPB41L4A-AS1. Notably, EMT has been found to not possess an unique gene expression program, but it rather involves distinct and partially overlapping gene signatures (Youssef et al., 2024). In Fig. 8D, the most upregulated gene is TIMP3, a matrix metallopeptidase inhibitor linked to a particular EMT signature that is less invasive and more profibrotic (EMT-T2, (Youssef et al., 2024)). Interestingly, we observed a strong upregulation of other genes linked to EMT-T2, such as TIMP1, FOSB, SOX9, JUNB, JUN and KLF4, whereas MPP genes (linked to EMT-T1, which is highly proteolytic and invasive) are generally downregulated or not expressed. With regards to N- and E-cadherin, the first does not pass our cutoff to be considered expressed, and the latter is not significantly changing. Vimentin is also not significantly dysregulated. All these examples are reported, which were added as Fig. 8E:

      The text has also been updated accordingly:

      “These findings suggest that proper EPB41L4A-AS1 expression is required for cellular proliferation, whereas its deficiency results in the onset of more aggressive and migratory behavior, likely linked to the increase of the gene signature of epithelial to mesenchymal transition (EMT) (Fig. 8D). Because EMT is not characterized by a unique gene expression program and rather involves distinct and partially overlapping gene signatures (Youssef et al., 2024), we checked the expression level of marker genes linked to different types of EMTs (Fig. 8E). The most upregulated gene in Fig. 8D is TIMP3, a matrix metallopeptidase inhibitor linked to a particular EMT signature that is less invasive and more profibrotic (EMT-T2) (Youssef et al., 2024). Interestingly, we observed a stark upregulation of other genes linked to EMT-T2, such as TIMP1, FOSB, SOX9, JUNB, JUN and KLF4, whereas MPP genes (linked to EMT-T1, which is highly proteolytic and invasive) are generally downregulated or not expressed. This suggests that the downregulation of EPB41L4A-AS1 is primarily linked to a specific EMT program (EMT-T2), and future studies aimed at uncovering the exact mechanisms and relevance will shed light upon a possible therapeutic potential of this lncRNA.”

      (12) Minor points:

      (a) What could be the explanation for why only the EPB41L4A-AS1 locus has an effect on the neighbouring gene?

      There might be multiple reasons why EPB41L4A-AS1 is able to modulate the expression of the neighboring genes. First, it is expressed from a TAD boundary exhibiting physical contacts with several genes in the two flanking TADs (Fig. 1F and 2A), placing it in the right spot to regulate their expression. Second, it is highly expressed when compared to most of the genes nearby, with transcription having been linked to the establishment and maintenance of TAD boundaries (Costea et al., 2023). Accordingly, the (partial) depletion of EPB41L4A-AS1 via GapmeRs transfection slightly reduces the contacts between the lncRNA and EPB41L4A loci (Fig. 2E and S4J), although this effect could also be determined by a premature transcription termination triggered by the GapmeRs. 

      There are a multitude of mechanisms by which lncRNAs with regulatory functions modulate the expression of one or more target genes in cis (Gil & Ulitsky, 2020), and our data do not unequivocally point to one of them. Distinguishing between these possibilities is a major challenge in the field and would be difficult to address in the context of this one study. It could be that the processive RNA polymerases at the EPB41L4A-AS1 locus are recruited to the neighboring loci, facilitated by the close proximity in the 3D space. It could also be possible that chromatin remodeling factors are recruited by the nascent RNA, and then promote and/or sustain the opening of chromatin at the target site. The latter possibility is intriguing, as this mechanism is proposed to be widespread among lncRNAs (Gil & Ulitsky, 2020; Oo et al., 2025) and we observed a significant reduction of H3K27ac levels at the EPB41L4A promoter region (Fig. 2D). Future studies combining chromatin profiling (e.g., CUT&RUN and ATAC-seq) and RNA pulldown experiments will shed light upon the exact mechanisms by which this lncRNA regulates the expression of target genes in cis and its interacting partners.

      (b) The scale bar is missing on all the images in the Supplementary Figures as well.

      The scale bars are present in the top-left figure of each panel. We acknowledge that due to the export as PNG, some figures (including those with microscopy images) display abnormal font sizes and aspect ratio. All images were created using consistent fonts, sizes and ratio, and are provided as high-quality PDF in the current submission.

      (13) Methods:

      The authors should double-check if they used sirn and LNA gapmers at 25 and 50um concentrations, as that is a huge dose. Most papers used these reagents in the range of 5-50nM maximum.

      We apologize for the typo, the text has been fixed. We performed the experiments at 25 and 50nM, respectively, as suggested by the manufacturer’s protocol.

      (14) Discussion:

      Which cell lines were used in reference 27 (Cheng et al., 2024 Cell) to study the role of SNORA13? It may be useful to include this in the discussion.

      We already mentioned the cell system in the discussion, and now we edited to include the specific cell line that was used:

      “A recent study found that SNORA13 negatively regulates ribosome biogenesis in TERT-immortalized human fibroblasts (BJ-HRAS<Sup>G12V</sup>), by decreasing the incorporation of RPL23 into the maturing 60S ribosomal subunits, eventually triggering p53-mediated cellular senescence(Cheng et al., 2024).”

      Reviewer #3 (Recommendations for the authors):

      Major comments on weaknesses:

      (1) The paper is quite disjointed:

      (a) Figures1/2 studied the cis- and potential trans target genes altered by EPB41L4A-AS1 knockdown. They also showed some data about EPB41L4A-AS1 overlaps a strong chromatin boundary.

      (b) Figures3/4/5 studied the role of SUB1 - as it is altered by EPB41L4A-AS1 knockdown - in affecting genes and snoRNAs, which may partially underlie the gene/snoRNA changes after EPB41L4A-AS1 knockdown.

      (c) Figure 6 showed that EPB41L4A-AS1 knockdown did not directly affect SNORA13, the snoRNA located in the intron of EPB41L4A-AS1. Thus, the upregulation of many snoRNAs is not due to SNORA13.

      (d) Figure 7 studied whether the changes of cis genes or snoRNAs are due to transcriptional stability.

      (e) Figure 8 studied cellular phenotypes after EPB41L4A-AS1 knockdown.

      These points are overly spread out and this dilutes the central theme of these results, which this Reviewer considered to be on cis or trans gene regulation by this lncRNA.The title of the paper implies EPB41L4A-AS1 knockdown affected trans target genes, but the paper did not focus on studying cis or trans effects, except briefly mentioning that many genes were changed in Figure 2. The many changes of snoRNAs are suggested to be partially explained by SUB1, but SUB1 itself is affected (>50%, Figure 3B) by EPB41L4A-AS1 knockdown, so it is unclear if these are mostly secondary changes due to SUB1 reduction. Given the current content of the paper, the authors do not have sufficient evidence to support that the changes of trans genes are due to direct effects or indirect effects. And so they are encouraged to revise their title to be more on snoRNA regulation, as this area took the majority of the efforts in this paper.

      We respectfully disagree with the reviewer. We show that the effect on the proximal genes are cis-acting, as they are not rescued by exogenous expression, whereas the majority of the changes observed in the RNA-seq datasets appear to be indirect, and the snoRNA changes, that indeed might be indirect and not necessarily involve direct interaction partners of the lncRNA, such as SUB1, appear to be trans-regulated, as they can be rescued partially by exogenous expression of the lncRNA. We also show that KD of the main cis-regulated gene, EPB41L4A, results in a much milder transcriptional response, further solidifying the contribution of trans-acting effects. While we agree that the snoRNA effects are interesting, we do not consider them to be the main result, as they are accompanied by many additional changes in gene expression, and changes in the subnuclear distribution of the key nucleolar proteins, so it is difficult for us to claim that EPB41L4A-AS1 is specifically relevant to the snoRNAs rather than to the more broad nucleolar biology. Therefore, we prefer not to mention snoRNAs specifically in the title.

      (2) EPB41L4A-AS1 knockdown caused ~2,364 gene changes. This is a very large amount of change on par with some transcriptional factors. It thus needs more scrutiny. First, on Page 9, second paragraph, the authors used|log2Fold-change| >0.41 to select differential genes, which is an unusual cutoff. What is the rationale? Often |log2Fold-change| >1 is more common. How many replicates are used? To examine how many gene changes are likely direct target genes, can the authors show how many of the cist-genes that are changed by EPB41L4A-AS1 knockdown have direct chromatin contacts with EPB41L4A-AS1 in HiC data? Is there any correlation between HiC contact with their fold changes? Without a clear explanation of cis target genes as direct target genes, it is more difficult to establish whether any trans target genes are directly affected by EPB41L4A-AS1 knockdown.

      A |log<sub>2</sub>Fold-change| >0.41 equals a change of 33% or more, which together with an adjusted P < 0.05 is a threshold that has been used in the past. All RNA-seq experiments have been performed in triplicates, in line with the standards in the field. While it is possible that the EPB41L4A-AS1 establishes multiple contacts in trans—a process that has been observed in at least another lncRNA, namely Firre but involving its mature RNA product—we do believe this to be less likely that the alternative, namely that the > 2,000 DEGs are predominantly result from secondary changes rather than genes directly regulated by EPB41L4A-AS1 contacts.

      In any case, we have inspected our UMI-4C data to identify other genes exhibiting higher contact frequencies than background levels, and thus, potentially regulated in cis. To this end, we calculated the UMI-4C coverage in a 10kb window centered around the TSS of the genes located on chromosome 5, which we subsequently normalized based on the distance from EPB41L4A-AS1, in order to account for the intrinsic higher DNA recovery the closer to the target DNA sequence. However, in our UMI-4C experiment we have employed baits targeting three different genes—EPB41L4A-AS1, EPB41L4A and STARD4—and therefore such approach assumes that the lncRNA locus has the most regulatory features in this region. As expected, we detected a strong negative correlation between the normalized coverage and the distance from the EPB41L4A-AS1 locus (⍴ = -0.51, p-value < 2.2e-16), and the genes in the two neighboring TADs exhibited the strongest association with the bait region (Author response image 5). The genes that we see are down-regulated in the adjacent TADs, namely NREP, MCC and MAN2A1 (Fig. 2F) show substantially higher contacts than background with the EPB41L4A-AS1 gene, thus potentially constituting additional cis-regulated targets of this lncRNA. We note that both SUB1 and NPM1 are located on chromosome 5 as well, albeit at distances exceeding 75 and 50 Mb, respectively, and they do not exhibit any striking association with the lncRNA locus.

      Author response image 5.

      UMI-4C coverage over the TSS of the genes located on chromosome 5. (A) Correlation between the normalized UMI-4C coverage over the TSS (± 5kb) of chromosome 5 genes and the absolute distance (in megabases, Mb) from EPB41L4A-AS1. (B) Same as in (A), but with the x axis showing the relative distance from EPB41L4A-AS1. In both cases, the genes in the two flanking TADs are colored in red and their names are reported.

      To increase the confidence in our RNA-seq data, we have now performed another round of polyA+ RNA-seq following EPB41L4A-AS1 knockdown using LNA1 or LNA2, as well as the previously used and an additional control GapmeR. The FPKMs of the control samples are highly-correlated both within replicates and between GapmeRs (Fig. S6A). More importantly, the fold-changes to control are highly correlated between the two on-target GapmeRs LNA1 and LNA2, regardless of the GapmeR used for normalization (Fig. S6B), thus showing that despite significant GapmeR-specific effects, the bulk of the response is shared and likely the direct result of the reduction in the levels of EPB41L4A-AS1. Notably, key targets NPM1 and MTREX (see discussion, Fig. S12A-C and comments to Reviewer 3) were found to be downregulated by both LNAs (Fig. S6C).

      However, we acknowledge that some of the dysregulated genes are observed only when using one GapmeR and not the other, likely due to a combination of indirect, secondary and non-specific effects, and as such it is difficult without short time-course experiments (Much et al., 2024) to infer the direct response. Supporting this, LNA2 yielded a total of 1,069 DEGs (617 up and 452 down) and LNA1 2,493 DEGs (1,328 up and 1,287 down), with the latter triggering a stronger response most likely as a result of the previously mentioned CDKN1A/p21 induction. Overall, 45.1% of the upregulated genes following LNA2 transfection were shared with LNA1, in contrast to only the 24.3% of the downregulated ones.

      We have now included these results in the Results section (see below) and in Supplementary Figure (Fig. S6).

      “Most of the consequences of the depletion of EPB41L4A-AS1 are thus not directly explained by changes in EPB41L4A levels. An additional trans-acting function for EPB41L4A-AS1 would therefore be consistent with its high expression levels compared to most lncRNAs detected in MCF-7 (Fig. S5G). To strengthen these findings, we have transfected MCF-7 cells with LNA1 and a second control GapmeR (NT2), as well as the previous one (NT1) and LNA2, and sequenced the polyadenylated RNA fraction as before. Notably, the expression levels (in FPKMs) of the replicates of both control samples are highly correlated with each other (Fig. S6A), and the global transcriptomic changes triggered by the two EPB41L4A-AS1-targeting LNAs are largely concordant (Fig. S6B and S6C). Because of this concordance and the cleaner (i.e., no CDKN1A upregulation) readout in LNA2-transfected cells, we focused mainly on these cells for subsequent analyses.”

      Figure 3B, SUB1 mRNA is reduced >half by EPB41L4A-AS1 KD. How much did SUB1 protein reduce after EPB41L4A-AS1 KD? Similarly, how much is the NPM1 protein reduced? If these two important proteins were affected by EPB41L4A-AS1 KD simultaneously, it is important to exclude how many of the 2,364 genes that changed after EPB41L4A-AS1 KD are due to the protein changes of these two key proteins. For SUB1, Figures S7E,F,G provided some answers. But NPM1 KD is also needed to fully understand such. Related to this, there are many other proteins perhaps changed in addition to SUB1 and NPM1, this renders it concerning how many of the EPB41L4A-AS1 KD-induced changes are directly caused by this RNA. In addition to the suggested study of cist targets, the alternative mechanism needs to be fully discussed in the paper as it remains difficult to fully conclude direct versus indirect effect due to such changes of key proteins or ncRNAs (such as snoRNAs or histone mRNAs).

      As requested by both Reviewer #2 and #3, we have performed WB for SUB1, NPM1 and FBL following EPB41L4A-AS1 KD with two targeting (LNA1 and LNA2) and the previous control GapmeRs. Interestingly, we did not detect any significant downregulation of either proteins (Author response image 3), although this might be the result of the high variability observed in the control samples. Moreover, the short timeframe in which the experiments have been conducted━that is, transient transfections for 3 days━might not be sufficient time for the existing proteins to be degraded, and thus, the downregulation is more evident at the RNA (Fig. 3B and Supplementary Figure 6C) rather than protein level.

      We acknowledge that many proteins might change simultaneously, and to pinpoint which ones act upstream of the plethora of indirect changes is extremely challenging when considering such large-scale changes in gene expression. In the case of SUB1 and NPM1━which were prioritized for their predicted binding to the lncRNA (Fig. 3A)━we show that the depletion of the former affects the latter in a similar way than that of the lncRNA (Fig. 5F). Moreover, snoRNAs changes are also similarly affected (as the reviewer pointed out, Fig. 4F), suggesting that at least this phenomenon is predominantly mediated by SUB1. Other effects might also be indirect consequences of cellular responses, such as the decrease in histone mRNAs (Fig. 4A) that might reflect the decrease in cellular replication (Fig. 8C) and cell cycle genes (Fig. 2I) (although a link between SUB1 and histone mRNA expression has been described (Brzek et al., 2018)). 

      Supporting the notion that additional proteins might be involved in driving the observed phenotypes, one of the genes that most consistently was affected by EPB41L4A-AS1 KD with GapmeRs is MTREX (also known as MTR4), that becomes downregulated at both the RNA and protein levels (now presented in the main text as Supplementary Figure 12). MTREX it’s part of the NEXT and PAXT complexes (Contreras et al., 2023), that target several short-lived RNAs for degradation, and the depletion of either MTREX or other complex members leads to the upregulation of such RNAs, that include PROMPTs, uaRNAs and eRNAs, among others. Given the lack in our understanding in snoRNA biogenesis from introns in mammalian systems(Monziani & Ulitsky, 2023), it is tempting to hypothesize a role for MTREX-containing complexes in trimming and degrading those introns and release the mature snoRNAs.  

      We updated the discussion section to include these observations:

      “Beyond its site of transcription, EPB41L4A-AS1 associates with SUB1, an abundant protein linked to various functions, and these two players are required for proper distribution of various nuclear proteins. Their dysregulation results in large-scale changes in gene expression, including up-regulation of snoRNA expression, mostly through increased transcription of their hosts, and possibly through a somewhat impaired snoRNA processing and/or stability. To further hinder our efforts in discerning between these two possibilities, the exact molecular pathways involved in snoRNAs biogenesis, maturation and decay are still not completely understood. One of the genes that most consistently was affected by EPB41L4A-AS1 KD with GapmeRs is MTREX (also known as MTR4), that becomes downregulated at both the RNA and protein levels (Fig. S12A-C). Interestingly, MTREX it is part of the NEXT and PAXT complexes(Contreras et al., 2023), that target several short-lived RNAs for degradation, and the depletion of either MTREX or other complex members leads to the upregulation of such RNAs, that include PROMPTs, uaRNAs and eRNAs, among others. It is therefore tempting to hypothesize a role for MTREX-containing complexes in trimming and degrading those introns, and releasing the mature snoRNAs. Future studies specifically aimed at uncovering novel players in mammalian snoRNA biology will both conclusively elucidate whether MTREX is indeed involved in these processes.”

      With regards to the changes in gene expression between the two LNAs, we provide a more detailed answer above and to the other reviewers as well.

      (3) A Strong discrepancy of results by different approaches of knockdown or overexpression:

      (a) CRISPRa versus LNA knockdown: Figure S4 - CRISPRa of EPB41L4A-AS1 did not affect EPB41L4A expression (Figure S4B). The authors should discuss how to interpret this result. Did CRISPRa not work to increase the nuclear/chromatin portion of EPB41L4A-AS1? Did CRISPRa of EPB41L4A-AS1 affect the gene in the upstream, the STARD4? Did CRISPRa of EPB41L4A-AS1 also affect chromatin interactions between EPB41L4A-AS1 and the EPB41L4A gene? If so, this may argue that chromatin interaction is not necessary for cis-gene regulation.

      There are indeed several possible explanations, the most parsimonious is that since the lncRNA is already very highly transcribed, the relatively modest effect of additional transcription mediated by CRISPRa is not sufficient to elicit a measurable effect. For this reason, we did not check by UMI-4C the contact frequency between the lncRNA and EPB41L4A upon CRISPRa.

      CRISPRa augments transcription at target loci, and thus, the nuclear and chromatin retention of EPB41L4A-AS1 are not expected to be affected. We did not check the expression of STARD4, because we focused on EPB41L4A which appears to be the main target locus according to Hi-C (Fig. 2A), UMI-4C (Fig. 2E and S4J) and GeneHancer (Fig. S1). 

      We already provide extensive evidence of a cis-regulation of EPB41L4A-AS1 over EPB41L4A, and show that EPB41L4A is lowly-expressed and likely has a limited role in our experimental settings. Thus, we respectfully propose that an in-deep exploration of the mechanism of action of this regulatory axis is out of scope of the current study, that instead focused more on the global effects of EPB41L4A-AS1 perturbation.

      (b) Related to this, while CRISPRa alone did not show an effect, upon LNA knockdown of EPB41L4A-AS1, CRISPRa of EPB41L4A-AS1 can increase EPB41L4A expression. It is perplexing as to why, upon LNA treatment, CRISPRa will show an effect (Figure S4H)? Actually, Figures S4H and I are very confusing in the way they are currently presented. They will benefit from being separated into two panels (H into 2 and I into two). And for Ectopic expression, please show controls by empty vector versus EPB41L4A-AS1, and for CRISPRa, please show sgRNA pool versus sgRNA control.

      The results are consistent with the parsimonious assumption mentioned above that the high transcription of the lncRNA at baseline is sufficient for maximal positive regulation of EPB41L4A, and that upon KD, the reduced transcription and/or RNA levels are no longer at saturating levels, and so CRISPRa can have an effect. We now mention this interpretation in the text:

      “Levels of EPB41L4A were not affected by increased expression of EPB41L4A-AS1 from the endogenous locus by CRISPR activation (CRISPRa), nor by its exogenous expression from a plasmid (Fig. S4B and S4C). The former suggests that endogenous levels of EPB41L4A-AS1—that are far greater than those of EPB41L4A—are sufficient to sustain the maximal expression of this target gene in MCF7 cells.”

      We apologize for the confusion regarding the control used in the rescue experiments in Fig. S4H and S4I. The “-” in the Ectopic overexpression and CRISPRa correspond to the Empty Vector and sgControl, respectively, and not the absence of any vector. We changed the text in the figure legends:

      “(H) Changes in EPB41L4A-AS1 expression after rescuing EPB41L4A-AS1 with an ectopic plasmid or CRISPRa following its KD with GapmeRs. In both panels (Ectopic OE and CRISPRa) the “-” samples represent those transfected with the Empty Vector or sgControl. Asterisks indicate significance relative to the –/– control (transfected with both the control GapmeR and vector). (I) Same as in (H), but for changes in EPB41L4A expression.”

      (c) siRNA versus LNA knockdown: Figure S3A showed that siRNA KD of EPB41L4A-AS1 does not affect EPB41L4A expression. How to understand this data versus LNA?

      As explained in the text, siRNA-mediated KD presumably affects mostly the cytoplasmic pool of EPB41L4A-AS1 and not the nuclear one, which we assume explains the different effects of the two perturbations, as observed for other lncRNAs (e.g., (Ntini et al., 2018)). However, we acknowledge that we do not know what aspect of the nuclear RNA biology is relevant, let it be the nascent EPB41L4A-AS1 transcription, premature transcriptional termination or even the nuclear pool of this lncRNA, and this can be elucidated further in future studies.

      (d) EPB41L4A-AS1 OE versus LNA knockdown: Figure 6F showed that EPB41L4A-AS1 OE caused reduction of EPB41L4A mRNA, particularly at 24hr. How to interpret that both LNA KD and OE of EPB41L4A-AS1 reduce the expression of EPB41L4A mRNA?

      We do not believe that the OE of EPB41L4A-AS1, and in particular the one elicited by an ectopic plasmid affects EPB41L4A RNA levels. In the experiment in Fig. 6F, EPB41L4A relative expression at 24h is ~0.65 (please note the log<sub>2</sub> scale in the graph), which is significant as reported. However, throughout this study (and as shown in Fig. S4C for the ectopic and Fig. S4B for the CRISPRa overexpression, respectively), we observed no such behavior, suggesting that the effect reported in Fig. 6F is the result of either that particular setting, and unlikely to reflect a general phenomenon.

      (e) Did any of the effects on snoRNAs or trans target genes after EPB41L4A-AS1 knockdown still appear by CRISPRa?

      As mentioned above, we did a limited number of experiments after CRISPRa, prompted by the fact that endogenous levels of EPB41L4A-AS1 are already high enough to sustain its functions. Pushing the expression even higher will likely result in no or artifactual effects, which is why we respectfully propose such experiments are not essential in this current work, which instead mostly relies on loss-of-function experiments.

      For issue 3, extensive data repetition using all these methods may be unrealistic, but key data discrepancy needs to be fully discussed and interpreted.

      Other comments on weakness:

      (1) This manuscript will benefit from having line numbers so comments from Reviewers can be made more specifically.

      We added line numbers as suggested by the reviewer.

      (2) Figure 2G, to distinguish if any effects of EPB41L4A-AS1 come from the cytoplasmic or nuclear portion of EPB41L4A-AS1, an siRNA KD RNA-seq will help to filter out the genes affected by EPB41L4A-AS1 in the cytoplasm, as siRNA likely mainly acts in the cytoplasm.

      This experiment would be difficult to interpret as while the siRNAs mostly deplete the cytoplasmic pool of their target, they can have some effects in the nucleus as well (e.g., (Sarshad et al., 2018)) and so siRNAs knockdown will not necessarily report strictly on the cytoplasmic functions.

      (3) Figure 2H, LNA knockdown of EPB41L4A should check the protein level reduction, is it similar to the change caused by knockdown of EPB41L4A-AS1?

      As suggested by reviewer #2, we have now replaced the EPB41L4A Western Blot that now shows the results with both LNA1 and LNA2. Please note that the previous Fig. 2C was a subset of this, i.e., we have previously cropped the results obtained with LNA1. Unfortunately, we did not have sufficient antibody to check for EPB41L4A protein reduction following LNA KD of EPB41L4A in a timely manner.

      (4) There are two LNA Gapmers used by the paper to knock down EPB41L4A-AS1, but some figures used LNA1, some used LNA2, preventing a consistent interpretation of the results. For example, in Figures 2A-D, LNA2 was used. But in Figures 2E-H, LNA1 was used. How consistent are the two in changing histone H3K27ac (like in Figure 2D) versus gene expression in RNA-seq? The changes in chromatin interaction appear to be weaker by LNA2 (Figure S4J) versus LNA1 (Figure 2E).

      As explained above and in response to Reviewer #1, we now provide more RNA-seq data for LNA1 and LNA2. We note that besides the unwanted and/or off-target effects, these two GapmeRs might be not equally effective in knocking down EPB41L4A-AS1, which could explain why LNA1 seems to have a stronger effect on chromatin than LNA2. Nonetheless, when we have employed both we have obtained similar and consistent results (e.g., Fig. 5A-D and 8A-C), suggesting that these and the other effects are indeed on target effects due to EPB41L4A-AS1 depletion.

      (5) It will be helpful if the authors provide information on how long they conducted EPB41L4A-AS1 knockdown for most experiments to help discern direct or indirect effects.

      The length of all perturbations was indicated in the Methods section, and we now mention them also  in the Results. Unless specified otherwise, they were carried out for 72 hours. We agree with the reviewer that having time course experiments can have added value, but due to the extensive effort that these will require, we suggest that they are out of scope of the current study.

      (6) In Figures 1C and F, the authors showed results about EPB41L4A-AS1 overlapping a strong chromatin boundary. But these are not mentioned anymore in the later part of the paper. Does this imply any mechanism? Does EPB41L4A-AS1 knockdown or OE, or CRISPRa affect the expression of genes near the other interacting site, STARD4? Do genes located in the two adjacent TADs change more strongly as compared to other genes far away?

      We discuss this point in the Discussion section:

      “At the site of its own transcription, which overlaps a strong TAD boundary, EPB41L4A-AS1 is required to maintain expression of several adjacent genes, regulated at the level of transcription. Strikingly, the promoter of EPB41L4A-AS1 ranks in the 99.8th percentile of the strongest TAD boundaries in human H1 embryonic stem cells(Open2C et al., 2024; Salnikov et al., 2024). It features several CTCF binding sites (Fig. 2A), and in MCF-7 cells, we demonstrate that it blocks the propagation of the 4C signal between the two flanking TADSs (Fig. 1F). Future studies will help elucidate how EPB41L4A-AS1 transcription and/or the RNA product regulate this boundary. So far, we found that EPB41L4A-AS1 did not affect CTCF binding to the boundary, and while some peaks in the vicinity of EPB41L4A-AS1 were significantly affected by its loss, they did not appear to be found near genes that were dysregulated by its KD (Fig. S11C). We also found that KD of EPB41L4A-AS1—which depletes the RNA product, but may also affect the nascent RNA transcription(Lai et al., 2020; Lee & Mendell, 2020)—reduces the spatial contacts between the TAD boundary and the EPB41L4A promoter (Fig. 2E). Further elucidation of the exact functional entity needed for the cis-acting regulation will require detailed genetic perturbations of the locus, that are difficult to carry out in the polypoid MCF-7 cells, without affecting other functional elements of this locus or cell survival as we were unable to generate deletion clones despite several attempts.”

      As mentioned in the text (pasted below) and in Fig. 2F, most genes in the two flanking TADs become downregulated following EPB41L4A-AS1 KD. While STARD4 – which was chosen because it had spatial contacts above background with EPB41L4A-AS1 – did not reach statistical significance, others did and are highlighted. Those included NREP, which we also discuss:

      “Consistently with the RT-qPCR data, KD of EPB41L4A-AS1 reduced EPB41L4A expression, and also reduced expression of several, but not all other genes in the TADs flanking the lncRNA (Fig. 2F).Based on these data, EPB41L4A-AS1 is a significant cis-acting activator according to TransCistor (Dhaka et al., 2024) (P=0.005 using the digital mode). The cis-regulated genes reduced by EPB41L4A-AS1 KD included NREP, a gene important for brain development, whose homolog was downregulated by genetic manipulations of regions homologous to the lncRNA locus in mice(Salnikov et al., 2024). Depletion of EPB41L4A-AS1 thus affects several genes in its vicinity.”

      (7) Related to the description of SUB1 regulation of genes are DNA and RNA levels: "Of these genes, transcripts of only 56 genes were also bound by SUB1 at the RNA level, suggesting largely distinct sets of genes targeted by SUB1 at both the DNA and the RNA levels." SUB1 binding to chromatin by Cut&Run only indicates that it is close to DNA/chromatin, and this interaction with chromatin may still likely be mediated by RNAs. The authors used SUB1 binding sites in eCLIP-seq to suggest whether it acts via RNAs, but these binding sites are often from highly expressed gene mRNAs/exons. Standard analysis may not have examined low-abundance RNAs close to the gene promoters, such as promoter antisense RNAs. The authors can examine whether, for the promoters with cut&run peaks of SUB1, SUB1 eCLIP-seq shows binding to the low-abundance nascent RNAs near these promoters.

      In response to a related comment by Reviewer 1, we now show that when considering expression level–matched control genes, knockdown of EPB41L4A-AS1 still significantly affects expression of SUB1 targets over controls. The results are presented in Supplementary Figure 7 (Fig. S7C).

      Based on this analysis, while there is a tendency of increased expression with increased SUB1 binding, when controlling for expression levels the effect of down-regulation of SUB1-bound RNAs upon lncRNA knockdown remains, suggesting that it is not merely a confounding effect. We have updated the text as follows:

      “We hypothesized that loss of EPB41L4A-AS1 might affect SUB1, either via the reduction in its expression or by affecting its functions. We stratified SUB1 eCLIP targets into confidence intervals, based on the number, strength and confidence of the reported binding sites. Indeed, eCLIP targets of SUB1 (from HepG2 cells profiled by ENCODE) were significantly downregulated following. EPB41L4A-AS1 KD in MCF-7, with more confident targets experiencing stronger downregulation (Fig. 3C). Importantly, this still holds true when controlling for gene expression levels (Fig. S7C), suggesting that this negative trend is not due to differences in their baseline expression.”

      (8) Figure 8, the cellular phenotype is interesting. As EPB41L4A-AS1 is quite widely expressed, did it affect the phenotypes similarly in other breast cancer cells? MCF7 is not a particularly relevant metastasis model. Can a similar phenotype be seen in commonly used metastatic cell models such as MDA-MB-231?

      We agree that further expanding the models in which EPB41L4A-AS1 affects cellular proliferation, migration and any other relevant phenotype is of potential interest before considering targeting this lncRNA as a therapeutic approach. However, given that 1) others have already identified similar phenotypes upon the modulation of EPB41L4A-AS1 in a variety of different systems (see Results and Discussion), and 2) we were most interested in the molecular consequences following the loss of this lncRNA, we respectfully suggest that these experiments are out of scope of the current study.

      References

      Bahar Halpern, K., Caspi, I., Lemze, D., Levy, M., Landen, S., Elinav, E., Ulitsky, I., & Itzkovitz, S. (2015). Nuclear Retention of mRNA in Mammalian Tissues. Cell Reports, 13(12), 2653–2662.

      Brabletz, T., Kalluri, R., Nieto, M. A., & Weinberg, R. A. (2018). EMT in cancer. Nature Reviews. Cancer, 18(2), 128–134.

      Brzek, A., Cichocka, M., Dolata, J., Juzwa, W., Schümperli, D., & Raczynska, K. D. (2018). Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression. BMC Molecular Biology, 19(1), 9.

      Cheng, Y., Wang, S., Zhang, H., Lee, J.-S., Ni, C., Guo, J., Chen, E., Wang, S., Acharya, A., Chang, T.-C., Buszczak, M., Zhu, H., & Mendell, J. T. (2024). A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence. Cell, 187(17), 4770–4789.e23.

      Conesa, C., & Acker, J. (2010). Sub1/PC4 a chromatin associated protein with multiple functions in transcription. RNA Biology, 7(3), 287–290.

      Contreras, X., Depierre, D., Akkawi, C., Srbic, M., Helsmoortel, M., Nogaret, M., LeHars, M., Salifou, K., Heurteau, A., Cuvier, O., & Kiernan, R. (2023). PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs. Nature Communications, 14(1), 6745.

      Costea, J., Schoeberl, U. E., Malzl, D., von der Linde, M., Fitz, J., Gupta, A., Makharova, M., Goloborodko, A., & Pavri, R. (2023). A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination. Molecular Cell, 83(5), 681–697.e7.

      Das, C., Hizume, K., Batta, K., Kumar, B. R. P., Gadad, S. S., Ganguly, S., Lorain, S., Verreault, A., Sadhale, P. P., Takeyasu, K., & Kundu, T. K. (2006). Transcriptional coactivator PC4, a chromatin-associated protein, induces chromatin condensation. Molecular and Cellular Biology, 26(22), 8303–8315.

      Dhaka, B., Zimmerli, M., Hanhart, D., Moser, M. B., Guillen-Ramirez, H., Mishra, S., Esposito, R., Polidori, T., Widmer, M., García-Pérez, R., Julio, M. K., Pervouchine, D., Melé, M., Chouvardas, P., & Johnson, R. (2024). Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates. Nucleic Acids Research, 52(6), 2821–2835.

      Didiot, M.-C., Ferguson, C. M., Ly, S., Coles, A. H., Smith, A. O., Bicknell, A. A., Hall, L. M., Sapp, E., Echeverria, D., Pai, A. A., DiFiglia, M., Moore, M. J., Hayward, L. J., Aronin, N., & Khvorova, A. (2018). Nuclear Localization of Huntingtin mRNA Is Specific to Cells of Neuronal Origin. Cell Reports, 24(10), 2553–2560.e5.

      Dongre, A., & Weinberg, R. A. (2019). New insights into the mechanisms of epithelial-mesenchymal transition and implications for cancer. Nature Reviews. Molecular Cell Biology, 20(2), 69–84.

      Dubois, J.-C., Bonnell, E., Filion, A., Frion, J., Zimmer, S., Riaz Khan, M., Teplitz, G. M., Casimir, L., Méthot, É., Marois, I., Idrissou, M., Jacques, P.-É., Wellinger, R. J., & Maréchal, A. (2025). The single-stranded DNA-binding factor SUB1/PC4 alleviates replication stress at telomeres and is a vulnerability of ALT cancer cells. Proceedings of the National Academy of Sciences of the United States of America, 122(2), e2419712122.

      Garavís, M., & Calvo, O. (2017). Sub1/PC4, a multifaceted factor: from transcription to genome stability. Current Genetics, 63(6), 1023–1035.

      Gil, N., & Ulitsky, I. (2020). Regulation of gene expression by cis-acting long non-coding RNAs. Nature Reviews. Genetics, 21(2), 102–117.

      Hou, Y., Gan, T., Fang, T., Zhao, Y., Luo, Q., Liu, X., Qi, L., Zhang, Y., Jia, F., Han, J., Li, S., Wang, S., & Wang, F. (2022). G-quadruplex inducer/stabilizer pyridostatin targets SUB1 to promote cytotoxicity of a transplatinum complex. Nucleic Acids Research, 50(6), 3070–3082.

      Jan, C. H., Friedman, R. C., Ruby, J. G., & Bartel, D. P. (2011). Formation, regulation and evolution of Caenorhabditis elegans 3’UTRs. Nature, 469(7328), 97–101.

      Kaypee, S., Ochiai, K., Shima, H., Matsumoto, M., Alam, M., Ikura, T., Kundu, T. K., & Igarashi, K. (2025). Positive coactivator PC4 shows dynamic nucleolar distribution required for rDNA transcription and protein synthesis. Cell Communication and Signaling : CCS, 23(1), 283.

      Lai, F., Damle, S. S., Ling, K. K., & Rigo, F. (2020). Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination. Molecular Cell, 77(5), 1032–1043.e4.

      Lee, J.-S., & Mendell, J. T. (2020). Antisense-Mediated Transcript Knockdown Triggers Premature Transcription Termination. Molecular Cell, 77(5), 1044–1054.e3.

      Lubelsky, Y., & Ulitsky, I. (2018). Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature, 555(7694), 107–111.

      Ly, S., Didiot, M.-C., Ferguson, C. M., Coles, A. H., Miller, R., Chase, K., Echeverria, D., Wang, F., Sadri-Vakili, G., Aronin, N., & Khvorova, A. (2022). Mutant huntingtin messenger RNA forms neuronal nuclear clusters in rodent and human brains. Brain Communications, 4(6), fcac248.

      Maranon, D. G., & Wilusz, J. (2020). Mind the Gapmer: Implications of Co-transcriptional Cleavage by Antisense Oligonucleotides. Molecular Cell, 77(5), 932–933.

      Monziani, A., & Ulitsky, I. (2023). Noncoding snoRNA host genes are a distinct subclass of long noncoding RNAs. Trends in Genetics : TIG, 39(12), 908–923.

      Mortusewicz, O., Roth, W., Li, N., Cardoso, M. C., Meisterernst, M., & Leonhardt, H. (2008). Recruitment of RNA polymerase II cofactor PC4 to DNA damage sites. The Journal of Cell Biology, 183(5), 769–776.

      Much, C., Lasda, E. L., Pereira, I. T., Vallery, T. K., Ramirez, D., Lewandowski, J. P., Dowell, R. D., Smallegan, M. J., & Rinn, J. L. (2024). The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation. Nature Communications, 15(1), 6821.

      Ntini, E., Louloupi, A., Liz, J., Muino, J. M., Marsico, A., & Ørom, U. A. V. (2018). Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin. Nature Communications, 9(1), 1636.

      Oo, J. A., Warwick, T., Pálfi, K., Lam, F., McNicoll, F., Prieto-Garcia, C., Günther, S., Cao, C., Zhou, YGavrilov, A. A., Razin, S. V., Cabrera-Orefice, A., Wittig, I., Pullamsetti, S. S., Kurian, L., Gilsbach, R., Schulz, M. H., Dikic, I., Müller-McNicoll, M., … Leisegang, M. S. (2025). Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers. Nature Communications, 16(1), 131.

      Open2C, Abdennur, N., Abraham, S., Fudenberg, G., Flyamer, I. M., Galitsyna, A. A., Goloborodko, A., Imakaev, M., Oksuz, B. A., Venev, S. V., & Xiao, Y. (2024). Cooltools: Enabling high-resolution Hi-C analysis in Python. PLoS Computational Biology, 20(5), e1012067.

      Potapova, T. A., Unruh, J. R., Conkright-Fincham, J., Banks, C. A. S., Florens, L., Schneider, D. A., & Gerton, J. L. (2023). Distinct states of nucleolar stress induced by anticancer drugs. https://doi.org/10.7554/eLife.88799.

      Ray, D., Laverty, K. U., Jolma, A., Nie, K., Samson, R., Pour, S. E., Tam, C. L., von Krosigk, N., Nabeel-Shah, S., Albu, M., Zheng, H., Perron, G., Lee, H., Najafabadi, H., Blencowe, B., Greenblatt, J., Morris, Q., & Hughes, T. R. (2023). RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Scientific Reports, 13(1), 5238.

      Salgado, S., Abreu, P. L., Moleirinho, B., Guedes, D. S., Larcombe, L., & Azzalin, C. M. (2024). Human PC4 supports telomere stability and viability in cells utilizing the alternative lengthening of telomeres mechanism. EMBO Reports, 25(12), 5294–5315.

      Salnikov, P., Korablev, A., Serova, I., Belokopytova, P., Yan, A., Stepanchuk, Y., Tikhomirov, S., & Fishman, V. (2024). Structural variants in the Epb41l4a locus: TAD disruption and Nrep gene misregulation as hypothetical drivers of neurodevelopmental outcomes. Scientific Reports, 14(1), 5288.

      Sarshad, A. A., Juan, A. H., Muler, A. I. C., Anastasakis, D. G., Wang, X., Genzor, P., Feng, X., Tsai, P.-F., Sun, H.-W., Haase, A. D., Sartorelli, V., & Hafner, M. (2018). Argonaute-miRNA Complexes Silence Target mRNAs in the Nucleus of Mammalian Stem Cells. Molecular Cell, 71(6), 1040–1050.e8.

      Tafforeau, L., Zorbas, C., Langhendries, J.-L., Mullineux, S.-T., Stamatopoulou, V., Mullier, R., Wacheul, L., & Lafontaine, D. L. J. (2013). The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of Pre-rRNA processing factors. Molecular Cell, 51(4), 539–551.

      Unfried, J. P., & Ulitsky, I. (2022). Substoichiometric action of long noncoding RNAs. Nature Cell Biology, 24(5), 608–615.

      Van Nostrand, E. L., Freese, P., Pratt, G. A., Wang, X., Wei, X., Xiao, R., Blue, S. M., Chen, J.-Y.,Cody, N. A. L., Dominguez, D., Olson, S., Sundararaman, B., Zhan, L., Bazile, C., Bouvrette, L. P. B., Bergalet, J., Duff, M. O., Garcia, K. E., Gelboin-Burkhart, C., … Yeo, G. W. (2020). A large-scale binding and functional map of human RNA-binding proteins. Nature, 583(7818), 711–719.

      Yang, K., Wang, M., Zhao, Y., Sun, X., Yang, Y., Li, X., Zhou, A., Chu, H., Zhou, H., Xu, J., Wu, M., Yang, J., & Yi, J. (2016). A redox mechanism underlying nucleolar stress sensing by nucleophosmin. Nature Communications, 7, 13599.

      Youssef, K. K., Narwade, N., Arcas, A., Marquez-Galera, A., Jiménez-Castaño, R., Lopez-Blau, C., Fazilaty, H., García-Gutierrez, D., Cano, A., Galcerán, J., Moreno-Bueno, G., Lopez-Atalaya, J. P., & Nieto, M. A. (2024). Two distinct epithelial-to-mesenchymal transition programs control invasion and inflammation in segregated tumor cell populations. Nature Cancer, 5(11), 1660–1680.

      Yu, L., Ma, H., Ji, X., & Volkert, M. R. (2016). The Sub1 nuclear protein protects DNA from oxidative damage. Molecular and Cellular Biochemistry, 412(1-2), 165–171.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Public Reviews: 

      Reviewer #1 (Public review): 

      Summary: 

      In their previous publication (Dong et al. Cell Reports 2024), the authors showed that citalopram treatment resulted in reduced tumor size by binding to the E380 site of GLUT1 and inhibiting the glycolytic metabolism of HCC cells, instead of the classical citalopram receptor. Given that C5aR1 was also identified as the potential receptors of citalopram in the previous report, the authors focused on exploring the potential of immune-dependent anti-tumor effect of citalopram via C5aR1. C5aR1 was found to be expressed on tumor-associated macrophages (TAMs) and citalopram administration showed potential to improve the stability of C5aR1 in vitro. Through macrophage depletion and adoptive transfer approaches in HCC mouse models, the data demonstrated the potential importance of C5aR1-expressing macrophage in the anti-tumor effect of citalopram in vivo. Mechanistically, their in vitro data suggested that citalopram may regulate the phagocytosis potential and polarization of macrophages through C5aR1. Next, they tried to investigate the direct link between citalopram and CD8+T cells by including an additional MASH-associated HCC mouse model. Their data suggest that citalopram may upregulate the glycolytic metabolism of CD8+T cells, probability via GLUT3 but not GLUT1-mediated glucose uptake. Lastly, as the systemic 5-HT level is down-regulated by citalopram, the authors analyzed the association between a low 5-HT and a superior CD8+T cell function against tumor. Although the data is informative, the rationale for working on additional mechanisms and logical link among different parts are not clear. In addition, some of the conclusion is also not fully supported by the current data. 

      Strengths: 

      The idea of repurposing clinical-in-used drugs showed great potential for immediate clinical translation. The data here suggested that the anti-depression drug, citalopram displayed immune regulatory role on TAM via a new target C5aR1 in HCC. 

      Comments on revised version: 

      The authors have addressed most of my concerns about the paper.

      We thank you the reviewer. We appreciate the reviewer’s constructive suggestions that helped improve the clarity and robustness of the study.

      Reviewer #2 (Public review):

      Summary: 

      Dong et al. present a thorough investigation into the potential of repurposing citalopram, an SSRI, for hepatocellular carcinoma (HCC) therapy. The study highlights the dual mechanisms by which citalopram exerts anti-tumor effects: reprogramming tumor-associated macrophages (TAMs) toward an anti-tumor phenotype via C5aR1 modulation and suppressing cancer cell metabolism through GLUT1 inhibition, while enhancing CD8+ T cell activation. The findings emphasize the potential of drug repurposing strategies and position C5aR1 as a promising immunotherapeutic target.

      Strengths:

      It provides detailed evidence of citalopram's non-canonical action on C5aR1, demonstrating its ability to modulate macrophage behavior and enhance CD8+ T cell cytotoxicity. The use of DARTS assays, in silico docking, and gene signature network analyses offers robust validation of drug-target interactions. Additionally, the dual focus on immune cell reprogramming and metabolic suppression presents a comprehensive strategy for HCC therapy. By highlighting the potential for existing drugs like citalopram to be repurposed, the study also emphasizes the feasibility of translational applications. During revision, the authors experimentally demonstrated that TAM has lower GLUT1, which further strengthens their claim of C5aR1 modulation-dependent TAM improvement for tumor therapy.

      Weaknesses:

      The authors proposed that CD8+ T cells have an TAM-independent role upon Citalopram treatment. However, this claim requires further investigation to confirm that the effect is truly "TAM independent".

      We appreciate the reviewer’s insightful comment regarding the interpretation of CD8<sup>+</sup> T cell roles. In this study, in vitro analyses show that citalopram directly enhances CD8<sup>+</sup>T cell activity, as evidenced by increased CFSE proliferation, upregulation of activation markers, and cytotoxic effector readouts (Figures S10A–E). Accordingly, we infer a TAM-independent CD8<sup>+</sup> T cell activation by citalopram in vitro.

      Our in vivo data indicate that the primary anti-tumor mechanism of citalopram involves targeting C5aR1<sup>+</sup> TAMs, which subsequently enhances CD8<sup>+</sup> T cell immunity. This conclusion is supported by the near-complete ablation of citalopram’s therapeutic effect upon TAM depletion with clodronate liposomes (Figure S5). Additionally, citalopram reduces serum serotonin (5-HT) levels (Figure 4E), recapitulating the serotonergic state of Tph1<sup>−/−</sup> mice. Notably, the anti-tumor effect and CD8<sup>+</sup> T cell activation induced by citalopram exceed those observed in Tph1<sup>−/−</sup> mice (Figures 4G–I), suggesting that 5-HT reduction contributes to CD8<sup>+</sup> T cell activation but operates alongside other mechanisms in vivo, prominently including TAM targeting. As suggested, we further tested CD8<sup>+</sup> T cell activity in the context of macrophage depletion. The result showed that citalopram did not further enhance CD8<sup>+</sup> T cell cytotoxicity after macrophage depletion, indicating that TAM-dependent pathways are central to CD8<sup>+</sup> T cell–mediated anti-tumor immunity and largely underlie the anti-tumor effects of citalopram.

      To accurately reflect our main findings, we had made several revisions to the manuscript. First, we have revised the title to “Citalopram exhibits immune-dependent anti-tumor effects by modulating C5aR1<sup>+</sup> TAMs”. In the Results section, the Conclusions have been updated to: “These data not only corroborate recent reports that SSRIs modulate CD8<sup>+</sup> T cell function via serotonergic-dependent mechanism, but also reveals additional in vivo regulatory avenues by which citalopram affects CD8<sup>+</sup> T cells, such as its ability to reprogram C5aR1<sup>+</sup> TAMs. Notably, in the context of macrophage depletion, CD8<sup>+</sup> T cell cytotoxicity was not further enhanced by citalopram, indicating that TAM-dependent pathways are central to CD8<sup>+</sup> T cell-mediated anti-tumor immunity and largely underlie the anti-tumor effects of citalopram”. In the Discussion part, we have included the following content: “Although citalopram directly stimulates CD8<sup>+</sup> T cells in vitro, the TAM-independent activation is not evident in vivo within the complex TME, as CD8<sup>+</sup> T cell responses are abolished by macrophage depletion, indicating that the in vivo effects of citalopram on CD8<sup>+</sup> T cells and tumor growth are largely TAM-dependent”.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Fig S5 and Fig 3: To improve clarity regarding the roles of TAMs and CD8+ T cells, can the authors experimentally demonstrate the macrophage-independent function of CD8+ T cells? An experiment in Fig 3J using or not using Clodro-Liposome to deplete TAMs would be more informative.

      We thank the reviewer for the insightful suggestion. In this study, in vitro analyses show that citalopram directly enhances CD8<sup>+</sup> T cell activity, as evidenced by increased CFSE proliferation, upregulation of activation markers, and cytotoxic effector readouts (Figures S10A–E). Therefore, we conclude a TAM-independent CD8<sup>+</sup> T cell activation induced by citalopram. Previously, in Figure S5, we analyzed the therapeutic effect of citalopram after macrophage depletion by clodronate liposomes and also probed the immune profiles. The result showed that CD8<sup>+</sup> T cell cytotoxic activities were not significantly affected by citalopram in this context (Figure S5E), indicating that the TAM-dependent pathway is central to CD8<sup>+</sup> T cell-mediated anti-tumor immunity and to the anti-tumor effects of citalopram. We have incorporated this result into the revised manuscript.

      Fig S4: The figure panel showing sample/treatment annotations is missing.

      Thank you for pointing this out. We have updated Fig. S4 to include explicit sample identifiers, treatment group labels, and drug concentrations.

      Since Glut3 is vital in both TAMs and CD8+ T cells, the authors should discuss the interaction between Glut3 and Citalopram. Additionally, include details about the structural homology between Glut1 and Glut3 in the discussion.

      Thank you for the suggestion. Citalopram was docked into the GLUT1 substrate-binding pocket, with the best poses showing an electrostatic interaction centered on E380 accompanied by hydrophobic contacts within the pocket (Our previous publication, Dong et al. Cell Reports 2024). Although GLUT1 and GLUT3 share a highly conserved core substrate-binding pocket, isoform-specific regulation arises from features outside the canonical site. Structural homology between GLUT1 and GLUT3 is high in the transmembrane core, but regulatory features, such as the cytosolic Sugar Porter (SP) motif network, the conserved A motif, lipid interfaces, and gating dynamics, differ between the two isoforms (PMID: 33536238). These regulatory differences can alter pocket accessibility, coupling to conformational transitions, and allosteric communication with the cytosol, such that a ligand binding GLUT1 in the inward-facing state may not stabilize a GLUT3 conformation that yields appreciable transport inhibition. Consistently, functional experiments have indicated robust GLUT1 engagement in cancer cells (Dong et al. Cell Reports 2024), while equivalent GLUT3 inhibition has not been observed in TAMs (Figure S8), suggesting isoform-selective targeting by citalopram. We have included these discussion in the revised manuscript.

      Fig 3O: Please clarify the statement regarding the requirements of CD8 T cells for the pro-tumor phenotype of C5aR1+ TAMs. Specify whether this relates to a pro- or anti-tumor effect of CD8 T cells.

      Thanks. As suggested, we have improved the statement as follows: “depletion of CD8<sup>+</sup> T cells abrogated the C5aR1<sup>+</sup> TAM-mediated enhancement of tumor growth (Figure 3O), suggesting that the anti-tumor effects of CD8<sup>+</sup> T cells are required for the pro-tumor phenotype of C5aR1<sup>+</sup> TAMs”.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This work presents an interesting circuit dissection of the neural system allowing a ctenophore to keep its balance and orientation in its aquatic environment by using a fascinating structure called the statocyst. By combining serial-section electron microscopy with behavioral recordings, the authors found a population of neurons that exists as a syncytium and could associate these neurons with specific functions related to controlling the beating of cilia located in the statocyst. The type A ANN neurons participate in arresting cilia beating, and the type B ANN neurons participate in resuming cilia beating and increasing their beating frequency.

      Moreover, the authors found that bridge cells are connected with the ANN neurons, giving them the role of rhythmic modulators.

      From these observations, the authors conclude that the control is coordination instead of feedforward sensory-motor function, a hypothesis that had been put forth in the past but could not be validated until now. They also compare it to the circuitry implementing a similar behavior in a species that belongs to a different phylum, where the nervous system is thought to have evolved separately.

      Therefore, this work significantly advances our knowledge of the circuitry implementing the control of the cilia that participate in statocyst function, which ultimately allows the animal to correct its orientation. It represents an example of systems neuroscience explaining how the nervous system allows an animal to solve a specific problem and puts it in an evolutionary perspective, showing a convincing case of convergent evolution.

      Strengths:

      The evidence for how the circuitry is connected is convincing. Pictures of synapses showing the direction of connectivity are clear, and there are good reasons to believe that the diagram inferred is valid, even though we can always expect that some connections are missing.

      The evidence for how the cilia change their beating frequency is also convincing, and the paradigm and recording methods seem pretty robust.

      The authors achieved their aims, and the results support their conclusions. This work impacts its field by presenting a mechanism by which ctenophores correct their balance, which will provide a template for comparison with other sensory systems.

      Thank you very much for these comments.

      Weaknesses:

      The evidence supporting the claim that the neural circuitry presented here controls the cilia beating is more correlational because it only relies on the fact that the location of the two types of ANN neurons coincides with the quadrants that are affected in the behavioral recordings. Discussing ways by which causality could be established might be helpful.

      We have now added additional discussions in a new “Future Directions” section explaining that for example calcium imaging or targeted neuron ablations could be used in future work to establish causality. This would require the development of genetic delivery techniques to e.g. introduce GCaMP calcium sensor or transgenic reporters.

      The explanation of the relevance of this work could be improved. The conclusion that the work hints at coordination instead of feedforward sensory-motor control is explained over only a few lines. The authors could provide a more detailed explanation of how the two models compete (coordination vs feedforward sensory-motor control), and why choosing one option over the other could provide advantages in this context.

      We added a more detailed explanation about the two types of model and why we believe that a coordination model is more compatible with our connectome data.

      “An alternative model for the function of the nerve net would be a feedforward sensory-motor system, in which balancer cells provide mechanosensory input to motor effectors via the nerve net, similar to a reflex arc. None of our observations support such a sensory-motor model. There are no synaptic pathways from balancer cells or any other sensory cells to the nerve net. The only synaptic input to ANNs comes from the bridge cells (discussed below) and from each other. The three synaptically interconnected ANNs may generate endogenous rhythm that controls balancer cilia and is influenced by bridge input. ANNs may also be influenced by neuropeptides secreted by other aboral organ neurons. Such chemical inputs may underlie the flexibility of gravitaxis and its modulation by other cues (e.g. light). Overall, the coordination model parsimoniously explains both the ANN wiring topology and the observed dynamics, whereas a simple feedforward reflex does not.”

      Since the fact that the ANN neurons form a syncytium is an important finding of this study, it would be useful to have additional illustrations of it. For instance, pictures showing anastomosing membranes could typically be added in Figure 2.

      We have now included a movie (Video 3) showing a volumetric reconstruction of a segment of an ANN neuron, which highlights the anastomosing morphology in greater detail than static images.

      “Video 3. Volumetric reconstruction of a single ANN Q1-4 neuron showing syncytial soma (cyan) and nuclei (magenta). The rotating view highlights the anastomosing morphology, although not all fine details could be reconstructed due to data limitations.”

      Also, to better establish the importance of the study, it could be useful to explain why the balancers’ cilia spontaneously beat in the first place (instead of being static and just acting as stretch sensors).

      We have discussed in more detail why it may be important for the balancer cilia to beat.

      “The observation that balancer cilia beat spontaneously, even in the absence of external tilt, suggests that they are active sensory oscillators rather than static stretch sensors. Their spontaneous beating could set a dynamic baseline of sensitivity, which can then be modulated by ANN inputs or sensory changes during tilt. Such a dynamic system may be more sensitive to small deflections and be more responsive [@Lowe1997]. Thus, the regulated beating of balancer cilia should not be seen as noise, but as an adaptive feature that enables flexible and robust graviceptive responses. The ctenophore balancer may thus use active ciliary oscillations for enhanced sensorimotor integration similar to other sensory systems [@Wan_2023].”

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, the authors describe the production of a high-resolution connectome for the statocyst of a ctenophore nervous system. This study is of particular interest because of the apparent independent evolution of the ctenophore nervous system. The statocyst is a component of the aboral organ, which is used by ctenophores to sense gravity and regulate the activity of the organ’s balancer cilia. The EM reconstruction of the aboral organ was carried out on a five-day-old larva of the model ctenophore Mnemiopsis leidyi. To place their connectome data in a functional context, the authors used high-speed imaging of ciliary beating in immobilized larvae. With these data, the authors were able to model the circuitry used for gravity sensing in a ctenophore larva.

      Strengths:

      Because of it apparently being the sister phylum to all other metazoans, Ctenophora is a particularly important group for studies of metazoan evolution. Thus, this work has much to tell us about how animals evolved. Added to that is the apparent independent evolution of the ctenophore nervous system. This study provides the first high-resolution connectomic analysis of a portion of a ctenophore nervous system, extending previous studies of the ctenophore nervous system carried out by Sid Tamm. As such, it establishes the methodology for high-resolution analysis of the ctenophore nervous system. While the generation of a connectome is in and of itself an important accomplishment, the coupling of the connectome data with analysis of the beating frequency of balancer cell cilia provides a functional context for understanding how the organization of the neural circuitry in the aboral organ carries out gravity sensing. In addition, the authors identified a new type of syncytial neuron in  Mnemiopsis. Interestingly, the authors show that the neural circuitry controlling cilia beating in Mnemiopsis shares features with the circuitry that controls ciliary movement in the annelid Platynereis, suggesting convergent evolution of this circuitry in the two organisms. The data in this paper are of high quality, and the analyses have been thoroughly and carefully done.

      Weaknesses:

      The paper has no obvious weaknesses.

      We thank the reviewer for these comments.

      Reviewer #3 (Public review):

      Summary:

      It has been a long time since I enjoyed reviewing a paper as much as this one. In it, the authors generate an unprecedented view of the aboral organ of a 5-day-old ctenophore. They proceed to derive numerous insights by reconstructing the populations and connections of cell types, with up to 150 connections from the main Q1-4 neuron.

      Strengths:

      The strengths of the analysis are the sophisticated imaging methods used, the labor-intensive reconstruction of individual neurons and organelles, and especially the mapping of synapses. The synaptic connections to and from the main coordinating neurons allow the authors to create a polarized network diagram for these components of the aboral organ. These connections give insight into the potential functions of the major neurons. This also gives some unexpected results, particularly the lack of connections from the balancer system to the coordinating system.

      Thank you for these positive comments on the paper.

      Weaknesses:

      There were no significant weaknesses in the paper - only a slate of interesting unanswered questions to motivate future studies.

      Recommendations for the authors:

      Reviewing Editor Comments:

      In consultation, the reviewers recommend that improving the evidence to “exceptional” would require additional perturbation experiments (e.g., ablation of specific neurons), as Reviewer 1 suggests. They also recommend adding a “Future Directions” section to the manuscript, because it opens up so many new experimental directions.

      We have added a new “Future Directions” section at the end of the Discussion. To carry out the proposed perturbation or calcium imaging experiments would require significant additional work and method development. We are actively working in establishing mRNA and DNA injection into ctenophore zygotes to enable live imaging, cell labelling or ablations in the future.

      Reviewer #1 (Recommendations for the authors):

      Suggestions for improved or additional experiments, data, or analyses:

      To establish causality (neurons control balancer cilia), an important experiment would be to manipulate each of these neuronal populations (e.g., by ablating them) and measure the effect of these ablations on the beating frequency of the balancer cilia of the four quadrants. Moreover, direct observation of neuronal activity (e.g., by using calcium imaging) would also provide more compelling evidence for neuronal control.

      We agree with the reviewer that such perturbation experiments would be needed to establish causality. Such experiments are currently still not possible in ctenophoes and would require significant technology development. We discuss such experiments in the “Future directions” section and also place this in the context of the currently available techniques in ctenophores. We are actively working on this but waiting for such technological breakthroughs and new experiments would significantly delay the publication of a version of record of the paper.

      Recommendations for improving the writing and presentation:

      ANN neurons are described in great detail, though SNN neurons are described more loosely. Perhaps a more detailed description of SNN neurons would be helpful.

      We added the information on SNNs to show that these cells are distinct from the ANN neurons. Since our focus is on the aboral organ, we did not aim for a comprehensive reconstruction of SNNs. Several of the processes of the SNNs are also truncated and outside our EM volume. We have nevertheless added additional details about the morphology and connectivity of SNN neurons.

      “Near the perifery of the aboral organ, we identified four further anastomosing nerve-net neurons. These resembled the previously reported syncytial subepithelial nerve net (SNN) neurons in the body wall of Mnemiopsis (Figure 2–figure supplement 1C–G) and were clearly distinct from the ANN neurons (both in location and morphology). SNN neurons show a blebbed morphology and contain dense core vesicles @Burkhardt2023 but no synapses.”

      Minor corrections to the text and figures:

      (1) Figure 2 C): “mitochondia” instead of “mitochondria”.

      corrected

      (2) Figure 3. Title: “balancer and and bridge”.

      corrected

      (3) Figure 3.C) “shown in xxx color”

      corrected

      Reviewer #2 (Recommendations for the authors):

      Clearer usage of the terms statocyst, aboral organ, aboral nerve net, statolith, dome, and lithocytes would be helpful. For readers not familiar with ctenophore anatomy, things can get a bit confusing. A single schematic with all of these terms would be helpful. In Figure 1E, there is a label “dc”. Should this be “do”?

      We have added an annotated schematic to Figure 1, explaining these terms.

      Figure 1C “The statocyst is a cavity-like organ enclosed by the dome cilia (do), which contains the statolith formed by lithocytes (li) and supported by the balancer cilia (bal).”

      Reviewer #3 (Recommendations for the authors):

      My comments are numerous, but mostly minor suggestions for improving the clarity.

      [Suggested insertions/changes are indicated by square brackets]

      (1) [It would be much easier to review this if there were line numbers, or with a double-spaced manuscript that was more accommodating for markup.]

      Thank you for this comment. We have increased the line spacing in the revised version. (We set the CSS line-height property on the html ‘body’ element to 2em).

      (2) The terms statolith, statocyst, and lithocytes can be confusing, so it would be nice to have an upfront definition of how they relate to each other.

      We have now explain these terms in the Introduction and also have improved the annotation of Figure 1.

      Figure1C. “The statocyst is a cavity-like organ enclosed by the dome cilia (do), which contains the statolith formed by lithocytes (li) and supported by the balancer cilia (bal).”

      (3) Statolith is spelled as statolyth in the early pages, but statolith in the later pages. I think -lith is more common, but in any case, these should be standardized.

      corrected to ‘statolith’

      ABSTRACT:

      (1) Differential load[s] on the balancer cilia [lead] to altered

      changed

      (2) We used volume electron microscopy (vEM) to image the aboral organ.

      changed

      (3) also form reciprocal connections with the bridge cells.

      corrected

      INTRODUCTION:

      (1) “identify conserved neuronal markers in ctenophores” - confusing - does this mean conserved across ctenophores, or conserved in ctenophores and other animals?

      changed to “classical neuronal markers”

      (2) “either increase or decrease their [ciliary] activity, indicating” - otherwise it sounds like the balancers are increasing activity.

      changed to “balancer cells may either increase or decrease their ciliary activity”

      (3) after “matches the setup used in high-speed imagine experiments”, it might be nice to add a statement like “Future studies could potentially investigate activity in the inverted orientation, when the statolith is suspended below the cilia, to see if the response differs.”

      In this sentence we referred to the orientation of the animals in our figures. There is a consensus among ctenophore researchers that when depicting ctenophores, the aboral organ should face downwards. However, for this paper we chose the opposite orientation to better match our experiments and help interpreting the results. We changed the text to: “In this study, we represent ctenophores with their aboral organ facing upwards (”balancer-up” posture), as this configuration facilitates intuitive interpretation of balance-like functions and matches the setup used in high-speed imaging experiments. ”

      We added the sentences “Future experiments could also explore how orientation affects the response of balancer cilia. For example, when the statolith is suspended below the cilia (the”balancer-down” posture), ciliary beating patterns may differ from what we observed here in the “balancer-up” configuration.” to the section Future Directions”.

      (4) “abolished by calcium[-]channel inhibitors”

      corrected

      (5) “By functional imaging, we uncovered” - It is not clear what functional imaging is. Maybe a fewword definition here, and be sure to explain in the methods.

      changed to “By high-speed ciliary imaging”. The details of the imaging are explained in the Methods section under “Imaging the Activity of Balancer Cilia”.

      RESULTS:

      (1) “five-day-old” - is it worth saying post-fertilization here?

      Thank you for pointing this out. In accordance with Presnell et al. (2022), we use post-hatching as the reference. We have revised the text in the Materials and Methods section to read: “5-day-old (5 days post-hatching)”

      (2) “We classified these cells into cell types [based on …]” - specify a bit about how you classified them based on morphology, the presence of organelles, etc.

      We added a clarification. “Our classification was based on i) ultrastructural features (e.g. number of cilia), ii) cell morphology (e.g. nerve net or bridge cells), iii) unique organelles (e.g. lamellate body, plumose cells), iv) and similarities to cell types previously described by EM. Our classification agrees with the cell types identified in the 1-day-old larva [@ferraioli2025].”

      (3) “CATMAID only supports [bifurcating] skeleton trees” - Correct?

      yes, a node in CATMAID cannot be fused to another node of the same skeleton to represent anastomoses

      FIGURE 1:

      (1) It is not worth redrawing and renumbering everything, but I wish the lateral view in A matched the rotated aboral view in B, instead of having to do two rotations to get the alignment to coincide. (Rotating panel B 90{degree sign} clockwise would make them match, but then it wouldn’t coincide with all the subsequent figures.)

      Thank you for the suggestion. We have replaced panel A with a lateral view that now matches panel B.

      (2) The labels on Figure 1 are a mix of two typefaces (Helvetica and Myriad?). They should be standardized to all use one typeface (preferably Helvetica).

      we have changed the font to Helvetica

      (3) Panel C legend: arrows are not really arrows. Say “Eye icons” or something like that. Can you show the location of the anal pores in the DIC image?

      Changed to ‘eye icons’. The anal pores are usually closed and only open briefly therefore it is not clear where exactly they would be, so indicating their position would be misleading.

      (4) Panel F, I cannot see the lines mentioned in the legend at all, except for maybe a tiny wisp in a couple of places. Either omit or make visible.

      changed to “The spheres indicate the position of nuclei in the reconstructed cells.”

      (5) Panel G. “Cells are color coded according to quadrants”… but unfortunately, the color scale is 90{degree sign} off of what is presented in the rest of the panels and the paper. Q1 and Q3 have been blue, but now Q2+4 are blue/purple, while Q1+3 are orange/yellow. Again, it seems like too much work to recolor panel G, but in future, it would be nice to maintain that consistency, especially since other panels specifically mention the consistent colors.

      We have changed the color code in panels B, C and E to match G and the subsequent panels/figures.

      RESULTS: Aboral synaptic nerve net

      (1)“We reconstructed three aboral nerve-net (ANN) neurons” - out of how many total? Were these three just the first ones traced, or are they likely to be all of the multi-domain neurons? One can’t tell if these are the top 3 (out of X), or if there are other multi-quad neurons that were not traced. Are there any Q1Q4 or Q2Q3 neurona? Specify overall composition.

      There are only three ANN neurons in the aboral organ. These are all completely reconstructed and contained within the volume. We have clarified this in the text. “We identified and reconstructed three aboral nerve-net (ANN) neurons, each exhibiting a syncytial morphology characterized by anastomosing membranes and multiple nuclei (ranging from two to five) (Figure 2A and B, Figure 2–figure supplement 1C). These three neurons are the only fully reconstructed ANN neurons contained within the volume. Several small ANN-like fragments were also observed at the periphery of the aboral organ, but their connectivity to the main ANN remains uncertain.”

      FIGURE 2:

      (1) Panel C: “N > 2 cells for each cell type” - is that supposed to say “N > 2 mitochondria”? More than 2 cells in all the types shown in the graph.

      It is number of cells for each cell type

      (2) Panel D: Is this the wrong caption? I can only see green and black circles, not red, yellow, or blue. Make them larger or “flat” (circled, not shaded spheres) if they are supposed to be visible

      Thank you for pointing this out. The caption was incorrect and has been corrected to match the figure.

      (3) Panel E: Amazing to see the cross-network connections!

      Thank you

      (4) Again, it is great to see the three ANN mapped out, but … are there other connections that weren’t mapped in this study? Other high-level coordinating neurons? ANN_Q1Q4 or Q2Q3?

      The reconstruction is complete and there are no other neurons or connections. Given the large size of ctenophore synapses, we are confident that we identified all or most synapses and their connections.

      RESULTS: Synaptic connectome

      (1) “displaying rotational symmetry” - This is one of the things I am most curious about. Where is the evidence of rotational symmetry in the network diagram? Is it the larger number of connections to Q2 and Q4? Any evidence of rotational symmetry, like Q1 and Q3 connect to Q2 and Q4 respectively, but not the other way around?

      changed to “displaying biradial symmetry”, we do not consider the slight difference in synapse number from ANN Q1-4 to the Q1-Q3 vs. Q2-Q4 balancers as significant or strong enough evidence for a single rotational symmetry (i.e. 180 degrees rotation)

      (2) “Surprisingly” - this *was* really surprising. There have to be some afferent neurons connecting from the balancers, don’t there? I can’t remember the connections to the SNN, but is there a tertiary set of ANNs that connect between the balancers and the top 3 ANNs? I would like a little more discussion about this.

      Indeed, this is why this is so surprising. Most people would have expected some output connections from the balancer to the nerve net or elsewhere. There are none. We have the complete balancer network and all balancer cells are ‘sink nodes’ (inputs only)(Figure3–figure supplement 1).

      we added a short statement in the beginning of the Bridge Cells as Feedback Regulators of Ciliary Rhythms section noting that no direct connections from the balancers to the ANN were found and that all balancer cells act as sink nodes (inputs only; Figure 3–figure supplement 1). This highlights that bridge cells are indeed the sole neuronal input to the ANN circuit.

      Figure 3:

      (1) As you know, during development, the diagonally opposite cells have a shared heritage and shared functionality. Are there neuronal signatures that correspond to the rotational symmetry that we see, for example, in the position of the anal pores?

      We did not find any evidence in neuronal complement for a diagonal symmetry, suggesting that neuronal organization does not simply mirror the organism’s rotational body symmetry.

      (2) Do you have the information to say whether there are any diagonal or asymmetric connections? Can’t tell if those would have shown up in the mapping efforts or if you focused on the major ones only.

      Based on our complete mapping, we did not find evidence for a diagonal pattern. The connectivity instead shows a biradial organization.

      (3) “extending across opposite quadrant regions” - to me, opposite would be diagonally opposite, but this looks like a set of cells between Q1 and Q2 is connecting to a sister-set in Q3+Q4. I wonder if, in a more detailed view, you could see whether this is a rotational correspondence, rather than a reflection. There are some subtle hints of this in the aboral view, with some cells on the right of the blue cluster and the left of the magenta cluster.

      changed to “extending across tentacular-axis-symmetric quadrant regions” for clarity

      (4) As with Figure 2, I do not see any circles/spheres that are yellow, red, or blue! There are some traces of what appear to be other neurons that have these colors, but nothing that would suggest the localization of mitochondria.

      Thank you for pointing this out. We have corrected the caption to match the figure, as in the previous item.

      (5) The connectivity map is very cool, but the caption does not seem to correspond to the version included in the manuscript. I don’t see any hexagons; all arrows seem to have the same thickness.

      changed to: “Complete connectivity map of the gravity-sensing neural circuit. Cells belonging to the same group are shown as diamonds, and the number of cells is added to their labels. The number of synapses is shown on the arrows.”

      RESULTS: Dynamics of balancer cilia

      (1) The orientation of the stage+larvae is a bit hard to follow. Maybe say the sagittal or tentacular plane is parallel to the sample stage and the gravity vector?

      we added “Larvae were oriented with their sagittal or tentacular plane parallel to the sample stage.”

      (2) “We could simultaneously image Q1(3) and Q2(4). The meaning of the numbers in () is not clear. Either way that I try to interpret it does not match the diagrams. Should this say viewing the tentacular plane, you can image Q1 and 4 or Q2 and 3?

      Thank you for spotting this mistake, we have changed to: “In larvae with their sagittal plane facing the objective, we could compare balancer-cilia movements between Q1 vs. Q2 or Q3 vs. Q4. In other larvae oriented in the tentacular plane, we could simultaneously image Q1 and Q4 or Q2 and Q3.”

      (3) Typo: episod[e]s were excluded

      Corrected

      DISCUSSION:

      This section is quite clean. Maybe mention some future directions:

      We have added a “Future Directions” section

      (1) Do these networks change during development? Five-days-old is still quite undeveloped - what would it look like in an adult specimen? Would you expect a larger version of the same or more diverse connections?

      As far as we know from work on aboral organs in adult ctenophores, the same structures and cells can be found. We do not know how the network will develop. We know that at 5 days the balancer is fully functional and the animals can orient and their behaviour is coordinated. So the wiring may not change extensively later in development. In the 1-day-old larva, Ferraioli et al. did not distinguish ANN neurons as a separate population, as these were merged with SNNs in their dataset. This suggests that significant cellular and circuit maturation likely occurs between 1 and 5 days.

      METHODS: Imaging the Activity of Balancer Cilia

      (1) “we selected only larvae whose aboral-oral axis was oriented nearly perpendicular to the gravitational vector”. Shouldn’t this be “nearly parallel to the gravity vector” not perpendicular?

      Thank you for spotting this, corrected.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      The study by Luden et al. seeks to elucidate the molecular functions of AHL15, a member of the AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) protein family, whose overexpression has been shown to extend plant longevity in Arabidopsis. To address this question, the authors conducted genome-wide ChIP-sequencing analyses to identify AHL15 binding sites. They further integrated these data with RNA-sequencing and ATAC-sequencing analyses to compare directly bound AHL15 targets with genes exhibiting altered expression and chromatin accessibility upon ectopic AHL15 overexpression.

      The analyses indicate that AHL15 preferentially associates with regions near transcription start sites (TSS) and transcription end sites (TES). Notably, no clear consensus DNA-binding motif was identified, suggesting that AHL15 binding may be mediated through interactions with other regulatory factors rather than through direct sequence recognition. The authors further show that AHL15 predominantly represses its direct target genes; however, this repression appears to be largely independent of detectable changes in chromatin accessibility.

      In addition to the AHL protein family, the globular H1 domain-containing high-mobility group A (GH1-HMGA) protein family also harbors AT-hook DNA-binding domains. Recent studies have shown that GH1-HMGA proteins repress FLC, a key regulator of flowering time, by interfering with gene-loop formation. The observed enrichment of AHL15 at both TSS and TES regions, therefore, raises the intriguing possibility that AHL15 may also participate in regulating gene-loop architecture. Consistent with this idea, the authors report that several direct AHL15 target genes are known to form gene loops.

      Overall, the conclusions of this study are well supported by the presented data and provide new mechanistic insights into how AHL family proteins may regulate gene expression.

      However, it is important to note that the genome-wide analyses in this study rely predominantly on ectopic overexpression of AHL15 at developmental stages when the gene is not usually expressed. Moreover, loss-of-function phenotypes for AHL15 have not been reported, leaving unresolved whether AHL15 plays a physiological role in regulating plant longevity under native conditions. It therefore remains possible that longevity control is mediated by other AHL family members rather than by AHL15 itself. In this regard, the manuscript's title would benefit from more accurately reflecting this broader implication.

      The ahl15 loss-of-function phenotype has previously been described in Karami et al., 2020 (Nat. Plants), Rahimi et al., 2022a (New Phyt.), and Rahimi et al., 2022b (Curr. Biol.), showing that ahl15 loss-of-function among others results in accelerated vegetative phase change and flowering, a reduced number of leaves produced by axillary meristems in short day grown plants and reduced secondary growth in the inflorescence stem. The dominant-negative ahl15 delta-G allele, expressing a mutant protein lacking the conserved G motif in the PPC domain, shows these phenotypes more clearly in the heterozygous ahl15 +/- background, and is embryo lethal in the homozygous ahl15 background (Karami et al., 2021, Nature Comm.). In addition, we recently show that leaf senescence is significantly accelerated in the ahl15 loss-of-function mutant (Luden et al., 2025, BioRxiv). These results show that AHL15 is involved in several aspects of ageing in Arabidopsis, and we will adjust the introduction to discuss these previous findings more explicitly.

      I agree with reviewer 1 on the possibility that multiple AHLs could have an effect on longevity, which is partially supported by the delayed flowering time observed in the AHL20, AHL27, or AHL29 overexpression lines (Karami et al., 2020, Street et al., 2008). However, the induction of the AHL15-GR fusion alone by DEX shows a clear delay of developmental phase transitions and the aging process in general, indicating that AHL15 by itself is able to extend longevity as other AHLs are not affected by DEX treatment (proven by the fact that their expression is not significantly changed in our RNA-seq analysis of DEX-treated 35S:AHL15-GR seedlings).

      Reviewer #2 (Public review):

      Summary:

      The manuscript by Luden et al. investigates the molecular function and DNA-binding modes of AHL15, a transcription factor with pleiotropic effects on plant development. The results contribute to our understanding of AHL15 function in development, specifically, and transcriptional regulation in plants, more broadly.

      Strengths:

      The authors developed a set of genetic tools for high-resolution profiling of AHL15 DNA binding and provided exploratory analyses of chromatin accessibility changes upon AHL15 overexpression. The generated data (CHiP-Seq, ATAC-Seq and RNA-Seq is a valuable resource for further studies. The data suggest that AHL15 does not operate as a pioneer TF, but is likely involved in gene looping.

      Weaknesses:

      While the overall message is conveyed clearly and convincingly, I see one major issue concerning motif discovery and interpretation. The authors state that because HOMER detected highly enriched motifs at frequencies below 1%, they conclude that "a true DNA binding motif would be present in a large portion of the AHL15 peaks (targets) and would be rare in other regions of the genome (background)."

      I agree that the frequency below 1% is unexpectedly low; however, this more likely reflects problems in data preprocessing or motif discovery rather than intrinsic biological properties of the transcriptional factor that possesses a DNA-binding domain and is known to bind AT_rich motifs. As it is, Figure 2 cannot serve as a main figure in the manuscript: it rather suggests that the generated CHiP-Seq peakset is dominated by noise (or motif discovery was done improperly) than that AHL15 binds nonspecifically.

      Since key methodological details on the HOMER workflow are missing in the M&M section, it is not possible to determine what went wrong. Looking at other results, i.e. the reasonably structured peak distribution around TSS/TTS and consistent overlap of the peaks between the replicas, I assume that the motif discovery step was done improperly.

      Therefore, I recommend redoing the motif analysis, for example, by restricting the search to the top-ranked peaks (e.g. TOP1000) and by using an appropriate background set (HOMER can generate good backgrounds, but it was not documented in the manuscript how the authors did it). If HOMER remains unsuccessful, the authors should consider complementary methods such as STREME or MEME, similar to the approach used for GH1-HMGA (https://pmc.ncbi.nlm.nih.gov/). If the peakset is of good quality, I would expect the analysis to identify an AT-rich motif with a frequency substantially higher than 1%-more likely in the range of at least 30%. If such a motif is detected, it should be reported clearly, ideally with positional enrichment information relative to TSS or TTS. It would also be informative to compare the recovered motif with known GH1-HMGA motifs.

      If de novo motif discovery remains inconclusive, the authors should, at a minimum, assess enrichment of known AHL binding motifs using available PWMs (e.g. from JASPAR). As it stands, the claim that "our ChIP-seq data show that AHL15 binds to AT-rich DNA throughout the Arabidopsis genome with limited sequence specificity (Figure 2A, Figure S2-S4)" is not convincingly supported.

      Another point concerns the authors' hypothesis regarding the role of AHL15 in gene looping. While I like this hypothesis and it is good to discuss it in the discussion section, the data presented are not sufficient to support the claim, stated in the abstract, that AHL15 "regulates 3D genome organization," as such a conclusion would require additional, dedicated experiments.

      The motifs discovered by HOMER are ranked by their enrichment over background, of which the highest-scoring motifs are very rare in the AHL15-bound targets, but even rarer in the background, which is why they score highly on the percent enrichment score. As expected by reviewer 2, we identified AT-rich motifs that were present in a larger percentage of AHL15 targets (found in 3-18% of targets, depending on the motif, see for example motif #5 in figure S4A), which can be seen at the right tail of the histograms shown in figures 2B-C and figures S2-S4B-C. However, these motifs were also common in the background and were therefore not considered as significantly enriched in the AHL15-bound regions, with a target:background ratio of <2. As most of these motifs were flagged by HOMER as possible false-positives, and to limit the size of the (supplemental) figures, we did not show each of the motifs identified by HOMER in table form. We can include the full tables of de novo motifs identified by HOMER, including possible false-positive results for clarification.

      Although the identification of AT-rich motifs shows that AHL15 (and very likely most other AHL proteins as well) binds AT-rich regions, it does not sufficiently explain the binding of AHL15 to its target genes, as these motifs are found at almost equal frequencies in non-AHL15-bound regions.  In addition, a sequence found at this frequency in the genomic background is, in our view, too unspecific to be considered as a transcription factor binding site. Based on this, we concluded that AHL15 lacks a specific binding motif that can define the genes it binds.

      We will update the methods section to include more details on the HOMER analysis, and will also run the analysis in the top1000 shared peaks as suggested by reviewer 2.

      Reviewer #3 (Public review):

      Summary:

      This study investigated the role of AHL15 in the regulation of gene expression using AHL15 overexpression lines. Their results do show that more genes are downregulated when AHL15 is upregulated, and its binding does not affect the chromatin accessibility. Further, they investigated AHL15 binds in regions depleted in histone modifications and other epigenetic signatures. Subsequently, they investigated the presence of AHL15 in the gene chromatin loops. They found overlaps with both upregulated and downregulated genes. The methods are appropriately described, but could be improved to include the analysis of self-looping gene boundaries.

      Strengths:

      Their study clearly showed a lack of any specific sequence enrichment in the AHL15 binding sites, other than these being AT-rich, suggesting that AHL proteins do not recognize a specific DNA sequence but are recruited to their AT-rich target sites in another way. The study does suggest significant enrichment of AHL15 binding sites at TSS and TES, and AHL15 sites are depleted of any histone marks. They also identified that AHL15 binding sites overlap with self-looping gene boundaries.

      Weaknesses:

      The claim that AHL15 acts as a repressor and genes regulated by it are downregulated needs to be investigated based on AHL15 binding sites, to show enrichment/ depletion of AHL15 binding sites in overexpressing genes and repressed genes. The authors should provide data to support plant longevity with AHL15 overexpression using the DEX-induced system to support the claims in the title. Calculation of the enrichment score of AHL15 peaks in the self-looping genes that are upregulated or downregulated, and discussion about the different effects of AHL15 binding on self-looping regions to regulate gene expression may be helpful to understand the significance of the study. Motif enrichment in upregulated and downregulated genes separately to identify binding sequence preferences may be useful. It is not clear how the overlap of AHL15 peaks with self-looping genes has been carried out.

      A metagenome plot of AHL15 binding around genes that are differentially expressed upon DEX treatment can be found in Figure 3F. This analysis shows that AHL15 binding near differentially expressed genes is more pronounced compared to all AHL15-bound genes, and that AHL15 binding near the TSS is especially enriched for upregulated genes.

      As also suggested by reviewer 2, we will run a motif enrichment analysis on the differentially expressed genes that are bound by AHL15 to see if any motifs are enriched compared to the background and overrepresented in the AHL15-bound genes.

      Plant longevity in 35S:AHL15-GR plants treated with DEX has been shown by Karami et al. (2020; Nature Plants). DEX treatment extended vegetative development after flowering in Arabidopsis and tobacco, enhanced overall biomass in Arabidopsis and tobacco, re-initiation of vegetative growth in senescent tobacco) and recently we showed that it delays leaf senescence in Arabidopsis (Luden et al., 2025, bioRxiv). All these observations will be discussed in more detail in the text. In addition, we show that 35S:AHL15-GR plants treated a single time with DEX at 10 days after germination show a significantly delayed flowering time in figure 4C-D of this manuscript.

      The enrichment of AHL15 ChIP-seq peaks in self-looping genes will be analyzed as suggested and compared to a random set of genes as a control, and the methods section will be updated to clarify how the analyses on self-looping genes were carried out.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      The authors present exciting new experimental data on the antigenic recognition of 78 H3N2 strains (from the beginning of the 2023 Northern Hemisphere season) against a set of 150 serum samples. The authors compare protection profiles of individual sera and find that the antigenic effect of amino acid substitutions at specific sites depends on the immune class of the sera, differentiating between children and adults. Person-to-person heterogeneity in the measured titers is strong, specifically in the group of children's sera. The authors find that the fraction of sera with low titers correlates with the inferred growth rate using maximum likelihood regression (MLR), a correlation that does not hold for pooled sera. The authors then measure the protection profile of the sera against historical vaccine strains and find that it can be explained by birth cohort for children. Finally, the authors present data comparing pre- and post- vaccination protection profiles for 39 (USA) and 8 (Australia) adults. The data shows a cohort-specific vaccination effect as measured by the average titer increase, and also a virus-specific vaccination effect for the historical vaccine strains. The generated data is shared by the authors and they also note that these methods can be applied to inform the bi-annual vaccine composition meetings, which could be highly valuable.

      We appreciate the reviewer’s clear summary of our work.

      Thanks to the authors for the revised version of the manuscript. A few concerns remain after the revision:

      (1) We appreciate the additional computational analysis the authors have performed on normalizing the titers with the geometric mean titer for each individual, as shown in the new Supplemental Figure 6. We agree with the authors statement that, after averaging again within specific age groups, "there are no obvious age group-specific patterns." A discussion of this should be added to the revised manuscript, for example in the section "Pooled sera fail to capture the heterogeneity of individual sera," referring to the new Supplemental Figure 6.

      However, we also suggested that after this normalization, patterns might emerge that are not necessarily defined by birth cohort. This possibility remains unexplored and could provide an interesting addition to support potential effects of substitutions at sites 145 and 275/276 in individuals with specific titer profiles, which as stated above do not necessarily follow birth cohort patterns.

      The reviewer is correct that there remains heterogeneity among the serum titers to different strains that we cannot easily explain via age group, and suggests that additional patterns could emerge. We certainly agree that explaining this heterogeneity remains an interesting goal, but as described in the manuscript we have analyzed the possible causes of the heterogeneity as exhaustively as possible given the available metadata. At this point, the most we can say is that the strain-specific neutralization titers are highly heterogeneous in a way that cannot be completely explained by birth cohort. We agree that further analysis of the cause is an area for future work, and have made all of our data available so that others can continue to explore additional hypotheses. It may be that these questions can only be answered by experiments on sera from newer cohorts where more detailed metadata on infection and vaccination history are available.

      (2) Thank you for elaborating further on the method used to estimate growth rates in your reply to the reviewers. To clarify: the reason that we infer from Fig. 5a that A/Massachusetts has a higher fitness than A/Sydney is not because it reaches a higher maximum frequency, but because it seems to have a higher slope. The discrepancy between this plot and the MLR inferred fitness could be clarified by plotting the frequency trajectories on a log-scale.

      For the MLR, we understand that the initial frequency matters in assessing a variant's growth. However, when starting points of two clades differ in time (i.e., in different contexts of competing clades), this affects comparability, particularly between A/Massachusetts and A/Ontario, as well as for other strains. We still think that mentioning these time-dependent effects, which are not captured by the MLR analysis, would be appropriate. To support this, it could be helpful to include the MLR fits as an appendix figure, showing the different starting and/or time points used.

      Multinomial logistic regression is a widely used technique to estimate viral growth rates from sequencing counts (PLoS Computational Biology, 20:e1012443; Nature, 597:703-708; Science, 376:1327-1332). As the reviewer points out, it does assume that the relative viral growth rates are constant over the time period analyzed. However, most of the patterns mentioned by the reviewer are not deviations from this assumption, but rather just due to the fact that frequencies are plotted on a linear scale. More specifically, our multinomial logistic regression implementation defines two parameters per variant: the initial frequency and the growth rate. The absolute variant growth rate is effectively the slope of the logit-transformed variant frequencies. Each variant's relative fitness depends on that variant's growth rate relative to a predefined baseline variant. Plotting frequencies on a logit scale does help emphasize the importance of the slope by showing exponential growth as a linear trajectory. We have added a new Supplemental Figure 9 that plots the frequencies from Figure 5A on a logit scale. As can be seen the frequency trajectories are closer to linear on the logit scale.

      We have updated the results text to clarify the nature of the fixed relative growth rates per strain and to refer to this new supplemental figure as follows:

      To estimate the evolutionary success of different human H3N2 influenza strains during 2023, we used multinomial logistic regression, which uses sequence counts to estimate fixed strain growth rates relative to a baseline strain for the entire analysis time period (in this case, 2023) [50–52]. Relative growth rates estimated by multinomial logistic regression represent relative fitnesses of strains over that time period. There were sufficient sequencing counts to reliably estimate growth rates in 2023 for 12 of the HAs for which we measured titers using our sequencing-based neutralization assay libraries (Figure 5a,b and Supplemental Figure 9). We estimated strain growth rates relative to the baseline strain of A/Massachusetts/18/2022. Note that these growth rates estimate how rapidly each strain grows relative to the baseline strain, rather than the absolute highest frequency reached by each strain. Each strain’s absolute growth rate corresponds to the slope of the strain’s logit-transformed frequencies at the end of the analysis time period (Supplemental Figure 9).

      As the reviewer notes, the multinomial logistic regression implementation assumes a fixed growth rate for each strain over the time period being analyzed. This limitation causes the inferred growth rates to emphasize the latest trends in the analysis time period. For example, at the end of December 2023 in Figure 5A, the A/Ontario/RV00796/2023 strain is growing rapidly and replacing all other variants. Correspondingly, the multinomial logistic regression infers a high growth rate for that Ontario strain relative to the A/Massachusetts/18/2022 baseline strain. However, the A/Massachusetts/18/2022 strain was growing relative to other strains in the first half of 2023 since it has a higher growth rate than they do. However, there are modest deviations from linearity on the logit scale shown in the added supplementary figure likely because the assumption of a fixed set of relative growth rates over the analyzed time period is an approximation.

      We have added the following text to the discussion to highlight this limitation of the multinomial logistic regression:

      Our comparisons of the neutralization titers to the growth rates of different H3N2 strains was limited by the fact that only a modest number of strains had adequate sequence data to estimate their growth rates. Strains with more sequencing counts tend to be those with moderate-to-high fitness, which therefore limited the dynamic range of growth rates across strains we were able to analyze. Relatedly, the multinomial logistic regression infers a single fixed growth rate per strain for the entire analysis time period of 2023, and cannot represent changes in relative fitness of strains over that relatively short time period. Additionally, because the strains for which we estimated growth rates are phylogenetically related it is difficult to assess the statistical significance of the correlation [53], so it will be important for future work to reassess the correlations with new neutralization data against the dominant strains in future years.

      (3) Regarding my previous suggestion to test an older vaccine strain than A/Texas/50/2012 to assess whether the observed peak in titer measurements is virus-specific: We understand that the authors want to focus the scope of this paper on the relative fitness of contemporary strains, and that this additional experimental effort would go beyond the main objectives outlined in this manuscript. However, the authors explicitly note that "Adults across age groups also have their highest titers to the oldest vaccine strain tested, consistent with the fact that these adults were first imprinted by exposure to an older strain." This statement gives the impression that imprinting effects increase titers for older strains, whereas this does not seem to be true from their results, but only true for A/Texas. It should be modified accordingly.

      We agree with the reviewer’s suggestion that the specific language describing the potential trend of adults having the highest titers to the oldest strain tested could be further caveated. To this end, we have made the following edits to the portion of the main text that they highlighted:

      Adults across age groups also have their highest titers to the oldest vaccine strain tested (Figure 6), consistent with the fact that these adults were likely first imprinted by exposure to an older strain more antigenically similar to A/Texas/50/2012 (the oldest strain tested here) than more recent strains. Note that a similar trend towards adult sera having higher titers to older vaccine strains was also observed in a more recent study we have performed using the same methodology described here [60].

      Notably, this trend of adults across age groups having the highest titers to the oldest vaccine strains tested has held true in subsequent work we’ve performed with H1N1 viruses (Kikawa et al., 2025 Virus Evolution, DOI: https://doi.org/10.1093/ve/veaf086). In that more recent study, we again saw that adults (cohorts EPIHK, NIID, and UWMC) tended to have their highest titers to the oldest cell-passaged strain tested (A/California/07/2009), whereas children (cohort SCH) had more similar neutralization titers across strains.  These additional data therefore support the idea that adults tend to have their highest titers to older vaccine strains, a finding that is also consistent with substantial prior work (eg, Science, 346:996-1000).

      Reviewer #2 (Public review):

      This is an excellent paper. The ability to measure the immune response to multiple viruses in parallel is a major advancement for the field, that will be relevant across pathogens (assuming the assay can be appropriately adapted). I only had a few comments, focused on maximising the information provided by the sera. These concerns were all addressed in the revised paper.

      We thank this reviewer for the summary of our work and their helpful comments in the first revision.

      Reviewer #3 (Public review):

      The authors use high throughput neutralisation data to explore how different summary statistics for population immune responses relate to strain success, as measured by growth rate during the 2023 season. The question of how serological measurements relate to epidemic growth is an important one, and I thought the authors present a thoughtful analysis tackling this question, with some clear figures. In particular, they found that stratifying the population based on the magnitude of their antibody titres correlates more with strain growth than using measurements derived from pooled serum data. The updated manuscript has a stronger motivation, and there is substantial potential to build on this work in future research.

      Comments on revisions:

      I have no additional recommendations. There are several areas where the work could be further developed, which were not addressed in detail in the responses, but given this is a strong manuscript as it stands, it is fine that these aspects are for consideration only at this point.

      We appreciate this reviewer’s summary of our work, and we are glad they feel the motivation is stronger in the revised manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      Summary: 

      Overall, this is a well-designed and carefully executed study that delivers clear and actionable guidance on the sample size and representative demographic requirements for robust normative modelling in neuroimaging. The central claims are convincingly supported. 

      Strengths: 

      The study has multiple strengths. First, it offers a comprehensive and methodologically rigorous analysis of sample size and age distribution, supported by multiple complementary fit indices. Second, the learning-curve results are compelling and reproducible and will be of immediate utility to researchers planning normative modelling projects. Third, the study includes both replication in an independent dataset and an adaptive transfer analysis from UK Biobank, highlighting both the robustness of the results and the practical advantages of transfer learning for smaller clinical cohorts. Finally, the clinical validation ties the methodological work back to clinical application.  

      We are grateful for the reviewer’s positive overall evaluation and for the constructive feedback, which has helped us refine and clarify the manuscript.

      Weaknesses: 

      There are two minor points for consideration: 

      (1) Calibration of percentile estimates could be shown for the main evaluation (similar to that done in Figure 4E). Because the clinical utility of normative models often hinges on identifying individuals outside the 5th or 95th percentiles, readers would benefit from visual overlays of model-derived percentile curves on the curves from the full training data and simple reporting of the proportion of healthy controls falling outside these bounds for the main analyses (i.e., 2.1. Model fit evaluation). 

      We thank the reviewer for this helpful point. To address this, we implemented two complementary analyses that evaluate the accuracy of percentile estimates in the main evaluation (Section 2.1, Model fit evaluation).

      (a) Percentage of healthy controls (HC) outside the extreme centiles (added to the main figure)

      For each sampling strategy and sample size, we now report the proportion of healthy controls falling outside the predicted 2.5th and 97.5th percentiles, to remain consistent with the 1.96 threshold used throughout the study. Under perfect calibration, this proportion should be close to 2.5%. This metric was computed for every ROI, model run, sample size, and sampling condition. The results are now shown in the main model-fit figure alongside MSLL, EV, Rho, SMSE, and ICC, and the corresponding statistics have been added throughout. This directly quantifies how well the centile estimates capture tail behavior, which is essential for the clinical interpretation of normative deviations. See the added plots to Figure 2 and Figure 3 (see also Table 2-3 in the revised main manuscript and replication in AIBL and transfer leaning experiments in Supplementary Materials Figure S1, S10-11, S18-19, S2829, Table S1-2, S5-6, S9-10). 

      (b) Centile curve overlays (added to the Supplementary Figures)

      To visually demonstrate calibration, we now include additional overlays of model-derived percentile curves against those obtained using the full training set. These are shown for key ROIs, multiple sample sizes and different sampling strategies in Supplementary Materials (Figure S9 and S27). These overlays illustrate where centile estimation diverges, particularly at age extremes. 

      Together, these additions provide both quantitative and qualitative evidence of percentile calibration across sampling regimes and sample sizes.

      (2) The larger negative effect of left-skewed sampling likely reflects a mismatch between the younger training set and the older test set; accounting explicitly for this mismatch would make the conclusions more generalizable. 

      We agree with the reviewer that the large negative effect of left-skewed training reflects a mismatch between the training and test age distributions. 

      To characterize the expected age distributions produced by each sampling strategy, we simulated the procedures used in the main analyses by repeatedly drawing training samples under all sampling conditions (representative, left-skewed, right-skewed, and the predefined sex-ratio settings). Simulations were performed at a fixed sample size (n = 200), generating 1000 samples per condition, and the resulting age distributions were summarized separately for males and females (Supplementary Materials section 5.1). These simulated distributions show that left-skewed sampling produces a more pronounced shift toward younger ages than the corresponding shift toward older ages under rightskewed sampling, particularly in OASIS-3, with smaller differences observed in AIBL (Tables S14– S15).

      To further quantify how these sampling-induced age profiles align with the empirical age structure of the test cohorts, we computed an age-bin coverage metric based on distribution intersection. Age was discretized into 20 quantile-based bins using the full training set of each dataset (OASIS-3 and AIBL) as reference.

      For each sampling strategy (Representative, Left-skewed, Right-skewed), sample size, and dataset, we generated 1000 independent training samples using the same sampling procedures as in the main analyses. For each sampled training set, age-bin count distributions were computed and compared to the corresponding HC test-set age-bin counts.

      Coverage was defined as:

      where, 𝑖 indexes age bins, 𝑛<sub>train</sub> and 𝑛<sub>test</sub> are the numbers of individuals in bin i in the sampled training set and HC test set, respectively. This metric quantifies the fraction of the test-set age distribution that is “covered” by the sampled training set and ranges from 0 (no test-set ages covered) to 1 (complete coverage of the test-set age distribution). For each condition, the mean and standard deviation of the coverage across repetitions were computed.

      We show that under left-skewed sampling, age coverage remains markedly reduced across all sample sizes in OASIS-3 in comparison with AIBL dataset (see Figures S37). This suggests that the poorer performance observed with left-skewed training may stem from a reduced coverage of the test age range. We added the following in the Discussion (page 27):

      “The left-skewed sampling had overall a greater effect than right-skewed sampling in both model evaluation and clinical validation, likely due to (1) the dataset’s original bias toward older individuals, making younger-skewed samples less representative, and (2) the older age structure of the AD population, which exacerbates mismatch when younger HC are used to calibrate models in the clinical population. This asymmetry is also reflected in the coverage analysis, where left-skewed sampling resulted in poorer age coverage of the target population at the same sample size (Supplementary Materials section 5.4.)”

      Reviewer #2:

      Summary: 

      The authors test how sample size and demographic balance of reference cohorts affect the reliability of normative models in ageing and Alzheimer's disease. Using OASIS-3 and replicating in AIBL, they change age and sex distributions and number of samples and show that age alignment is more important than overall sample size. They also demonstrate that models adapted from a large dataset (UK Biobank) can achieve stable performance with fewer samples. The results suggest that moderately sized but demographically well-balanced cohorts can provide robust performance. 

      Strengths: 

      The study is thorough and systematic, varying sample size, age, and sex distributions in a controlled way. Results are replicated in two independent datasets with relatively large sample sizes, thereby strengthening confidence in the findings. The analyses are clearly presented and use widely applied evaluation metrics. Clinical validation (outlier detection, classification) adds relevance beyond technical benchmarks. The comparison between within-cohort training and adaptation from a large dataset is valuable for real-world applications. 

      The work convincingly shows that age alignment is crucial and that adapted models can reach good performance with fewer samples. However, some dataset-specific patterns (noted above) should be acknowledged more directly, and the practical guidance could be sharper. 

      We are grateful for the reviewer’s positive overall evaluation and for the constructive comments that guided our revisions strengthened the manuscript.

      Weaknesses: 

      The paper uses a simple regression framework, which is understandable for scalability, but limits generalization to multi-site settings where a hierarchical approach could better account for site differences. This limitation is acknowledged; a brief sensitivity analysis (or a clearer discussion) would help readers weigh trade-offs. 

      We thank the reviewer for this insightful point. We agree that hierarchical Bayesian regression provides clear advantages in multi-site settings, particularly when site-level variability is substantial or when federated learning is required. In our case, both OASIS-3 and AIBL include only a small number of sites, and the primary aim of the study was to isolate the effects of sample size and covariate composition rather than to model site-related structure. For these reasons, implementing HBR was beyond the scope of the present work, but we fully acknowledge its relevance for studies with larger or more heterogeneous site configurations. To clarify this distinction, we added a dedicated paragraph in the Discussion (page 28) that situates warped BLR and HBR within different data scenarios and outlines the circumstances under which each approach is preferable.

      “From a methodological perspective, the choice between warped BLR and HBR should primarily be guided by the structure of site effects and by computational constraints. HBR explicitly models sitelevel variation through hierarchical random effects, enabling information sharing across sites and supporting federated-learning implementations in which site-specific updates can be combined without sharing raw data (Bayer et al., 2022; Kia et al., 2021; Maccioni et al., 2025). This structure provides more stable estimates when site-specific sample sizes are small or acquisition differences are substantial. In contrast, wrapped BLR treats site as a fixed-effect covariate when site adjustment is required and does not implement hierarchical pooling, but offers simpler inference and substantially lower computational cost while accommodating non-Gaussian data distributions through the warping transformation (C. J. Fraza et al., 2021). These properties make wrapped BLR practical in settings where site heterogeneity is limited or adequately controlled, whereas HBR may be preferable in strongly multisite contexts or when federated learning is required for privacy-preserving data integration.”

      Other than that, there are some points that are not fully explained in the paper: 

      (1) The replication in AIBL does not fully match the OASIS results. In AIBL, left-skewed age sampling converges with other strategies as sample size grows, unlike in OASIS. This suggests that skew effects depend on where variability lies across the age span. 

      Recommendation: Replication differences across datasets (age skew): 

      In OASIS, left-skewed (younger-heavy) training harms performance and does not fully recover with more data; in AIBL, performance under left-skew appears to converge toward the other conditions as training size grows. Given AIBL's smaller size and older age range, please explain this discrepancy. Does this imply that the effect of skew depends on where biological variability is highest across the age span (e.g., more variability from ~45-60 in OASIS vs {greater than or equal to}60 in AIBL), rather than on "skew" per se? If so, the paper should say explicitly that skewness must be interpreted relative to the age-variability profile of the target population, not just counts. 

      We thank the reviewer for this thoughtful comment. To examine whether differences in age-related variability could explain the replication patterns, we quantified how regional variance changed with age by computing age-binned variance profiles in the HC training sets of OASIS-3 and AIBL. Age was discretized into 10 quantile-based bins for each dataset separately. For each ROI and each age bin, we calculated the sample variance of the ROI values within that bin. The bin center was defined as the mean age of individuals in the corresponding bin. We then summarized variance across ROIs by computing, for each age bin, the median variance and its interquartile range (25th–75th percentile). These summary profiles (median and IQR across ROIs as a function of bin-centered age) are shown in Author response image 1. As shown in this plot, OASIS-3 and AIBL display comparable levels of variance across their respective age ranges, and the profiles do not suggest pronounced shifts in variability that would account for the divergent behavior of the left-skewed models.

      Author response image 1.

      Median ROI variance across age bins for OASIS-3 and AIBL. Shaded areas represent variability across regions within each age bin.

      Instead, the coverage analysis recommended by the reviewer in comment #5 and introduced in our response to Reviewer 1, comment #2 indicates that the replication differences between OASIS-3 and AIBL are primarily driven by the age coverage of the sampled training sets relative to the test cohorts. In AIBL, which has a narrower and predominantly older age range, left-skewed sampling shows slightly lower coverage than right-skewed sampling, but coverage increases steadily with sample size, and the strategies converge as n grows. In contrast, OASIS-3 spans a broader lifespan and is itself skewed toward older ages; under left-skewed sampling, coverage of the test-set age range increases more slowly and remains comparatively lower even at large n. This slower recovery of age coverage explains why leftskewed performance does not recover in OASIS-3 and why the discrepancies between left- and rightskewed sampling are more pronounced in this dataset. The corresponding age-coverage curves are reported in Supplementary Figures S37. 

      Furthermore, this difference is also reflected in the expected age distributions obtained from repeated simulations of the sampling procedures (Supplementary Materials section 5.1. Tables S14–S15), where left-skewed sampling induces a larger shift toward younger ages than right-skewed sampling induces toward older ages, especially in OASIS-3, with smaller differences observed in AIBL. 

      For more details on both analyses see also our response to Reviewer 1, comment #2.

      (2) Sex imbalance effects are difficult to interpret, since sex is included only as a fixed effect, and residual age differences may drive some errors. 

      Recommendation: Sex effects may be confounded with age:

      Because sex is treated only as a fixed effect, it is unclear whether errors under sex-imbalance scenarios partly reflect residual age differences between female and male subsets. Please report (or control for) age distributions within each sex-imbalance condition, and clarify whether the observed error changes are truly attributable to sex composition rather than age composition. 

      To address the concern that sex-imbalance effects could be driven by residual age differences we now explicitly report the age distributions by sex for the original training and test datasets, as well as the expected age distributions induced by each sampling condition, obtained by repeated simulation of the sampling procedure (Supplementary Materials section 5.1, Tables S13-15). Table S13 shows very similar distributions of age for HC train and test sets across sexes within each dataset. Tables S14–S15 further show that, within each sampling strategy, the age distributions of females and males are highly similar, including under sex-imbalanced conditions. These summaries confirm that the sampling procedures do not introduce systematic age-structure differences between sexes.

      In addition, we extended the statistical models for tOC and MSE to explicitly include age, sex, and all higher-order interactions with the diagnosis, sample size, and sex-ratio sampling (Supplementary Materials section 5.2., Tables S17 for direct training, and S19 for transferred models). For completion we also included age and sex for age samplings models (Supplementary Tables S16 for direct training, S18 for transferred models). These analyses revealed no significant main effects of age under seximbalanced sampling and only very small effect sizes in isolated higher-order interactions. Together, these results indicate that age did not introduce residual confounding in our analyses.

      We now report in the Results section (page 15) the following: 

      “Supplementary analysis (Tables S17,19) also showed that main effect of age was not significant for either MSE or tOC, and no significant age × sex-ratio interactions were observed. While some higherorder interactions involving age, diagnosis, and sex-ratio reached statistical significance, all associated effect sizes were very small and inconsistent across outcomes, indicating that the observed error changes are not driven by residual age confounding.”

      And in the Methods section (page 36): 

      “Age distributions were summarized separately for males and females in the original training and test sets (Supplementary Table S13) and the expected age distributions resulting from the skewed-age sampling and the sex-imbalance sampling procedures were obtained by repeated simulations at a fixed sample size and are reported in Supplementary Tables S14–S15.”

      (3) In Figure 3, performance drops around n≈300 across conditions. This consistent pattern raises the question of sensitivity to individual samples or sub-sampling strategy. 

      Recommendation: Instability around n ≈ 300 (Figure 3):

      Several panels show a consistent dip in performance near n=300. What drives this? Is the model sensitive to particular individuals being included/excluded at that size, or does it reflect an interaction with the binning/selection scheme? A brief ablation (e.g., alternative sub-sampling seeds or bins) would help rule out artefacts. 

      We thank the reviewer for highlighting this point. To assess whether the observed dip at n=300 reflected sensitivity to the specific individuals selected or to the sub-sampling scheme, we re-ran the analysis at n = 300 using 20 independent random seeds (Supplementary Materials sections 5.3.). This ablation showed no systematic decrease in performance across repetitions, indicating that the original effect was driven by stochastic sampling variability rather than a stable model instability or binning interaction. We now report this control analysis in the Supplementary Materials (Figure S36). We have clarified this point in the Results page 10:

      “A consistent dip in performance was observed around n = 300 for the left-skewed sampling condition in the original analysis (Figure 3). To assess whether this reflected sensitivity to the specific subsampling or stochastic sampling variability, we repeated the analysis for this specific sample using 20 independent random seeds (Figure S36); the absence of a consistent effect across repetitions indicates that the original pattern was driven by sampling variability rather than a systematic model artifact.”

      (4) The total outlier count (tOC) analysis is interesting but hard to generalize. For example, in AIBL, left-skew sometimes performs slightly better despite a weaker model fit. Clearer guidance on how to weigh model fit versus outlier detection would strengthen the practical message. 

      Recommendation: Interpreting total outlier count (tOC): 

      The tOC findings are interesting but hard to operationalize. In AIBL, even for n>40, left-skewed training sometimes yields slightly better tOC discrimination and other strategies plateau. Does this mean that a better model fit on the reference cohort does not necessarily produce better outlier-based case separation? Please add a short practical rule-set: e.g., when optimizing for deviation mapping/outlier detection, prioritize coverage of the patient-relevant age band over global fit metrics; report both fit and tOC sensitivity to training-set age coverage. 

      We thank the reviewer for this important point. Apparent improvements in tOC-based separation under left-skewed training should not be interpreted as indicating a better model or superior deviation mapping. In particular, in AIBL, left-skew can sometimes yield slightly larger group differences in tOC despite weaker overall model fit. This reflects an inflation of deviation magnitude in AD rather than improved separation per se. Crucially, relative ranking between HC and AD remains preserved across sampling strategies, as shown by the classification analysis in the main manuscript (Figure 5C), indicating that enhanced tOC contrast under left-skew does not translate into improved case discrimination. Instead, it reflects a systematic shift in deviation scale due to age-mismatched training.

      We now clarify this distinction in the Discussion of the main manuscript on page 26:

      “Importantly, apparent increases in HC–AD separation in total outlier count should not be interpreted as evidence of superior model quality. Age-mismatched training can rescale deviation magnitudes and inflate tOC in specific subgroups without improving true case–control separability, as shown by classification task (Figure 5C). Model fit metrics and outlier-based measures, therefore capture complementary but distinct aspects of normative model behavior and should be interpreted jointly rather than in isolation.”

      (5) The suggested plateau at n≈200 seems context dependent. It may be better to frame sample size targets in relation to coverage across age bins rather than as an absolute number. 

      Recommendation: "n≈200" as a plateau is context-dependent: 

      The suggested threshold for stable fits (about 200 people) likely depends on how variable the brain features are across the covered ages. Rather than an absolute number, consider reporting a coverageaware target, such as a minimum per-age-bin coverage or an effective sample size relative to the age range. This would make the guidance transferable to cohorts with different age spans. 

      We agree that the observed performance plateau around n≈200 is context dependent and may shift with the covered age range, anatomical variability, and feature of interest. In the present study, this stabilization was evaluated within the specific datasets and age spans considered and extending it to broader lifespan or different biological contexts will require dedicated future work.

      To clarify this point, we added an explicit age-coverage analysis in the Supplementary Materials (section 5.4.) as introduced in response to reviewer 1 on comment #2. This analysis shows that, under representative sampling, the point at which age coverage becomes complete closely coincides with the saturation of model fit and stability metrics. At the same time, we note that normative models operate in continuous covariate space, such that reliable interpolation can still be achieved even when intermediate age ranges are less densely sampled, provided that surrounding age ranges are sufficiently represented. This makes rigid minimum per-bin requirements difficult to define in a generalizable way.

      Rather than proposing a universal sample-size threshold, we now emphasize that both learning-curve analyses and age-coverage assessments offer a more transferable way to identify when performance approaches saturation for a given dataset. This clarification is now included in the Discussion on page 25:

      “This is further supported by the coverage analysis reported in the Supplementary Materials (section 5.4), which shows that under representative sampling, the point of full age coverage closely coincides with the saturation of model fit and stability metrics. Rather than proposing a universal sample size threshold, we therefore encourage readers to perform learning-curve analyses, complemented by age coverage assessments, in their own datasets to empirically assess when performance approaches saturation for their specific age range and population.”

      And we also address it in the limitations page 29: 

      “In addition, the observed stabilization of model performance around 200–300 participants was evaluated within the specific age ranges and cohorts examined here and may shift in broader lifespan settings or in populations with different sources of biological variability.”

      (5) Minor inconsistency in training-set size: 

      The manuscript mentions 691 in Methods, but the figures/scripts label is 692. Please correct for consistency. 

      Thank you for pointing out this inconsistency, the error in the methods section has been corrected.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This valuable study provides insights into the role of Pten mutations in SHH-medulloblastoma, by using mouse models to resolve the effects of heterozygous vs homozygous mutations on proliferation and cell death throughout tumorigenesis. The experiments presented are convincing, with rigorous quantifications and orthogonal experimentation provided throughout, and the models employing sporadic oncogene induction, rather than EGL-wide genetic modifications, represent an advancement in experimental design. However, the study remains incomplete, such that the biological conclusions do not extend greatly from those in the extant literature; this could be addressed with additional experimentation focused on cell cycle kinetic changes at early stages, as well as greater characterization of macrophage phenotypes (e.g., microglia vs circulating monocytes). The work will be of interest to medical biologists studying general cancer mechanisms, as the function of Pten may be similar across tumor types.

      We appreciate the summary of the importance of our work and agree that it provides a foundation for future experiments addressing underlying mechanisms including the role of macrophages in tumor progression/regression

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This paper investigates how Pten loss influences the development of medulloblastoma using mouse models of Shh-driven MB. Previous studies have shown that Pten heterozygosity can accelerate tumorigenesis in models where the entire GNP compartment has MB-promoting mutations, raising questions about how Pten levels and context interact, especially when cancer-causing mutations are more sporadic. Here, the authors create an allelic series combining sporadic, cell-autonomous induction of SmoM2 with Pten loss in granule neuron progenitors. In their models, Pten heterozygosity does not significantly impact tumor development, whereas complete Pten loss accelerates tumour onset. Notably, Pten-deficient tumours accumulate differentiated cells, reduced cell death, and decreased macrophage infiltration. At early stages, before tumour establishment, they observe EGL hyperplasia and more pre-tumour cells in S phase, leading them to suggest that Pten loss initially drives proliferation but later shifts towards differentiation and accumulation of death-resistant, postmitotic cells. Overall, this is a well-executed and technically elegant study that confirms and extends earlier findings with more refined models. The phenotyping is strong, but the mechanistic insight is limited, especially with respect to dosage effects and macrophage biology.

      Strengths:

      The work is carefully executed, and the models-using sporadic oncogene induction rather than EGL-wide genetic manipulations-represent an advance in experimental design. The deeper phenotyping, including singlecell RNA-seq and target validation, adds rigor.

      Weaknesses:

      The biological conclusions largely confirm findings from previous studies (Castellino et al, 2010; Metcalf et al, 2013), showing that germline or conditional Pten heterozygosity accelerates tumorigenesis, generates tumors with a very similar phenotype, including abundant postmitotic cells, and reduced cell death.

      We respectfully would like to point out that we have added new insights not covered in the previous more abbreviated studies. First, we are the first to show that in a sporadic model, heterozygous loss of Pten does not lead to accelerated or more aggressive disease. This is an important finding, since this is the case for many patients and only germline PTEN mutant humans are likely to have more aggressive tumors. Also, the previous studies did not examine tumor progress by analyzing neonatal stages or analyze spinal cord metastasis. We found a different phenotype at some early stages then at end stage, thus they provide new insights. Our study also is the only one to apply a mosaic analysis to study cell behaviors at early stages of progression, including proliferation and differentiation/survival. We are also the first to demonstrate a reduction in macrophages in Pten mutant SHH-MB.

      The second stated goal - to understand why Pten dosage might matter - remains underdeveloped. The difference between earlier models using EGL-wide SmoA1 or Ptch loss versus sporadic cell-autonomous SmoM2 induction and Pten loss in this study could reflect model-specific effects or non-cell-autonomous contributions from Pten-deficient neighbouring cells in the EGL, for example. However, the study does not explore these possibilities. For instance, examining germline Pten loss in the sporadic SmoM2 context could have provided insight into whether dosage effects are cell-autonomous or dependent on the context.

      We thank the reviewer for suggesting this experiment and agree it would be an informative one for other groups to perform as a follow up to our work to allow a direct comparison in the same sporadic SHH-MB model of mosaic vs germline loss of Pten. Also, we would like to point out that we do show a dosage effect of lowering vs removing Pten when only sporadic GCPs also have an activating mutation in SMO. Please see above comments for additional new mechanistic insight we have provided.

      The observations on macrophages are intriguing but preliminary. The reduction in Iba1+ cells could reflect changes in microglia, barrier-associated macrophages, or infiltrating peripheral macrophages, but these populations are not distinguished. Moreover, the functional relevance of these immune changes for tumor initiation or progression remains unexplored.

      We agree, further studies of the influence of Pten mutations on macrophage phenotypes will be interesting.

      Reviewer #2 (Public review):

      The authors sought to answer several questions about the role of the tumor suppressor PTEN in SHHmedulloblastoma formation. Namely, whether Pten loss increases metastasis, understanding why Pten loss accelerates tumor growth, and the effect of single-copy vs double-copy loss on tumorigenesis. Using an elegant mouse model, the authors found that Pten mutations do not increase metastasis in a SmoD2-driven SHH-medulloblastoma mouse model, based on extensive characterization of the presence of spinal cord metastases. Upon examining the cellular phenotype of Pten-null tumors in the cerebellum, the authors made the interesting and puzzling observation that Pten loss increased the differentiation state of the tumor, with fewer cycling cells, seemingly in contrast to the higher penetrance and decreased latency of tumor growth.

      The authors then examined the rate of cell death in the tumor. Interestingly, Pten-null tumors had fewer dying cells, as assessed by TUNEL. In addition, the tumors expressed differentiation markers NeuN and SyP, which are rare in SHH-MB mouse models. This reduction in dying cells is also evident at earlier stages of tumor growth. By looking shortly after Pten-loss induction, the authors found that Pten loss had an immediate impact on increasing the proliferative state of GCPs, followed by enhancing the survival of differentiated cells. These two pro-tumor features together account for the increased penetrance and decreased latency of the model. While heterozygous loss of Pten also promoted proliferation, it did not protect against cell death.

      Interestingly, loss of Pten alone in GCPs caused an increase in cerebellar size throughout development. The authors suggest that Pten normally constrains GCP proliferation, although they did not check whether reduced cell death is also contributing to cerebellum size.

      Lastly, the authors examined macrophage infiltration and found that there was less macrophage infiltration in the Pten-null tumors. Using scRNA-seq, they suggest that the observed reduction in macrophages might be due to an immunosuppressive tumor microenvironment.

      This mouse model will be of high relevance to the medulloblastoma community, as current models do not reflect the heterogeneity of the disease. In addition, the elegant experimentation into Pten function may be relevant to cancer biologists outside of the medulloblastoma field.

      Strengths:

      The in-depth characterisation of the mouse model is a major strength of the study, including multiple time points and quantifications. The single-cell sequencing adds a nice molecular feature, and this dataset may be relevant to other researchers with specific questions of Pten function.

      Weaknesses:

      One weakness of the study was the examination of the macrophage phenotype, which did not include quantification (only single images), so it is difficult to assess whether this reduction of macrophages holds true across multiple samples. Future studies will also be needed to assess whether Pten-mutated patient medulloblastomas also have a differentiation phenotype, but this is difficult to assess given the low number of samples worldwide.

      We thank the reviewer for highlighting the importance of our sporadic mutant approach and new findings. As stated above, we agree, further studies of the influence of Pten mutations on macrophage phenotypes will be interesting as well as of human samples once large numbers can be obtained. All conclusions about macrophages are based on analyzing 3 independent tumors/genotype, which was stated in the Figure legends, and for all end stage tumors the sections were collected from one lateral edge of the tumor to the midline and for earlier stage from one side of the brain to the other, thus we believe the reported phenotypes are consistent within tumor and stages

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Minor points 

      (1) The authors should state explicitly that early EGL analyses sample the same cerebellar region across animals (e.g., matched lobule or distance from the midline) because position-dependent effects are possible. 

      We agree this is an important aspect of the rigor of the study and are sorry this was not clear enough. We had stated in the legends to Figures 4 and 5 that midline sections were analyzed and when it was not the entire EGL quantified the region analyzed was shown, but we now include more details in all relevant Figure legends and in the Methods section. 

      (2) It is not clear from Figure 3i-k that TUNEL density in Syp-high regions differs between Pten+/- and Pten-/- tumors. 

      We have added a new graph as Figure 3 Supplemental Figure 1D with this direct comparison. Indeed, there is no difference between the Syp-high regions of Pten+/- and Pten-/- tumors as these regions of Pten+/- tumors have no detectable PTEN protein and thus have the same behavior as Pten-/- tumors (reduced cell death).

      (3) The authors interpret the increase in the %EdU+ GFP+ cells in the EGL as evidence of a faster cell cycle. However, EdU labeling alone does not demonstrate altered cell cycle kinetics; this would require a dedicated assay. It would also be informative to combine EdU with Ki67 staining. This could clarify whether the effect reflects changes in differentiation - for example, if a higher proportion of GFP+ pre-tumor cells remain Ki67+-or whether the increase in EdU simply reflects a greater fraction of cells being in cycle. Such an analysis might even reveal no change in cycling if the proliferation index in controls is lower. 

      We are sorry we did not make our analysis sufficiently clear in Figure 5 and Figure 6. The quantification of EdU+ cells was restricted to the outer EGL (region defined by containing GFP+ and EdU+ cells) where all cells should be Ki67+.  We cannot perform co-staining of Ki67 and GFP, since antigen retrieval for Ki67 removes the epitope for our GFP antibody. We have revised the wording in the figure legends and results sections.  

      (4) Some of the stains are unconvincing - for example, Figure 2 E,F, the p27 staining is difficult to distinguish from the background, Figure 7G,E- CD31+ blood vessels are difficult to see. 

      As requested, in Fig. 2 we adjusted the level of the green color for P27 to reduce the background in A, B, E , F using Photoshop. In Fig. 7G, H we adjusted the level of the green color for CD31 to reduce the background.  

      (5) Line 158: "unlike a SmoA2 model with germline or broad deletion of Pten in the cerebellum, where heterozygous deletion is sufficient..." That paper refers to the Neuro-D2SmoA1 mouse model. So this statement should be clarified.  

      We have made this edit.

      Reviewer #2 (Recommendations for the authors): 

      (1) I find the final discussion paragraph about Kmt2d does not add much to the study, as it seems obvious that the mechanisms of tumor formation would differ between two different tumor suppressor genes, but this is only my opinion. 

      We respectfully think it is interesting, even if expected, so have left it in the Discussion.

      (2) There is also a typo on line 342 that changes the meaning of the sentence: mTORC1 signaling is significantly 'unregulated'; 

      We thank the reviewer for noticing this mistake. We have changed 'unregulated' to ‘upregulated’.

      (3) Figure 9Q,R mislabeled: not mTORC1, but instead UPR  

      Asns is included in the mTOR pathway in Hallmark MTOR1 signaling as well as in the Unfolded Protein Response gene list. We have made a note of this in the Figure legend.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Dixit and colleagues investigate the role of FRG1 in modulating nonsense-mediated mRNA decay using human cell lines and zebrafish embryos. They present data from experiments that test the effect of normal, reduced or elevated levels of FRG1 on NMD of a luciferase-based NMD reporter and on endogenous mRNA substrates of NMD. They also carry out experiments to investigate FRG1's influence on UPF1 mRNA and protein levels, with a particular focus on the possibility that FRG1 regulates UPF1 protein levels through ubiquitin-mediated proteolysis of UPF1. The experiments described also test whether DUX4's effect on UPF1 protein levels and NMD could be mediated through FRG1. Finally, the authors also present experiments that test for physical interaction between UPF1, the spliceosome and components of the exon junction complex.

      Strengths:

      A key strength of the work is its focus on an intriguing model of NMD regulation by FRG1, which is of particular interest as FRG1 is positively regulated by DUX4, which has been previously implicated in subjecting UPF1 to proteosome-mediated degradation and thereby causing NMD inhibition. The data that shows that DUX4-mediated effect on UPF1 levels is diminished upon FRG1 depletion suggests that DUX4's regulation of NMD could be mediated by FRG1.

      Weaknesses:

      A major weakness and concern is that many of the key conclusions drawn by the authors are not supported by the data, and there are also some significant concerns with experimental design. More specific comments below describe these issues:

      (1) Multiple issues lower the confidence in the experiments testing the effect of FRG1 on NMD.

      (a) All reporter assays presented in the manuscript are based on quantification of luciferase activity, and in most cases, the effect on luciferase activity is quite small. This assay is the key experimental approach throughout the manuscript. However, no evidence is provided that the effect captured by this assay is due to enhanced degradation of the mRNA encoding the luciferase reporter, which is what is implied in the interpretation of these experiments. Crucially, there is also no control for the reporter that can account for the effects of experimental manipulations on transcriptional versus post-transcriptional effects. A control reporter lacking a 3'UTR intron is described in Barid et al, where the authors got their NMD reporter from. Due to small effects observed on luciferase activity upon FRG1 depletion, it is necessary to not only measure NMD reporter mRNA steady state levels, but it will be equally important to ascertain that the effect of FRG1 on NMD is at the level of mRNA decay and not altered transcription of NMD substrates. This can be accomplished by testing decay rates of the beta-globin reporter mRNA.

      We thank the reviewer for raising these points and for the careful evaluation of our experimental approach. Here we provide our response to comment (a) in three parts

      Reliance on luciferase-based reporter assays

      While luciferase-based NMD reporter assays represent an important experimental component of this study, our conclusions do not rely exclusively on this approach. The reporter-based findings are independently supported by RNA sequencing analyses of FRG1-perturbed cells, which demonstrate altered abundance of established PTC-containing NMD target transcripts. This genome-wide analysis provides an unbiased and physiologically relevant validation of FRG1 involvement in NMD regulation.

      All reporter assays presented in the manuscript are based on quantification of luciferase activity, and in most cases, the effect on luciferase activity is quite small.

      We respectfully disagree with the comment that the magnitude of the luciferase effects is low. Increased expression of FRG1, which leads to reduced UPF1 levels, results in a ~3.5-fold increase in relative luciferase activity (Fig. 1C), indicating a robust effect. Furthermore, in the in vivo zebrafish model, FRG1 knockout causes a pronounced decrease in relative luciferase activity (Fig. 1H), consistent with elevated UPF1 levels and enhanced NMD activity.

      It is also important to note that FRG1 functions as a negative regulator of UPF1; therefore, its depletion is expected to increase UPF1 levels. However, excessive elevation of UPF1 is likely constrained by additional regulatory mechanisms, which may limit the observable effects of FRG1 knockdown or knockout. In line with this, our previous study (1) demonstrated that FRG1 positively regulates multiple NMD factors while exerting an inverse regulatory effect on UPF1. This dual role suggests that FRG1 may act as a compensatory modulator of the NMD machinery, which likely explains the relatively subtle net effects observed in FRG1 knockdown/knockout conditions in vitro (Fig. 1A and 1B). This interpretation is explicitly discussed in the manuscript (Discussion, paragraph para 4).

      However, no evidence is provided that the effect captured by this assay is due to enhanced degradation of the mRNA encoding the luciferase reporter, which is what is implied in the interpretation of these experiments. Crucially, there is also no control for the reporter that can account for the effects of experimental manipulations on transcriptional versus post-transcriptional effects. A control reporter lacking a 3'UTR intron is described in Barid et al, where the authors got their NMD reporter from. Due to small effects observed on luciferase activity upon FRG1 depletion, it is necessary to not only measure NMD reporter mRNA steady state levels, but it will be equally important to ascertain that the effect of FRG1 on NMD is at the level of mRNA decay and not altered transcription of NMD substrates. This can be accomplished by testing decay rates of the beta-globin reporter mRNA.

      Thank you for your suggestion. We will test decay rates of the beta-globin reporter mRNA.

      (b) It is unusual to use luciferase enzymatic activity as a measurement of RNA decay status. Such an approach can at least be justified if the authors can test how many-fold the luciferase activity changes when NMD is inhibited using a chemical inhibitor (e.g., SMG1 inhibitor) or knockdown of a core NMD factor.

      We respectfully disagree that the use of luciferase enzymatic activity as a readout for NMD is unusual. Multiple prior studies have successfully employed identical or closely related luciferase-based/fluorescence-based reporters to quantify NMD activity (2–5). Importantly, the goal of our study was not to measure RNA decay kinetics per se, but rather to assess how altered FRG1 levels influence the functional efficiency of the NMD pathway. Given that FRG1 is a structural component of the spliceosome C complex (6) and is previously indirectly linked to NMD regulation (1,7) this approach was well-suited to address our central question.

      As suggested by the reviewer, we will also assess luciferase activity following pharmacological inhibition of NMD to further validate the reporter system's responsiveness.

      (c) The concern about the direct effect of FRG1 on NMD is further amplified by the small effects of FRG1 knockout on steady-state levels of endogenous NMD targets (Figure 1A and B: ~20% reduction in reporter mRNA in MCF7 cells; Figure 1M, only 18 endogenous NMD targets shared between FRG1_KO and FRG1_KD).

      The modest changes observed upon FRG1 loss do not preclude a direct role in NMD. As detailed in our response to comment (a) and discussed in paragraph 4 of the Discussion, limited effects on steady-state levels of endogenous NMD targets are expected given the buffering capacity of the NMD pathway and the contribution of compensatory regulatory mechanisms.

      (d) The question about transcriptional versus post-transcriptional effects is also important in light of the authors' previous work that FRG1 can act as a transcriptional regulator.

      We agree that distinguishing between transcriptional and post-transcriptional effects is important, particularly in light of our previous work demonstrating that FRG1 can function as a transcriptional regulator of multiple NMD genes (1). Consistent with this, the current manuscript shows that FRG1 influences the transcript levels of UPF1. In addition, we demonstrate that FRG1 regulates UPF1 at the protein level. We therefore conclude that FRG1 regulates UPF1 dually, at both transcriptional and post-transcriptional levels, supporting a dual role for FRG1 in the regulation of NMD.

      This conclusion is further supported by prior studies indicating post-transcriptional functions of FRG1. FRG1 is a nucleocytoplasmic shuttling protein(8), interacts with the NMD factor ROD1 (7), and has been identified as a component of the spliceosomal C complex (6). FRG1 has also been reported to associate with the hnRNPK family of proteins (8), which participate in extensive protein–protein interaction networks. Collectively, these observations are consistent with a role for FRG1 in regulating NMD components at multiple levels.

      (2) In the experiments probing the relationship between DUX4 and FRG1 in NMD regulation, there are some inconsistencies that need to be resolved.

      (a) Figure 3 shows that the inhibition of NMD reporter activity caused by DUX4 induction is reversed by FRG1 knockdown. Although levels of FRG1 and UPF1 in DUX4 uninduced and DUX4 induced + FRG1 knockdown conditions are similar (Figure 5A), why is the reporter activity in DUX4 induced + FRG1 knockdown cells much lower than DUX4 uninduced cells in Figure 3?

      We appreciate the reviewer’s comment. Figures 3 and 5A represent independent experiments in which FRG1 knockdown was achieved by transient transfection. As such, variability in transfection efficiency is expected and likely accounts for the quantitative difference. We want to highlight that compared to DUX4_induced lane (Fig. 5A, lane 2), when we knock down FRG1 on the DUX4_induced background, it shows a clear increase in the UPF1 level (Fig. 5A, lane 3). We will add one more replicate to 5 A with better FRG1_KD transfection to the experiment.

      (b) In Figure 3, it is important to know the effect of FRG1 knockdown in DUX4 uninduced conditions.

      We thank the reviewer for this thoughtful suggestion. The effect of FRG1 knockdown under DUX4-uninduced conditions is presented in Figure 1A, where FRG1 levels are reduced without altering DUX4 expression. In contrast, Figure 3 is specifically designed to assess the rescue effect—namely, how reduction of FRG1 expression under DUX4-induced conditions influences NMD efficiency. Therefore, inclusion of an FRG1 knockdown–only group in Figure 3 was not relevant to the objective of this experiment.

      (c) On line 401, the authors claim that MG132 treatment leads to "time-dependent increase in UPF1 protein levels" in Figure 5C. However, upon proteasome inhibition, UPF1 levels significantly increase only at 8h time point, while the change at 12 and 24 hours is not significantly different from the control.

      We thank the reviewer for this observation and agree that the statement of a “time-dependent increase in UPF1 protein levels” was inaccurate. A significant increase is observed only at the 8 h time point following MG132 treatment, with no significant changes at 12 h or 24 h. The text will be revised accordingly to reflect Figure 5C.

      (3) There are multiple issues with experiments investigating ubiquitination of UPF1:

      (a) Ubiquitin blots in Figure 6 are very difficult to interpret. There is no information provided either in the text or figure legends as to which bands in the blots are being compared, or about what the sizes of these bands are, as compared to UPF1. Also, the signal for Ub in most IP samples looks very similar to or even lower than the input.

      We agree that the ubiquitin blots in Figure 6 require clearer presentation. In the revised figure, we will annotate the ubiquitin immunoblots to indicate the region corresponding to UPF1 (~140 kDa), which is the relevant molecular weight for interpretation. Because UPF1 is polyubiquitinated, ubiquitinated species are expected to appear as multiple bands rather than a single discrete signal; therefore, ubiquitination was assessed across the full blot. Importantly, interpretation is based on comparisons between UPF1 immunoprecipitated samples within each panel (Fig. 6C–F), rather than between input and IP lanes. For example, in Figure 6 C UPF1 IP FRG1_KD compared to UPF1 IP FRG1_Ex, in Figure 6 D UPF1 IP FRG1_WT compared to UPF1 IP FRG1_KO, in Figure 6 E UPF1 IP FRG1_KO compared to UPF1 IP FRG1_KO+FRG1_Ex, and in Figure 6 F UPF1 IP FRG1_Ex compared to UPF1 IP FRG1_Ex+MG132 TRT.

      (b) Western blot images in Figure 6D appear to be adjusted for brightness/contrast to reduce background, but are done in such a way that pixel intensities are not linearly altered. This image appears to be the most affected, although some others have also similar patterns (e.g., Figure 5C).

      We thank the reviewer for raising this point. The appearance noted in Figure 6D was not due to non-linear alteration of pixel intensities, but rather resulted from the poor quality of the ubiquitin antibody, which required prolonged exposure times. To address this, we replaced the antibody and repeated the ubiquitin immunoblots shown in Figures 6D, 6E, and 6F.

      For Figure 5C, only uniform contrast adjustment was applied for clarity. Importantly, all adjustments were performed linearly and applied to the entire image. Raw, unprocessed images for all blots are provided in the Supplementary Information. Updated versions of Figures 5 and 6 will be included in the revised manuscript.

      (4) The experiments probing physical interactions of FRG1 with UPF1, spliceosome and EJC proteins need to consider the following points:

      (a) There is no information provided in the results or methods section on whether immunoprecipitations were carried out in the absence or presence of RNases. Each RNA can be bound by a plethora of proteins that may not be functionally engaged with each other. Without RNase treatment, even such interactions will lead to co-immunoprecipitation. Thus, experiments in Figure 6 and Figure 7A-D should be repeated with and without RNase treatment.

      We thank the reviewer for this important point. The co-immunoprecipitation experiments shown in Figures 6 and 7A–D were performed in the absence of RNase treatment; this information was inadvertently omitted and will be added to the Methods section and the relevant figure legends. To directly assess whether the observed interactions are RNA-dependent, we will repeat the key co-immunoprecipitation experiments in the presence of RNase treatment and include these results in the revised manuscript.

      (b) Also, the authors claim that FRG1 is a "structural component" of EJC and NMD complexes seems to be an overinterpretation. As noted in the previous comment, these interactions could be mediated by a connecting RNA molecule.

      We thank the reviewer for this insightful comment. As noted, previous studies have suggested that FRG1 interacts with components of the EJC and NMD machinery. Specifically, Bertram et al. (6) identified FRG1 as a component of the spliceosomal C complex via Cryo-EM structural analysis, and pull-down studies have shown direct interaction between FRG1 and ROD1, a known EJC component (7). These findings support a protein-protein interaction rather than one mediated solely by RNA. To further address the reviewer’s concern, we will perform key co-immunoprecipitation experiments in the presence of RNase treatment to distinguish RNA-dependent from RNA-independent interactions.

      (c) A negative control (non-precipitating protein) is missing in Figure 7 co-IP experiments.

      We agree that including a non-precipitating protein as a negative control is important, and we will perform the co-IP experiment incorporating this control.

      (d) Polysome analysis is missing important controls. FRG1 and EIF4A3 co-sedimentation with polysomes could simply be due to their association with another large complex (e.g., spliceosome), which will also co-sediment in these gradients. This possibility can at least be tested by Western blotting for some spliceosome components across the gradient fractions. More importantly, a puromycin treatment control needs to be performed to confirm that FRG1 and EIF4A3 are indeed bound to polysomes, which are separated into ribosome subunits upon puromycin treatment. This leads to a shift of the signal for ribosomal proteins and any polysome-associated proteins to the left.

      As recommended, we will examine the distribution of a spliceosome component across the gradient fractions to assess potential co-sedimentation. Additionally, we will perform a puromycin treatment control to confirm that FRG1 and EIF4A3 are genuinely associated with polysomes.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Palo et al present a novel role for FRG1 as a multifaceted regulator of nonsense-mediated mRNA decay (NMD). Through a combination of reporter assays, transcriptome-wide analyses, genetic models, protein-protein interaction studies, ubiquitination assays, and ribosome-associated complex analyses, the authors propose that FRG1 acts as a negative regulator of NMD by destabilizing UPF1 and associating with spliceosomal, EJC, and translation-related complexes. Overall, the data, while consistent with the authors' central conclusions, are undermined by several claims-particularly regarding structural roles and mechanistic exclusivity. To really make the claims presented, further experimental evidence would be required.

      Strengths:

      (1) The integration of multiple experimental systems (zebrafish and cell culture).

      (2) Attempts to go into a mechanistic understanding of the relationship between FGR1 and UPF1.

      Weaknesses:

      (1) Overstatement of FRG1 as a structural NMD component.

      Although FRG1 interacts with UPF1, eIF4A3, PRP8, and CWC22, core spliceosomal and EJC interactions (PRP8-CWC22 and eIF4A3-UPF3B) remain intact in FRG1-deficient cells. This suggests that, while FRG1 associates with these complexes, this interaction is not required for their assembly or structural stability. Without further functional or reconstitution experiments, the presented data are more consistent with an interpretation of FRG1 acting as a regulatory or accessory factor rather than a core structural component.

      We thank the reviewer for this clarification. We would like to emphasize that we do not claim FRG1 to be a core structural component of either the spliceosome or the EJC. Consistent with the reviewer’s interpretation, our data indicate that FRG1 deficiency does not disrupt the structural integrity of these complexes. Our intended conclusion is that FRG1 functions as a regulatory or accessory factor in NMD rather than being required for complex assembly or stability. We will carefully revise the manuscript to remove any language that could be interpreted as an overstatement. In addition, we are currently performing further experiments to better define the association of FRG1 with the EJC.

      (2) Causality between UPF1 depletion and NMD inhibition is not fully established.

      While reduced UPF1 levels provide a plausible explanation for decreased NMD efficiency, the manuscript does not conclusively demonstrate that UPF1 depletion drives all observed effects. Given FRG1's known roles in transcription, splicing, and RNA metabolism, alterations in transcript isoform composition and apparent NMD sensitivity may arise from mechanisms independent of UPF1 abundance. To directly link UPF1 depletion to altered NMD efficiency, rescue experiments testing whether UPF1 re-expression restores NMD activity in FRG1-overexpressing cells would be important.

      As suggested, to directly test causality, we will perform rescue experiments to determine whether UPF1 re-expression restores NMD activity in FRG1-overexpressing MCF7 cells.

      (3) Mechanism of FRG1-mediated UPF1 ubiquitination requires clarification.

      The ubiquitination assays support a role for FRG1 in promoting UPF1 degradation; however, the mechanism underlying this remains unexplored. The relationship between FRG1-UPF1 what role FRG1 plays in this is unclear (does it function as an adaptor, recruits an E3 ubiquitin ligase, or influences UPF1 ubiquitination indirectly through transcriptional or signaling pathways?).

      We agree with the reviewer that the precise mechanism by which FRG1 promotes UPF1 ubiquitination remains to be defined. Our ubiquitination assays support a role for FRG1 in facilitating UPF1 degradation; however, whether FRG1 functions directly as an adaptor or E3 ligase, or instead influences UPF1 stability indirectly, is currently unclear. Notably, a prior study by Geng et al. reported that DUX4 expression alters the expression of numerous genes involved in protein ubiquitination, including multiple E3 ubiquitin ligases (9), and FRG1 itself has been reported to be upregulated upon DUX4 expression in muscle cells. We will expand the Discussion to address these potential mechanisms and place our findings in the context of indirect transcriptional or signaling pathways that may regulate UPF1 proteolysis. A detailed mechanistic dissection of FRG1-mediated ubiquitination is beyond the scope of the present study.

      (4) Limited transcriptome-wide interpretation of RNA-seq data.

      Although the RNA-seq data analysis relies heavily on a small subset of "top 10" genes. Additionally, the criteria used to define NMD-sensitive isoforms are unclear. A more comprehensive transcriptome-wide summary-indicating how many NMD-sensitive isoforms are detected and how many are significantly altered-would substantially strengthen the analysis.

      We thank the reviewer for this comment and agree that the current presentation may place a disproportionate emphasis on a limited subset of genes. These genes were selected as illustrative examples from an isoform-level analysis performed using IsoformSwitchAnalyzeR (ISAR) (10); however, we acknowledge that this approach does not fully convey the transcriptome-wide scope of the analysis.

      Using quantified RNA-seq data, ISAR was employed to identify significant isoform switches and transcripts predicted to be NMD-sensitive. Isoforms were annotated using GENCODE v47, and NMD sensitivity was assigned based on the established 50-nucleotide rule, as described in the Materials and Methods. To address the reviewer’s concern, we will revise the Results section to include a transcriptome-wide summary derived from the ISAR analysis.

      (5) Clarification of NMD sensor assay interpretation.

      The logic underlying the NMD sensor assay should be explained more clearly early in the manuscript, as the inverse relationship between luciferase signal and NMD efficiency may be counterintuitive to readers unfamiliar with this reporter system. Inclusion of a schematic or brief explanatory diagram would improve accessibility.

      We agree with the reviewer and would provide a schematic as well as the experimental setup diagram to improve accessibility to the readers.

      (6) Potential confounding effects of high MG132 concentration.

      The MG132 concentration used (50 µM) is relatively high and may induce broad cellular stress responses, including inhibition of global translation (its known that proteosome inhibition shuts down translation). Controls addressing these secondary effects would strengthen the conclusion that UPF1 stabilization specifically reflects proteasome-dependent degradation would be essential.

      We acknowledge the reviewer’s concern regarding the relatively high concentration of MG132 used in this study. While proteasome inhibition can indeed induce global translation inhibition, our interpretation is based on the specific stabilization of UPF1 observed under these conditions. Since inhibition of global translation would generally reduce protein levels rather than cause selective accumulation, the observed increase in UPF1 is unlikely to result from translational effects. To address this point, we plan to repeat selected experiments using a lower MG132 concentration to further confirm that UPF1 stabilization reflects proteasome-dependent degradation.

      (7) Interpretation of polysome co-sedimentation data.

      While the co-sedimentation of FRG1 with polysomes is intriguing, this approach does not distinguish between direct ribosomal association and co-migration with ribosome-associated complexes. This limitation should be explicitly acknowledged in the interpretation.

      We acknowledge that polysome co-sedimentation alone cannot definitively distinguish between direct ribosomal binding and co-migration with ribosome-associated complexes. Importantly, our interpretation does not rely solely on this assay; when combined with co-immunoprecipitation and proximity ligation assay results, the data consistently support an association of FRG1 with the exon junction complex. We are also conducting additional experiments with appropriate controls to further validate the specificity of FRG1’s association with ribosomes and to address the possibility of nonspecific co-migration.

      (8) Limitations of PLA-based interaction evidence.

      The PLA data convincingly demonstrate close spatial proximity between FRG1 and eIF4A3; however, PLA does not provide definitive evidence of direct interaction and is known to be susceptible to artefacts. Moreover, a distance threshold of ~40 nm still allows for proteins to be in proximity without being part of the same complex. These limitations should be clearly acknowledged, and conclusions should be framed accordingly.

      We thank the reviewer for highlighting this important point. We agree that PLA indicates close spatial proximity but does not constitute definitive evidence of direct interaction and can be susceptible to artefacts. We will explicitly acknowledge this limitation in the revised manuscript. Importantly, our conclusions are not solely based on PLA data; they are supported by complementary co-immunoprecipitation and polysome co-sedimentation assays, which provide biochemical evidence consistent with an association between FRG1 and eIF4A3.

      Reviewer #3 (Public review):

      The manuscript by Palo and colleagues demonstrates identification of FRG1 as a novel regulator of nonsense-mediated mRNA decay (NMD), showing that FRG1 inversely modulates NMD efficiency by controlling UPF1 abundance. Using cell-based models and a frg1 knockout zebrafish, the authors show that FRG1 promotes UPF1 ubiquitination and proteasomal degradation, independently of DUX4. The work further positions FRG1 as a structural component of the spliceosome and exon junction complex without compromising its integrity. Overall, the manuscript provides mechanistic insight into FRG1-mediated post-transcriptional regulation and expands understanding of NMD homeostasis. The authors should address the following issues to improve the quality of their manuscript.

      (1) Figure 7A-D, appropriate positive controls for the nuclear fraction (e.g., Histone H3) and the cytoplasmic fraction (e.g., GAPDH or α-tubulin) should be included to validate the efficiency and purity of the subcellular fractionation.

      We thank the reviewer for the suggestion. We will include appropriate positive controls for the nuclear fraction (Histone H3) and the cytoplasmic fraction (GAPDH or α-tubulin) in Figure 7A–D to validate the efficiency and purity of the subcellular fractionation.

      (2) To strengthen the conclusion that FRG1 broadly impacts the NMD pathway, qRT-PCR analysis of additional core NMD factors (beyond UPF1) in the frg1⁻/⁻ zebrafish at 48 hpf would be informative.

      We appreciate the reviewer’s insightful comment. We will perform qRT-PCR analysis of additional core NMD factors in the frg1⁻/⁻ zebrafish at 48 hpf to further strengthen the conclusion that FRG1 broadly impacts the NMD pathway.

      (3) Figure labels should be standardized throughout the manuscript (e.g., consistent use of "Ex" instead of mixed terms such as "Oex") to improve clarity and readability.

      We thank the reviewer for noticing the inconsistency. We will ensure that all figure labels are standardized throughout the manuscript (e.g., using “Ex” consistently) to improve clarity and readability.

      (4) The methods describing the generation of the frg1 knockout zebrafish could be expanded to include additional detail, and a schematic illustrating the CRISPR design, genotyping workflow, and validation strategy would enhance transparency and reproducibility.

      We appreciate the reviewer’s suggestion and will expand the Methods section to provide additional detail on the generation of the frg1 knockout zebrafish. A schematic illustrating the CRISPR design, genotyping workflow, and validation strategy will also be included to enhance transparency and reproducibility.

      (5) As FRG1 is a well-established tumor suppressor, additional cell-based functional assays under combined FRG1 and UPF1 perturbation (e.g., proliferation, migration, or survival assays) could help determine whether FRG1 influences cancer-associated phenotypes through modulation of the NMD pathway.

      We thank the reviewer for this thoughtful and constructive suggestion. While FRG1 is indeed a well-established tumor suppressor, incorporating additional cell-based functional assays under combined FRG1 and UPF1 perturbation would significantly broaden the scope of the current study. The present work is focused on elucidating the molecular relationship between FRG1 and the NMD pathway. Investigation of downstream cancer-associated phenotypes represents an important and interesting direction for future studies, but is beyond the scope of the current manuscript.

      (6) Given the claim that FRG1 inversely regulates NMD efficacy via UPF1, an epistasis experiment such as UPF1 overexpression in an FRG1-overexpressing background followed by an NMD reporter assay would provide stronger functional validation of pathway hierarchy.

      We agree with the reviewer’s suggestion. To strengthen the functional validation of the proposed pathway hierarchy, we will perform an epistasis experiment by overexpressing UPF1 in an FRG1-overexpressing background and assess NMD activity using an established NMD reporter assay. The results of this experiment will be included in the revised manuscript.

      References

      (1) Palo A, Patel SA, Shubhanjali S, Dixit M. Dynamic interplay of Sp1, YY1, and DUX4 in regulating FRG1 transcription with intricate balance. Biochim Biophys Acta Mol Basis Dis. 2025 Mar;1871(3):167636.

      (2) Sato H, Singer RH. Cellular variability of nonsense-mediated mRNA decay. Nat Commun. 2021 Dec 10;12(1):7203.

      (3) Baird TD, Cheng KCC, Chen YC, Buehler E, Martin SE, Inglese J, et al. ICE1 promotes the link between splicing and nonsense-mediated mRNA decay. eLife. 2018 Mar 12;7:e33178.

      (4) Chu V, Feng Q, Lim Y, Shao S. Selective destabilization of polypeptides synthesized from NMD-targeted transcripts. Mol Biol Cell. 2021 Dec 1;32(22):ar38.

      (5) Udy DB, Bradley RK. Nonsense-mediated mRNA decay uses complementary mechanisms to suppress mRNA and protein accumulation. Life Sci Alliance. 2022 Mar;5(3):e202101217.

      (6) Bertram K, El Ayoubi L, Dybkov O, Agafonov DE, Will CL, Hartmuth K, et al. Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome. Mol Cell. 2020 Oct 1;80(1):127-139.e6.

      (7) Brazão TF, Demmers J, van IJcken W, Strouboulis J, Fornerod M, Romão L, et al. A new function of ROD1 in nonsense-mediated mRNA decay. FEBS Lett. 2012 Apr 24;586(8):1101–10.

      (8) Sun CYJ, van Koningsbruggen S, Long SW, Straasheijm K, Klooster R, Jones TI, et al. Facioscapulohumeral muscular dystrophy region gene 1 is a dynamic RNA-associated and actin-bundling protein. J Mol Biol. 2011 Aug 12;411(2):397–416.

      (9) Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, et al. DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Dev Cell. 2012 Jan 17;22(1):38–51.

      (10) Vitting-Seerup K, Sandelin A. The Landscape of Isoform Switches in Human Cancers. Mol Cancer Res MCR. 2017 Sep;15(9):1206–20.

    1. Author response:

      eLife Assessment 

      This study presents a valuable finding on maternal SETDB1 as a key chromatin repressor that shuts down the 2C gene program and enables normal mouse embryonic development. The evidence supporting the claims of the authors is solid, although the inclusion of a causality test, a mechanistic understanding of SETDB1 targeting, and phenotypic quantification would have greatly strengthened the study. The work will be of broad interest to biologists working on embryonic development, stem cells and gene regulation.

      Thank you for this positive evaluation of our work. Please find the point-by point responses to the Reviewer’s comments below.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary: 

      During the earliest stages of mouse development, the zygote and 2-cell (2C) embryo are totipotent, capable of generating all embryonic and extra-embryonic lineages, and they transiently express a distinctive set of "2C-stage" genes, many driven by MERVL long terminal repeat (LTR) promoters. Although activation of these transcripts is a normal feature of totipotency, they must be rapidly silenced as development proceeds to the 4-cell and 8-cell stages; failure to shut down the 2C program results in developmental arrest. This study examines the role of maternal SETDB1, a histone H3K9 methyltransferase, in suppressing the 2C transcriptional network. Using an oocyte-specific conditional knockout that removes maternal Setdb1 while leaving the paternal allele intact, the authors demonstrate that embryos lacking maternal SETDB1 arrest during cleavage, with very few progressing beyond the 8-cell stage and no morphologically normal blastocysts forming. Transcriptomic analyses reveal persistent expression of MERVL-LTR-driven transcripts and other totipotency markers, indicating a failure to terminate the totipotent state. Together, the data demonstrate that maternally deposited SETDB1 is required to silence the MERVL-driven 2C program and enable the transition from totipotency to pluripotency. More broadly, the work identifies maternal SETDB1 as a key chromatin repressor that deposits repressive H3K9 methylation to shut down the transient 2C gene network and to permit normal preimplantation development. 

      Strengths: 

      (1) Closes a key knowledge gap. 

      The study tackles a central open question - how embryos exit the totipotent 2-cell (2C) state - and provides direct in vivo evidence that epigenetic repression is required to terminate the 2C program for development to proceed. By identifying maternal SETDB1 as the responsible factor, the work substantially advances our understanding of the maternal-to-zygotic transition and early lineage specification. 

      (2) Clean genetics paired with rigorous genomics. 

      An oocyte-specific Setdb1 knockout cleanly isolates a maternal-effect requirement, ensuring that early phenotypes arise from loss of maternal protein. The resulting cleavage-stage arrest is unambiguous (most embryos stall before or around the 8-cell stage). State-of-the-art single-embryo RNA-seq across stages - well-matched to low-cell-number constraints - captures genome-wide mis-expression, including persistent 2C transcripts in mutants, strongly supporting the conclusions. 

      (3) Compelling molecular linkage to phenotype. 

      Transcriptome data show that without maternal SETDB1, embryos fail to repress a suite of 1-cell/2C-specific genes by the 8-cell stage. The tight correlation between continued activation of the MERVL-driven totipotency network and developmental arrest provides a specific molecular explanation for the observed failure to progress. 

      (4) Mechanistic insight grounded in chromatin biology. 

      SETDB1, a H3K9 methyltransferase classically linked to heterochromatin and transposon repression, targets MERVL LTRs and MERVL-driven chimeric transcripts in early embryos. Bioinformatic evidence indicates that these loci normally acquire H3K9me3 during the 2C→4C transition. The data articulate a coherent mechanism: maternal SETDB1 deposits repressive H3K9me3 at 2C gene loci to shut down the totipotency network, extending observations from ESC systems to bona fide embryos. 

      (5) Broad implications for development and stem-cell biology. 

      By pinpointing a maternal gatekeeper of the totipotent-to-pluripotent transition, the work suggests that some cases of cleavage-stage arrest (e.g., in IVF) may reflect faulty epigenetic silencing of transposon-driven genes. It also informs stem-cell efforts to control totipotent-like states in vitro (e.g., 2C-like cells), linking epigenetic reprogramming, transposable-element regulation, and developmental potency.

      We thank Reviewer 1 for recognizing the strengths in our work and for the suggestions below.

      Weaknesses: 

      (1) Causality not directly demonstrated. 

      The link among loss of SETDB1, persistence of 2C transcripts, and developmental arrest is compelling but remains correlative. No rescue experiments test whether dampening the 2C/MERVL program restores development. Targeted interventions-e.g., knocking down key 2C drivers (such as Dux) or pharmacologically curbing MERVL-linked transcription in maternal Setdb1 mutants-would strengthen the claim that unchecked 2C activity is causal rather than a by-product of other SETDB1 functions.

      We agree that rescue experiments might strengthen causality. Those experiments, however, would be extremely challenging technically because the knockdowns would need to be precisely timed to follow (and not prevent) the wave of 2c-specific activation. Knocking down 2c drivers in the zygote, for example, may prevent switching on the totipotency program. In addition, while sustained MERVL expression—such as that induced by forced DUX expression—disrupts totipotency exit and embryo development (1, 2), derepression of transcription is very broad in Setdb1<sup>mat-/+</sup> embryos and knocking down individual 2C drivers may not be sufficient to rescue development or restore the exit from totipotency.

      (2) Limited mechanistic resolution of SETDB1 targeting. 

      The study establishes a requirement for maternal SETDB1 but does not define how it is recruited to MERVL loci. Given SETDB1's canonical cooperation with TRIM28/KAP1 and KRAB-ZNFs, upstream sequence-specific factors and/or pre-existing chromatin features likely guide targeting. Direct occupancy and mark-placement evidence (e.g., SETDB1/TRIM28 CUT&RUN or ChIP, and H3K9me3 profiling at MERVL LTRs during the 2C→4C window) would convert inferred mechanisms into demonstrated ones.

      We do show H3K9me3 patterns at MERVL LTRs during the early2c-late2c-2c-4c-8c-morula window from a published dataset. Please see the genome browser images in Figures 4C, 4D, 4E, 6D, 6E and Figure S6. We agree that mapping of SETDB1/TRIM28 to those locations would strengthen the mechanistic insight. However, ChIPseq or CUT&RUN of those proteins in preimplantation embryos are not technically feasible. We do provide genetic evidence for the collaboration between SETDB1 and DUXBL, a DNA-binding factor, by showing that DUXBL cannot switch off its top targets without SETDB1 (Figure 6). Future studies will characterize the molecular mechanisms underlying this (likely indirect) collaboration. We do not think that DUXBL and SETDB1 directly interact, because such interaction was not detected by DUXBL IP-MS (3).

      (3) Narrow scope on MERVL; broader epigenomic consequences underexplored. 

      Maternal SETDB1 may restrain additional repeat classes or genes beyond the 2C network. A systematic repeatome analysis (LINEs/SINEs/ERV subfamilies) would clarify specificity versus a general loss of heterochromatin control. Moreover, potential effects on imprinting or DNA methylation balance are not examined; perturbations there could also contribute to arrest. Bisulfite-based DNA methylation maps at imprinted loci and allele-specific expression analyses would help rule in/out these mechanisms.

      We did examine genes and repeat elements beyond the 2c network. We evaluated gene and TE expression changes using four-way comparisons. Please find the results regarding gene expression in Figure 1C-J, Figure S2, Figure S3, Figure S4., Table S2, Table S3, and Table S4. Please find results on TE expression in Figure S5. Table S6, Table S7, and Table S8 and in the text. We agree that DNA methylation may be altered in Setdb1<sup>mat-/+</sup> embryos. In our hands, evaluating this possibility using bisulfite sequencing requires a larger number of embryos than what we can feasibly obtain (the number of obtained mutant embryos is very small). Regarding imprinted gene expression, one cannot fully assess and interpret imprinted gene expression in preimplantation stage embryos before the maternally deposited transcripts are gone. We reported earlier that clear somatic parental-specific patterns of imprinted gene expression may only start later in development, around 8.5 dpc (4).

      (4) Phenotype quantitation and transcriptomic breadth could be clearer. 

      The developmental phenotype is described qualitatively ("very few beyond 8-cell") without precise stage-wise arrest rates or representative morphology. Tabulated counts (2C/4C/8C/blastocyst), images, and statistics would increase clarity. On the RNA-seq side, the narrative emphasizes known 2C markers; reporting novel/unannotated misregulated transcripts, as well as downregulated pathways (e.g., failure to activate normal 8-cell programs, metabolism, or early lineage markers), would present a fuller portrait of the mutant state.

      Tabulated counts are displayed in Figure 1A, and morphology is shown in Figure S1A. We do say that 4% Setdb1<sup>mat-/+</sup> embryos reached the 8-cel stage by 2.5 dpc. We recovered zero Setdb1<sup>mat-/+</sup> blastocysts at 4.5 dpc (not shown). On the RNA-seq side we do report a more global assessment of transcription of genes and TEs (please see above at point 3), including novel chimeric transcripts (Table S6). Developmental pathways are shown in Figure S3 and Figure S4. Metabolic pathways are displayed in Figure S2.

      Reviewer #2 (Public review): 

      Zeng et al. report that Setdb1-/- embryos fail to extinguish the 1- and 2-cell embryo transcriptional program and have permanent expression of MERVL transposable elements. The manuscript is technically sound and well performed, but, in my opinion, the results lack conceptual novelty.

      (1) The manuscript builds on previous observations that: 1, Setbd1 is necessary for early mouse development, with knockout embryos rarely reaching the 8-cell stage; 2, SETB1 mediates H3K9me3 deposition at transposable elements in mouse ESCs; 3, SETB1silences MERVLs to prevent 2CLC-state acquisition in mouse ESCs. The strength of the current work is the demonstration that this is not due to a general transcriptional collapse; but otherwise, the findings are not surprising. The well-known (several Nature papers of years ago) crosstalk between m6A RNA modification and H3K9me3 in preventing 2CLC generation also partly compromises the novelty of this work.

      We thank the Reviewer for appreciating the technical quality of our work. Regarding novelty, please consider that prior work in ES cells included contradictory findings (please see our Introduction). Prior embryology work (please see our Introduction) did not explain the preimplantation-stage phenotype. We highly appreciate those earlier works. Our work here answers the expectations drawn from prior studies and unequivocally shows that SETDB1 carries out the developmentally essential function of suppressing MERVLs and the 2-cell program in the mouse embryo.

      (2) The conclusions regarding H3K9me3 deposition are inferred based on previously reported datasets, but there is no direct demonstration.

      Dynamic H3K9me3 deposition is displayed at MERVL LTRs during the early2c-late2c-2c-4c-8c-morula window (Figures 4C, 4D, 4E, 6D, 6E and Figure S6) from a published work that has very high-quality data. We agree that demonstrating loss off H3K9me3 in Setdb1<sup>mat-/+</sup> embryos would confirm that the H3K9me3 histone methyltransferase function of SETDB1 (as opposed to any, yet unidentified, non-HMT specific activity of SETDB1) is responsible for shutting down MERVL LTRs. However, ChIP-seq, CUT&RUN, or similar assays are not feasible due to the rarity of Setdb1<sup>mat-/+</sup> embryos.

      (3) The detection of chimeric transcripts is somewhat unreliable using short-read sequencing.

      We used single embryo total RNA-seq and we report detecting chimeric transcripts (Table S6), which is considered more reliable than mRNA-seq for detecting chimeric transcripts, because many are not polyadenylated. We acknowledge, however, that long-read sequencing, which recently is becoming available, but which is still very expensive, is currently the most powerful method for detecting chimeric transcripts. This, however, does not affect the major conclusions or the significance of our work.

    1. Author response:

      The following is the authors’ response to the original reviews

      Comment to both reviewers:

      We are very grateful for the thoughtful and constructive comments from both reviewers. During the revision, and in direct response to these comments, we performed additional control experiments for the cellular fluorescence measurements. These new data revealed that the weak increase in green fluorescence reported in our original submission does not depend on retron-expressed Lettuce RT-DNA or the DFHBI-1T fluorophore, but instead reflects stress-induced autofluorescence of E. coli (e.g. upon inducer and antibiotic treatment).

      We also benchmarked the fluorogenic properties of Lettuce against the RNA FLAP Broccoli and found that Lettuce is ~100-fold less fluorogenic under optimal in vitro conditions. Consequently, with the currently available, in vitro- but not in vivo-optimized Lettuce variants, intracellular fluorescence cannot be reliably detected by microscopy or flow cytometry. We have therefore removed the original flow cytometry / and in-culture-fluorescence data and no longer claim detectable intracellular Lettuce fluorescence.

      In the revised manuscript, we now directly demonstrate that retron-produced Lettuce RT-DNA can be purified from cells and remains functional ex vivo with a gel-based fluorophore-binding assays. Together, these data clarify the current limitations of DNA-based FLAPs for in vivo imaging, while still establishing retrons as a viable platform for intracellular production of functional DNA aptamers.

      Reviewer #1 (Public Review):

      Summary:

      The authors use an interesting expression system called a retron to express single-stranded DNA aptamers. Expressing DNA as a single-stranded sequence is very hard - DNA is naturally double-stranded. However, the successful demonstration by the authors of expressing Lettuce, which is a fluorogenic DNA aptamer, allowed visual demonstration of both expression and folding. This method will likely be the main method for expressing and testing DNA aptamers of all kinds, including fluorogenic aptamers like Lettuce and future variants/alternatives.

      Strengths:

      This has an overall simplicity which will lead to ready adoption. I am very excited about this work. People will be able to express other fluorogenic aptamers or DNA aptamers tagged with Lettuce with this system.

      We thank the reviewer for their thoughtful assessment and appreciate their encouraging remarks.

      Weaknesses:

      Several things are not addressed/shown:

      (1) How stable are these DNA in cells? Half-life?

      We thank the reviewer for this insightful question.

      Retron RT-DNA forms a phage surveillance complex with the associated RT and effector protein[1-4]. Moreover, considering the unique ‘closed’ structure of RT-DNA[5] (with the ends of msr and msd bound either by 2’-5’ linkage and base paired region) and its noncoding function, we hypothesized that the RT-DNA must be exceptionally stable. Nevertheless, we attempted to determine half-life of the RT-DNA using qPCR for Eco2 RT-DNA. To this end, we designed an assay where we would first induce RT-DNA expression, use the induced cells to start a fresh culture without the inducers. We would then take aliquots from this fresh culture at different timepoints and determine RT-DNA abundance by qPCR.

      We induced RT-DNA expression of retron Eco2 in BL21AI cells as described in the Methods. After overnight induction, cells were washed to remove IPTG and arabinose, diluted to OD<sub>600</sub> = 0.2 into fresh LB without inducers, and grown at 37°C. At the indicated time points, aliquots corresponding to OD<sub>600</sub> = 0.1 were boiled (95°C, 5 min), and 1 µL of the lysate was used as template in 20 µL qPCR reactions (see revised Methods for details).

      Assuming RT-DNA degradation would occur by active degradation mechanisms (nuclease-mediated degradation) and dilution (cell growth and division), we determined the rate of degradation by the following equation

      where  is the degradation rate constant and the ratio is the dilution factor which takes into account dilution by cell division. OD<sub>600</sub>(t) was determined by fitting the OD<sub>600</sub> measurements by the following the equation describing logistic growth:

      Which yields the plots shown in Figure 2–figure supplement 1.

      After substituting OD<sub>600</sub>(t) by the function in equation (2), we fit the experimental data for the fold-change of the RT-DNA to equation (1). Interestingly, the best fit (red) was obtained with a  converging towards zero suggesting that the half-life of the RT-DNA is beyond the detection limit of our assay. To showcase typical half-lives of RNA, which are in the range of minutes in growing E. coli cells[6], we refitted the data using constant half-life of 15 and 30 minutes. In both cases, simulated curve deviated significantly from the experimental data further confirming that the half-life of the RT-DNA is probably orders of magnitude higher than the doubling time of E. coli under these optimal conditions. While we cannot exclude that the RT-DNA is still produced as a result of promotor leakiness, but we expect this effect to be low as the expression of RT-DNA in E. coli AI cells requires both the presence of IPGT and arabinose, which were thoroughly removed before inoculating the growth media with the starter culture. Overall, our data therefore argues for an exceptional stability of the RT-DNA in growing bacterial cells.

      We have now included this new experimental data in the supplementary information.

      (2) What concentration do they achieve in cells/copy numbers? This is important since it relates to the total fluorescence output and, if the aptamer is meant to bind a protein, it will reveal if the copy number is sufficient to stoichiometrically bind target proteins. Perhaps the gels could have standards with known amounts in order to get exact amounts of aptamer expression per cell?

      The copy number of RT-DNA can be estimated based on the qPCR experiments. We use a pET28a plasmid, which is low-copy with typical copy number 15-20 per cell[7]. We determined the abundance of RT-DNA over plasmid/RT-DNA, upon induction, to be 8-fold, thereby indicating copy number of Eco2 RT-DNA to be roughly around 100-200. Assuming an average aqueous volume of E. coli of 1 femtoliter[6], the concentration of RT-DNA is ~250-500 nM. We have added this information to the revised version of the manuscript.

      (3) Microscopic images of the fluorescent E. coli - why are these not shown (unless I missed them)? It would be good to see that cells are fluorescent rather than just showing flow sorting data.

      In the original submission, we used flow cytometry as an orthogonal method to quantify the fluorescence output of intracellularly expressed Lettuce aptamer, anticipating that it would provide high-throughput, quantitative information on a large population of cells. During the revision, additional controls revealed that the weak increase in fluorescence we had previously attributed to Lettuce expression was in fact a stress-induced autofluorescence signal that occurred independently of retron RT-DNA and DFHBI-1T. We have therefore removed these data from the manuscript and no longer claim detectable intracellular Lettuce fluorescence.

      To understand this limitation, we compared the in vitro fluorescence of Lettuce with that of the RNA FLAP Broccoli, which is commonly used for RNA live-cell imaging. Under optimal in vitro conditions, Lettuce shows ~100-fold lower fluorescence output than Broccoli (new Figure 3–figure supplement 5). Given this poor fluorogenicity and the low intracellular concentration of retron RT-DNA (now derived from the qPCR experiments), we conclude that the current Lettuce variants are below the detection threshold for in vivo imaging in our system. We now explicitly discuss this limitation and the need for further (in vivo) evolution of DNA-based FLAPs in the revised manuscript.

      (4) I would appreciate a better Figure 1 to show all the intermediate steps in the RNA processing, the subsequent beginning of the RT step, and then the final production of the ssDNA. I did not understand all the processing steps that lead to the final product, and the role of the 2'OH.

      We thank the referee for this comment. We have now made changes to Figure 1, showing the intermediate steps as well as a better illustration of the 2’-5’ linkage.

      (5) I would like a better understanding or a protocol for choosing insertion sites into MSD for other aptamers - people will need simple instructions.

      We appreciate the reviewer for bringing up this important point. We simulated the ssDNA structure using Vienna RNA fold with DNA parameters. Based on the resulting structure, we inserted Lettuce sequence in the single stranded and/or loop regions to minimise interference with the native msd fold. We have now included this information in the description of Figure 3.

      (6) Can the gels be stained with DFHBI/other dyes to see the Lettuce as has been done for fluorogenic RNAs?

      Yes. We have now included experiments where we performed in-gel staining with DFHBI-1T for both chemically synthesized Eco2-Lettuce surrogates as well as the heterologously expressed Eco2-Lettuce RT-DNA. We have added this data to the revised Figure 3 (panel C and E).

      (7) Sometimes FLAPs are called fluorogenic RNA aptamers - it might be good to mention both terms initially since some people use fluorogenic aptamer as their search term.

      We thank the referee for this useful suggestion. We have now included both terms in the introduction of the revised version.

      (8) What E coli strains are compatible with this retron system?

      Experimental and bioinformatic analysis have shown that retrons abundance varies drastically across different strains of E. coli[8-10]. For example, in an experimental investigation of 113 independent clinical isolates of E. coli, only 7 strains contained RT-DNA[8]. In our experiments, we have found that BL21AI strain is compatible with plasmid-borne Eco2. The fact that this strain has a native retron system (Eco1) allowed us to use it as internal standard. However, we were also able express Eco2 RT-DNA in conventional lab strains such as E. coli Top 10 (data not shown), indicating both ncRNA and the RT alone are sufficient for intracellular RT-DNA synthesis.

      (9) What steps would be needed to use in mammalian cells?

      We appreciate the reviewer’s thoughtful inquiry. Expression of retrons has been demonstrated in mammalian cells by Mirochnitchenko et al[11] and Lopez et al[12]. For example, Lopez et al demonstrate expression of retrons in mammalian cell lines using the Lipofectamine 3000 transfection protocol (Invitrogen) and a PiggyBac transposase system[12]. We also mention this in the discussion section of the revised manuscript. Expression of retron-encoded DNA aptamers in mammalian cells should be possible with these systems.

      (10) Is the conjugated RNA stable and does it degrade to leave just the DNA aptamer?

      We are grateful to the reviewer for their perceptive question. This usually depends on the specific retron system. For example, in case of certain retron systems such as retron Sen2, Eco4 and Eco7, the RNA is cleaved off, leaving behind just the ssDNA. In our case, with retron Eco2, the RNA remains stably bound to the ssDNA, thereby maintaining a stable hybrid RNA-DNA structure[10,13]. During the extraction of RT-DNA, the conjugated RNA is degraded during the RNase digestion step, and therefore is not visible in the gel images.

      Reviewer #2 (Public Review):

      Summary:

      This manuscript explores a DNA fluorescent light-up aptamer (FLAP) with the specific goal of comparing activity in vitro to that in bacterial cells. In order to achieve expression in bacteria, the authors devise an expression strategy based on retrons and test four different constructs with the aptamer inserted at different points in the retron scaffold. They only observe binding for one scaffold in vitro, but achieve fluorescence enhancement for all four scaffolds in bacterial cells. These results demonstrate that aptamer performance can be very different in these two contexts.

      Strengths:

      Given the importance of FLAPs for use in cellular imaging and the fact that these are typically evolved in vitro, understanding the difference in performance between a buffer and a cellular environment is an important research question.

      The return strategy utilized by the authors is thoughtful and well-described.

      The observation that some aptamers fail to show binding in vitro but do show enhancement in cells is interesting and surprising.

      We appreciate the reviewer’s thorough assessment.

      Weaknesses:

      This study hints toward an interesting observation, but would benefit from greater depth to more fully understand this phenomenon. Particularly challenging is that FLAP performance is measured in vitro by affinity and in cells by enhancement, and these may not be directly proportional. For example, it may be that some constructs have much lower affinity but a greater enhancement and this is the explanation for the seemingly different performance.

      We thank the reviewer for this insightful comment. In response, we conducted a series of additional control experiments to better understand the apparent discrepancy between the in vitro and in vivo data. These experiments revealed that the previously reported increase in intracellular green fluorescence is independent of retron-expressed Lettuce RT-DNA and DFHBI-1T, and instead reflects stress-induced autofluorescence of E. coli upon inducer and antibiotic treatment. Our original negative controls (empty wild-type Eco2, uninduced cells in the presence of DFHBI-1T) were therefore not sufficient to rule out this effect.

      As a consequence, we have removed the earlier FACS data from the manuscript and no longer claim detectable intracellular Lettuce fluorescence. The reviewer’s comment prompted us to re-examine the fluorogenicity of our constructs in vitro. We found that the 4Lev4 construct folds poorly and produces very low signal in in-gel staining assays with DFHBI-1T. In contrast, the 8LE variant (8-nt P1 stem at position v4) shows the highest fluorescence in these in-gel assays (new Figure 3C). Nevertheless, even this construct remains 100-fold less fluorogenic than the RNA-based FLAP Broccoli (new Figure 3–figure supplement 5), and we were unable to detect its intracellular fluorescence above background (new Figure 3–figure supplement 4).

      To still directly demonstrate that retron-embedded Lettuce domains that are synthesized under intracellular conditions are functional, we modified our strategy in the revision and purified the expressed RT-DNA from E. coli, followed by in-gel staining with DFHBI-1T (new Figure 3E). Despite the challenge of obtaining sufficient amounts of ssDNA, this ex vivo approach clearly shows that the retron-produced Lettuce RT-DNA retains fluorogenic activity.

      The authors only test enhancement at one concentration of fluorophore in cells (and this experimental detail is difficult to find and would be helpful to include in the figure legend). This limits the conclusions that can be drawn from the data and limits utility for other researchers aiming to use these constructs.

      We appreciate this excellent suggestion. In the original experiments, the DFHBI-1T concentration in cells was chosen based on published conditions for live-cell imaging of the Broccoli RNA aptamer[14], which is substantially more fluorogenic than Lettuce. Motivated by the reviewer’s comment, we explored different fluorophore concentrations and additional controls to optimize the in vivo readout. These experiments showed that the weak intracellular fluorescence signal is dominated by stress-induced autofluorescence[15] (possibly due to the weaker antitoxin activity of the modified msd) and does not depend on the presence of Lettuce RT-DNA or DFHBI-1T.

      Given the combination of low Lettuce fluorogenicity and low intracellular RT-DNA levels, we concluded that varying the fluorophore concentration alone does not provide a meaningful way to deconvolute these confounding factors in cells. Instead, we shifted our focus to a more direct assessment of Lettuce activity: we now demonstrate that retron-produced Lettuce RT-DNA can be purified from E. coli and retains fluorogenic activity in an in-gel staining assay with DFHBI-1T (new Figure 3E). We believe this revised strategy provides a clearer and more quantitative characterization of the system’s capabilities and limitations than the initial in vivo fluorescence measurements.

      The FLAP that is used seems to have a relatively low fluorescence enhancement of only 2-3 fold in cells. It would be interesting to know if this is also the case in vitro. This is lower than typical FLAPs and it would be helpful for the authors to comment on what level of enhancement is needed for the FLAP to be of practical use for cellular imaging.

      In the revised manuscript, we directly address this point by comparing the in vitro fluorescence of Lettuce (DNA) and Broccoli (RNA) under optimized buffer conditions. These experiments show that Broccoli is nearly two orders of magnitude more fluorogenic than Lettuce (new Figure 3-figure supplement 5). Thus, the low enhancement observed for Lettuce in cells is consistent with its intrinsically poor fluorogenicity in vitro.

      Based on this comparison and on reported properties of RNA FLAPs such as Broccoli, we conclude that robust cellular imaging typically requires substantially higher fluorogenicity and dynamic range than currently provided by DNA-based Lettuce. In other words, under our conditions, Lettuce is close to or below the practical detection limit for in vivo imaging, whereas Broccoli performs well. We now explicitly state in the Discussion that further evolution and optimization of DNA FLAPs will be required to achieve fluorescence enhancements that are suitable for routine cellular imaging, and we position our work as a first demonstration that functional DNA aptamers can be produced in cells via retrons, while also delineating the current sensitivity limits.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Addgene accession numbers are not listed - how is this plasmid obtained?

      The sequence was obtained from Millman et al[16], and ordered as gblock from IDT. The gblock was then cloned into a pET28a vector by Gibson assembly. We have now included this in the methods section.

      Reviewer #2 (Recommendations For The Authors):

      Page 2, line 40 - FLAPS should be FLAPs

      We have corrected this typo in the revised version.

      References

      (1) Rousset, F. & Sorek, R. The evolutionary success of regulated cell death in bacterial immunity. Curr. Opin. Microbiol. 74, 102312; 10.1016/j.mib.2023.102312 (2023).

      (2) Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084; 10.1126/science.aba0372 (2020).

      (3) Carabias, A. et al. Retron-Eco1 assembles NAD+-hydrolyzing filaments that provide immunity against bacteriophages. Mol. Cell 84, 2185-2202.e12; 10.1016/j.molcel.2024.05.001 (2024).

      (4) Wang, Y. et al. DNA methylation activates retron Ec86 filaments for antiphage defense. Cell Rep. 43, 114857; 10.1016/j.celrep.2024.114857 (2024).

      (5) Wang, Y. et al. Cryo-EM structures of Escherichia coli Ec86 retron complexes reveal architecture and defence mechanism. Nat. Microbiol. 7, 1480–1489; 10.1038/s41564-022-01197-7 (2022).

      (6) Milo, R. & Phillips, R. Cell biology by the numbers (Garland Science Taylor & Francis Group, New York NY, 2016).

      (7) Sathiamoorthy, S. & Shin, J. A. Boundaries of the origin of replication: creation of a pET-28a-derived vector with p15A copy control allowing compatible coexistence with pET vectors. PLOS ONE 7, e47259; 10.1371/journal.pone.0047259 (2012).

      (8) Sun, J. et al. Extensive diversity of branched-RNA-linked multicopy single-stranded DNAs in clinical strains of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 86, 7208–7212; 10.1073/pnas.86.18.7208 (1989).

      (9) Rice, S. A. & Lampson, B. C. Bacterial reverse transcriptase and msDNA. Virus Genes 11, 95–104; 10.1007/BF01728651 (1995).

      (10) Simon, A. J., Ellington, A. D. & Finkelstein, I. J. Retrons and their applications in genome engineering. Nucleic Acids Res. 47, 11007–11019; 10.1093/nar/gkz865 (2019).

      (11) Mirochnitchenko, O., Inouye, S. & Inouye, M. Production of single-stranded DNA in mammalian cells by means of a bacterial retron. J. Biol. Chem. 269, 2380–2383; 10.1016/S0021-9258(17)41956-9 (1994).

      (12) Lopez, S. C., Crawford, K. D., Lear, S. K., Bhattarai-Kline, S. & Shipman, S. L. Precise genome editing across kingdoms of life using retron-derived DNA. Nat. Chem. Biol. 18, 199–206; 10.1038/s41589-021-00927-y (2022).

      (13) Lampson, B. C. et al. Reverse transcriptase in a clinical strain of Escherichia coli: production of branched RNA-linked msDNA. Science 243, 1033–1038; 10.1126/science.2466332 (1989).

      (14) Filonov, G. S., Moon, J. D., Svensen, N. & Jaffrey, S. R. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J. Am. Chem. Soc. 136, 16299–16308; 10.1021/ja508478x (2014).

      (15) Renggli Sabine, Keck Wolfgang, Jenal Urs & Ritz Daniel. Role of Autofluorescence in Flow Cytometric Analysis of Escherichia coli Treated with Bactericidal Antibiotics. J. Bacteriol. 195, 4067–4073; 10.1128/jb.00393-13. (2013).

      (16) Millman, A. et al. Bacterial Retrons Function In Anti-Phage Defense. Cell 183, 1551-1561.e12; 10.1016/j.cell.2020.09.065 (2020).

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Zhang and colleagues examine neural representations underlying abstract navigation in entorhinal cortex (EC) and hippocampus (HC) using fMRI. This paper replicates a previously identified hexagonal modulation of abstract navigation vectors in abstract space in EC in a novel task involving navigating in a conceptual Greeble space. In HC, the authors identify a three-fold signal of the navigation angle. They also use a novel analysis technique (spectral analysis) to look at spatial patterns in these two areas and identify phase coupling between HC and EC. Interestingly, the three-fold pattern identified in the hippocampus explains quirks in participants' behavior where navigation performance follows a three-fold periodicity. Finally, the authors propose a EC-HPC PhaseSync Model to understand how the EC and HC construct cognitive maps. The wide array and creativity of the techniques used is impressive but because of their unique nature, the paper would benefit from more details on how some of these techniques were implemented.

      Comments on revisions:

      Most of my concerns were adequately addressed, and I believe the paper is greatly improved. I have two more points. I noticed that the legend for Figure 4 still refers to some components of the previous figure version, this should be updated to reflect the current version of the figure. I also think the paper would benefit from more details regarding some of the analyses.

      Specifically, the phase-amplitude coupling analysis should have a section in the methods which should be sure to clarify how the BOLD signals were reconstructed.

      (1)“…I noticed that the legend for Figure 4 still refers to some components of the previous figure version, this should be updated to reflect the current version of the figure…”.

      Thank you for pointing this out. We have revised the legend of Figure 4 by removing the significance notation “***: p < 0.001”, which referred to elements from a previous version of the figure.

      (2)“…I also think the paper would benefit from more details regarding some of the analyses. Specifically, the phase-amplitude coupling analysis should have a section in the methods which should be sure to clarify how the BOLD signals were reconstructed”.

      We agree and appreciate the reviewer’s helpful suggestion. We have added a dedicated subsection entitled “Phase–amplitude coupling” to the Materials and Methods, in which we provide a detailed description of how the EC and HPC BOLD signals were reconstructed and how the coupling analysis was implemented. Correspondingly, we refined the description of this analysis in the Results section under “Phase synchronization between the HPC and EC activity”. The revised sections have been included below for your convenience. 

      Materials and Methods: Phase–amplitude coupling

      To quantify the spatial peak relationship between EC and HPC BOLD activity, we implemented a cross-frequency amplitude–phase coupling analysis in the directional space (Canolty et al., 2006). Rather than analyzing raw BOLD signals, we reconstructed 6-fold EC activity and 3-fold HPC activity in each voxel using sinusoidal modulation weights (β<sub>sine</sub> and β<sub>cosine</sub>) estimated from the raw BOLD signals. Specifically, activity was modeled as β<sub>cosine</sub>cos(kθ) + β<sub>sine</sub>sin(kθ), where k denotes the rotational symmetry. This approach selectively captures the hypothesized spatial symmetries of neural activity (e.g., 6-fold or 3-fold periodicity) as a function of movement direction. For this coupling analysis, we used participants’ original movement directions (i.e., without applying orientation calibration). The reconstructed 6-fold EC and 3-fold HPC activity were then converted into analytic representations using the Hilbert transform, yielding the instantaneous phase of the HPC (ϕ<sub>HPC</sub>) and the amplitude envelope of the EC (A<sub>ERC</sub>). HPC phases were classified into nine bins. The composite analytic signal, defined as z = A<sub>ERC</sub>e<sup>iϕHPC</sup>, was used to compute the modulation index M (Canolty et al., 2006), defined as the absolute value of the mean of z values, quantifying the scalar coupling strength between EC amplitude and HPC phase within each bin. A surrogate dataset, a null distribution of the modulation indices (M<sup>-</sup>), was generated by spatially offsetting the EC amplitude relative to the HPC phase across all possible spatial lags. The mean of this surrogate distribution was used as the baseline reference against which the observed coupling strength was compared.

      Results: Phase synchronization between the HPC and EC activity

      To examine whether the spatial phase structure in one region could predict that in another, we tested whether the orientations of the 6-fold EC and 3-fold HPC periodic activities, estimated from odd-numbered sessions using sinusoidal modulation with rotationally symmetric parameters, were correlated across participants. A cross-participant circular correlation was conducted between the spatial phases of the two areas to quantify the spatial correspondence of their activity patterns (EC: purple dots; HPC: green dots) (Jammalamadaka & Sengupta, 2001). The analysis revealed a significant circular correlation (Fig. 4a; r = 0.42, p < 0.001), as reflected by the continuous color progression across the participants (i.e., the colored lines connecting each pair of the EC and HPC dots in Fig. 4a), suggesting that participants with smaller hippocampal phases (green, outer ring) tended to have smaller entorhinal phases (purple, inner ring), and vice versa.

      In addition to the across-participant phase correlation, we further examined the spatial alignment between the 6-fold EC and 3-fold HPC activity patterns. Given that the spatial phase of the HPC is hypothesized to depend on EC projections, particularly along the three primary axes of the hexagonal code, we examined whether the periodic activities of the EC and HPC were spatially peak-aligned. Notably, unlike previous studies that focused on temporal coherence of neural oscillations (Buzsaki, 2006; Maris et al., 2011; Friese et al., 2013), our analysis focused on periodic coupling between brain areas in the directional space. To test spatial peak alignment between EC and HPC, a cross-frequency spatial coupling analysis (adapted from the amplitude–phase coupling framework; Canolty et al., 2006) was employed to identify at which HPC phase the EC exhibited maximal amplitude modulation. If the activities of both areas were peak-aligned (i.e., no peak offset), a strong coupling at phase 0 of the HPC would be expected as shown by the one-cyclebased schema in Fig. 4b. In doing so, the instantaneous phase of the HPC and the amplitude envelope of the EC were extracted from the reconstructed activity using the Hilbert transform (see methods for details). HPC phases were classified into nine bins, and the modulation index (M), quantifying the scalar coupling strength between EC amplitude and HPC phase, was computed within each bin. As a result, significant coupling was observed in the bin centered at phase 0 of the HPC (Fig. 4c; t(32) = 2.57, p = 0.02, Bonferroni-corrected across tests; Cohen’s d = 0.45). In contrast, no significant coupling was found in other bins (p > 0.05). To rule out the possibility that the observed coupling was driven by a potential harmonic (integer multiple) relationship between the 3-fold and 6-fold periodicities, we additionally conducted control analyses using 9-fold and 12-fold EC components. However, no significant coupling was observed in these controls (Fig. 4c; p > 0.05). Together, these results confirmed selective alignments of spatial peaks between the 6fold EC and 3-fold HPC periodicity in the conceptual direction domain.

      Reviewer #2 (Public review):

      The authors report results from behavioral data, fMRI recordings, and computer simulations during a conceptual navigation task. They report 3-fold symmetry in behavioral and simulated model performance, 3-fold symmetry in hippocampal activity, and 6-fold symmetry in entorhinal activity (all as a function of movement directions in conceptual space). The analyses seem thoroughly done, and the results and simulations are very interesting.

      We thank the reviewer for the positive assessment of our work.

      We thank both reviewers again for their constructive and insightful feedback, which has substantially strengthened the manuscript.

    1. Author response:

      The following is the authors’ response to the current reviews.

      Reviewer #2 (Public review):

      Summary:

      In the manuscript entitled "Ω-Loop mutations control dynamics 2 of the active site by modulating the 3 hydrogen-bonding network in PDC-3 4 β-lactamase", Chen and coworkers provide a computational investigation of the dynamics of the enzyme Pseudomonas-derived chephalosporinase 3 (PDC3) and some mutants associated with increased antibiotic resistance. After an initial analysis of the enzyme dynamics provided by RMSD/RMSF, the author conclude that the mutations alter the local dynamics within the omega loop and the R2 loop. The authors show that the network of hydrogen bonds in disrupted in the mutants. Constant pH calculations showed that the mutations also change the pKa of the catalytic lysine 67 and pocket volume calculations showed that the mutations expand the catalytic pocket. Finally, time-independent componente analysis (tiCA) showed different profiles for the mutant enzyme as compared to the wild type.

      Strengths:

      The scope of the manuscript is definitely relevant. Antibiotic resistance is an important problem and, in particular, Pseudomonas aeruginosa resistance is associated with an increasing number of deaths. The choice of the computational methods is also something to highlight here. Although I am not familiar with Adaptive Bandit Molecular Dynamics (ABMD), the description provided in the manuscript that this simulation strategy is well suited for the problem under evaluation.

      Weaknesses:

      In the revised version, the authors addressed my concerns regarding their use of the MSM, and in my view, their conclusions are now much more robust and well-supported by the data. While it would be very interesting to see a quantitative correlation between the effects of the mutations observed in the MD data and relevant experimental findings, I understand that this may be beyond the scope of the manuscript.

      Thank you for the careful evaluation and constructive comments. Regarding the suggestion of a more quantitative correlation with experimental observables, we agree that this would be valuable, and we have noted it as an important direction for future work.

      Reviewer #3 (Public review):

      Summary:

      This manuscript aims to explore how mutations in the PDC-3 3 β-lactamase alter its ability to bind and catalyse reactions of antibiotic compounds. The topic is interesting and the study uses MD simulations and to provide hypotheses about how the size of the binding site is altered by mutations that change the conformation and flexibility of two loops that line the binding pocket. Some greater consideration of the uncertainties and how the method choice affect the ability to compare equilibrium properties would strengthen the quantitative conclusions. While many results appear significant by eye, quantifying this and ensuring convergence would strengthen the conclusions.

      Strengths:

      The significance of the problem is clearly described the relationship to prior literature is discussed extensively.

      Comments on revised version:

      I am concerned that the authors state in the response to reviews that it is not possible to get error bars on values due to the use of the AB-MD protocol that guides the simulations to unexplored basins. Yet the authors want to compare these values between the WT and mutants. This relates to RMSD, RMSF, % H-bond and volume calculations. I don't accept that you cannot calculate an uncertainty on a time averaged property calculated across the entire simulation. In these cases you can either run repeat simulations to get multiple values on which to do statistical analysis, or you can break the simulation into blocks and check both convergence and calculate uncertainties.

      We thank the reviewer for raising this point. We would like to clarify that we did not intend to state that error bars are impossible to obtain under AB-MD. In fact, we reported error bars for several quantities derived from the AB-MD trajectories (we also broke the trajectories into blocks and calculated uncertainties for RMSF in our first-round response as you suggested). However, these data are closely related to your concern about comparing quantitative information without an appropriate reweighting of the ensemble. Therefore, in the revised manuscript, we removed quantitative analyses that were calculated directly from the raw AB-MD trajectories. Instead, the quantitative comparisons are now obtained from MSM analysis. We report pocket volumes and key interaction metrics for MSM metastable states, with corresponding error bars for these MSM-based quantities (Figure 6 and its supplementary figure).

      I note that the authors do provide error bars on the volumes, but the statistics given for these need closer scrutiny (I cant test this without the raw data). For example the authors have p<0.0001 for the following pair of volumes 1072 {plus minus} 158 and 1115 {plus minus} 242, or for SASA p<0.0001 is given for 2 identical numbers 155+/- 3.

      Thank you for this comment. As noted above, we have removed the table from the manuscript, and the pocket-volume results together with their error bars are now shown in Figure 6. To address the concern raised here and to avoid making the same mistake in future analyses, we re-examined how the statistics were computed. We believe the very small p-values were caused by treating per-frame MD values as independent observations in two-sample t-tests. Because consecutive MD frames are strongly time-correlated, they do not satisfy the independence assumption, which can greatly overestimate the effective sample size and lead to artificially small p-values. For the SASA, a p < 0.0001 is reported even though both values are shown as 155 ± 3. This is due to rounding, which can hide subtle underlying differences.

      I also remain concerned about comparisons between simulations run with the AB-MD scheme. While each simulation is an equilibrium simulation run without biasing forces, new simulations are seeded to expand the conformational sampling of the system. This means that by definition the ensemble of simulations does not represent and equilibrium ensemble. For example, the frequency at which conformations are sampled would not be the same as in a single much longer equilibrium simulation. While you may be able to see trends in the differences between conditions run in this way, I still don't understand how you can compare quantitative information without some method of reweighing the ensemble. It is not clear that such a rewieghting exists for this methods, in which case I advise some more caution in the wording of the comparisons made from this data.

      At this stage I don't feel the revision has directly addressed the main comments I raised in the earlier review, although there is a stronger response to the comments of Reviewer #2.

      We thank the reviewer for reiterating this important point, and we agree with the underlying concern. Although AB-MD generates unbiased trajectories, the ensemble of simulations does not represent an equilibrium ensemble. As a result, statistics computed by simply concatenating all AB-MD trajectories should not be used for quantitative comparisons. In the original version, we acknowledge that we reported several quantitative descriptors directly from concatenated AB-MD frames, including (i) distributions of χ1 torsions, (ii) mean pocket volumes and SASA, and (iii) percentages of some key interactions. We agree that this was not appropriate given the adaptive sampling protocol. In the revised manuscript, we have removed these quantitative analyses.

      We retained RMSD and RMSF analyses, but we have revised their wording and clarified their purpose. RMSD and RMSF are used only to summarize the structural variability and residue-level mobility observed across the collected trajectory segments and to motivate the selection of structural features for MSM construction. The manuscript now states: “Because AB-MD adaptively seeds new unbiased trajectories to expand conformational sampling, RMSD and RMSF are used here to summarize the structural variability and per-residue mobility observed across the collected trajectories.”

      Regarding the reviewer’s question about reweighting, the Markov state model (MSM) provides a principled framework to obtain the stationary distribution π from the transition probability matrix T<sub>τ</sub>. The resulting π<sub>i</sup> gives the equilibrium weight of each microstate i, and the corresponding discrete free energy can be written as F<sup>i</sup>=−k<sub>B</sub>Tln(π<sub>i</sup>). PCCA then coarse-grains the microstate space into a small number of metastable states. In the revised manuscript, quantitative comparisons are therefore derived from the MSM at the level of these metastable states, rather than from unweighted counts of concatenated AB-MD frames.

      Accordingly, we have revised the sections “E219K and Y221A mutations facilitate proton transfer” and “Substitutions enlarge the active-site pocket to accommodate bulkier R1 and R2 groups of β-lactams”, and we have added new figures in Figure 6 and its figure supplement. The adjustments to the quantitative analyses do not affect our original conclusions.


      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      This manuscript uses adaptive sampling simulations to understand the impact of mutations on the specificity of the enzyme PDC-3 β-lactamase. The authors argue that mutations in the Ω-loop can expand the active site to accommodate larger substrates.

      Strengths:

      The authors simulate an array of variants and perform numerous analyses to support their conclusions. The use of constant pH simulations to connect structural differences with likely functional outcomes is a strength.

      Weaknesses:

      I would like to have seen more error bars on quantities reported (e.g., % populations reported in the text and Table 1).

      We appreciate this point. Here, the population we analyze is intended to showcase conformational differences across variants rather than to estimate equilibrium occupancies. Although each system includes 100 trajectories, they were generated using an adaptive-bandit protocol. The protocol deliberately guides towards underexplored basins, therefore conformational heterogeneity betweentrajectories is expected by design. For example, in E219K the MSM decomposition shows that in states 1, 6, and 7 the K67(NZ)–S64(OG) distance is almost entirely > 6 Å, whereas in states 2 and 3 it is almost entirely < 3.5 Å (Figure 5—figure supplement 12). These distances suggest that the hydrogen bond fraction is approximately zero in states 1, 6, and 7, and close to one in states 2 and 3. In addition, the mean first passage time of the Markov state models suggests that the formation and disruption of this hydrogen bond occur on the microsecond timescale, which is far longer than the length of each individual trajectory (300 ns). Consequently, across the 100 replicas, some trajectories exhibit very low fractions, while others display the opposite trend. Under such bimodal, protocol-induced heterogeneity, computing an error bar across trajectories mainly visualizes the protocol’s dispersion and risks being misread as thermodynamic uncertainty, which is not central to our aim of comparing conformational differences between wild-type PDC-3 and variants. We therefore do not include the error bars. 

      Reviewer #2 (Public review):

      Summary:

      In the manuscript entitled "Ω-Loop mutations control dynamics of the active site by modulating the 3 hydrogen-bonding network in PDC-3 4 β-lactamase", Chen and coworkers provide a computational investigation of the dynamics of the enzyme Pseudomonas-derived cephalosporinase 3 (PDC3) and some mutants associated with increased antibiotic resistance. After an initial analysis of the enzyme dynamics provided by RMSD/RMSF, the author concludes that the mutations alter the local dynamics within the omega loop and the R2 loop. The authors show that the network of hydrogen bonds is disrupted in the mutants. Constant pH calculations showed that the mutations also change the pKa of the catalytic lysine 67, and pocket volume calculations showed that the mutations expand the catalytic pocket. Finally, time-independent component analysis (tiCA) showed different profiles for the mutant enzyme as compared to the wild type.

      Strengths:

      The scope of the manuscript is definitely relevant. Antibiotic resistance is an important problem, and, in particular, Pseudomonas aeruginosa resistance is associated with an increasing number of deaths. The choice of the computational methods is also something to highlight here. Although I am not familiar with Adaptive Bandit Molecular Dynamics (ABMD), the description provided in the manuscript suggests that this simulation strategy is well-suited for the problem under evaluation.

      Weaknesses:

      In the description of many of their results, the authors do not provide enough information for a deep understanding of the biochemistry/biophysics involved. Without these issues addressed, the strength of the evidence is of concern.

      We thank the reviewer for pointing out the need for deeper discussion of the biochemical and biophysical implications of our results. In our manuscript, we begin by examining basic structural metrics (e.g., RMSD and RMSF) which clearly indicate that the major conformational changes occur in the Ω-loop and the R2 loop. We have now added a paragraph to describe the importance of the Ωloop and highlighted it in the revised manuscript on lines 142-166 of page 6. This observation guided our subsequent focus on these regions, as well as on the catalytic site. Our analysis revealed notable alterations in the hydrogen bonding network—especially in interactions involving the K67-S64, K67N152, K67-G220, Y150-A292, and N287-N314 pairs. These observations led us to conclude that:

      (1) Mutations E219K and Y221A facilitate the proton transfer of catalytic residues. This is consistent with prior experimental data showing that these substitutions produce the most pronounced increase in sensitivity to cephalosporin antibiotics (lines 210-212 in page 8 of the revised manuscript). 

      (2) Substitutions enlarge the active-site pocket to accommodate bulkier R1 and R2 groups of β-lactams.This is in line with MIC measurements reported by Barnes et al. (2018), which showed that mutants with larger active-site pockets exhibit markedly greater sensitivity to cephalosporins with bulky side chains than others (lines 249-259 in pages 10).

      Furthermore, we applied Markov state models (MSMs) to explore the timescales of the transitions between these different conformational states. We believe that these methodological steps support our conclusions.

      Reviewer #3 (Public review):

      Summary:

      This manuscript aims to explore how mutations in the PDC-3 3 β-lactamase alter its ability to bind and catalyse reactions of antibiotic compounds. The topic is interesting, and the study uses MD simulations to provide hypotheses about how the size of the binding site is altered by mutations that change the conformation and flexibility of two loops that line the binding pocket. However, the study doesn't clearly describe the way the data is generated. While many results appear significant by eye, quantifying this and ensuring convergence would strengthen the conclusions.

      Strengths:

      The significance of the problem is clearly described, and the relationship to prior literature is discussed extensively.

      Weaknesses:

      The methods used to gain the results are not explained clearly, meaning it was hard to determine exactly how some data was obtained. The convergence and uncertainties in the data were not adequately quantified. The text is also a little long, which obscures the main findings.

      We thank the reviewer for the suggestion. We respectfully ask the reviewer to specify which aspects of the data-generation methods are unclear so that we can include the necessary details in the next revision. Moreover, all statistics that are reported in the manuscript are obtained from extensive analyses of 300,000 simulation frames. The Markov state models have been validated by the ITS plots and Chapman-Kolmogorov (CK) test. The two-sample t-tests were also carried out for the volume and SASA.

      Reviewer #2 (Recommendations for the authors):

      (1) Figure 1D focus on the PDC3 catalytic site. However, the authors mentioned before that the enzyme has two domains, an alpha domain and an alpha/beta domain. The reader would benefit from a more detailed description of the enzyme, its active site, AND the location of the mutants under investigation in the figure.

      We have updated Figure 1D and marked the positions of all mutations (V211A/G, G214A/R, E219A/G/K and Y221A/H), which have now been highlighted as spheres.

      (2) Since in the journal format, the results come before the methods. It would be interesting to add a brief description of where the results came from. For example, in the first section of the results, the authors describe the flexibility of the omega loop and the R2 loop. However, the reader won't know what kind of simulation was used and for how long, for example. A sentence would add the required context for a deeper understanding here.

      At the beginning of the Results and Discussion section we now state: “To investigate how the mutations in the Ω-loop affect PDC-3 dynamics, adaptive-bandit molecular dynamics (AB-MD) simulations were carried out for each system. 100 trajectories of 300 ns each (totaling 30 μs per system) were run.”

      (3) Still in the same section, the authors don't define what change in RMSF is considered significant. For example, I can't see a relevant change in the RMSF for the omega loop between the et enzyme and the E219 mutants in Figure 2D. A more objective definition would be of benefit here.

      Our analysis reveals that while the wild-type PDC-3 and the G214A, G214R, E214G, and Y221A variants exhibit an average per-residue RMSF of around 4 Å in the Ω-loop, the V211A and V211G variants show markedly lower values (around 1.5 Å), and the E219K and Y221H variants exhibit intermediate values between 2 and 2.5 Å. In addition, the fluctuations around the binding site should be seen collectively along with the fluctuations in the R2-loop. Importantly, we urge the reviewer to focus on the MDLovofit analysis in Figure 2C, where the dynamic differences between the core and the fluctuating loops is clearly evident.  

      (4) In line 138, the authors state that "Therefore, the flexibility of these proteins is mainly caused by the fluctuations in the Ω-loops and R2-loop". This is quite a bold statement to be drawn at this point. First of all, there is no mention of it in the manuscript, but is there any domain movement? Figure 2C clearly shows that there is some mobility in omega and R2 loops. But there is no evidence shown in the manuscript that shows that "the flexibility of these proteins is mainly caused by the fluctuations in the" loops. Please consider rephrasing this sentence or adding more data, if available.

      We have revised the wording to take the reviewer’s concern into account. The sentence now states: “Therefore, flexibility of PDC-3 is predominantly localized to the Ω- and R2-loops, whereas the remainder of the structure is comparatively rigid.” To further explain to the reviewer, the β lactamase enzymes are fairly rigid structures, where no large-scale domain motions occur. Instead, the enzyme communicates structurally via cross correlation of loop dynamics ( https://doi.org/10.7554/eLife.66567 ).  

      (5) I guess, the most relevant question for the scope of the paper is not answered in this section. The authors show that the mobility of the omega- and R2-loops is altered by some mutations. Why is that? I wish I could see a figure showing where the mutations are and where the loops are. This question will come back in other sections.

      We have updated Figure 1D to mark the positions of all mutations (V211A/G, G214A/R, E219A/G/K and Y221A/H) as spheres. The Ω- and R2-loops are also highlighted. All mutations map to the Ω-loop, indicating that these substitutions directly perturb this region. Notably, K67 forms a hydrogen bond with the backbone of G220 within the Ω-loop and another with the phenolic hydroxyl of Y150. Y150, in turn, hydrogen-bonds with A292 in the R2 loop. Together, the residue interaction network (G220– K67–Y150–A292) suggest a pathway by which Ω-loop mutations propagate their effects to the R2 loop.

      (6) The authors then analyze the network of polar residues in the active site and the hydrogen bonds observed there. For the K67-N152 hydrogen bond, for example, there is a reduction in the occupancy from ~70% in the wild-type enzyme to ~30% and 40% in the mutants E219K and Y221, respectively. This finding is interesting. The question that remains is "why is that"? From the structural point of view, how does the replacement of E219 with a Lysine alter the hydrogen bond formation between K67 and N152? Is it due to direct competition? Solvent rearrangement? The reader is left without a clue in this section. Also, Figure 3B won't help the reader, since the mutated residues are not shown there. Please consider adding some information about why the authors believe that the mutations are disrupting the active site hydrogen bond network and showing it in Figure 3B.

      We appreciate the comment and have updated Figures 1D and 3B to highlight the mutation sites. The change from ~70% in the wild type to ~30–40% in the E219K and Y221T variants reported in Table 1 refers to the S64–K67 hydrogen bond. In the wild type, K67 forms an additional hydrogen bond with G220 on the Ω-loop, which helps anchor the K67 side chain in a geometry that favors the S64–K67 interaction. In the variants, the mutations reshape the Ω-loop and frequently disrupt the K67–G220 contact. The loss of this local anchor increases the conformational dispersion of K67, which is consistent with the observed reduction of the S64–K67 occupancy. Furthermore, our observation that the mutations are disrupting the active-site hydrogen-bond network is a data-driven conclusion rather than a subjective inference. Across ten systems, our AB-MD simulations provided 30 µs of sampling per system. Saving one frame every nanosecond yielded 30,000 conformations per system and 300,000 in total. All hydrogen-bond and salt-bridge statistics were computed over this full ensemble. Thus, the conclusion that the mutations disrupt the active-site hydrogen-bond network follows directly from these ensemble statistics. 

      (7) The pKa calculations and the pocket volume calculations show that the mutations expand the volume of the catalytic site and alter the microenvironment. Is there any change in the solvation associated with these changes? If the volume expands and the environment becomes more acidic, are there more water molecules in the mutants as compared to the wt enzyme? If so, can changes in solvation be associated with the changes in the hydrogen bond network? Would a simulation in the presence of a substrate be meaningful here? ( I guess it would!).

      Regarding solvation, we observe a modest increase in transient water occupancy associated with the increase in volume of the pocket. The conserved deacylation water molecule is the most important and is always present throughout the simulation. Additional waters enter and leave the pocket but do not form persistent interactions that measurably perturb the hydrogen-bond network of the Ω- and R2-loops. We agree that simulations with a bound substrate would be informative. However, our study focuses on how Ω-loop mutations modulate the active site of apo PDC-3 and its variants. Within this scope, we find: (i) Amino acid substitutions change the flexibility of Ω-loops and R2-loops; (ii) E219K and Y221A mutations facilitate the proton transfer; (iii) Substitutions enlarge the active-site pocket to accommodate bulkier R1 and R2 groups of β-lactams.

      (8) I have some concerns regarding the Markov State Modeling as shown here. After a time-independent component analysis, the authors show the projections on the components, which is different between wild wild-type enzyme and the mutants, and draw some conclusions from these changes. For example, the authors state that "From the metastable state results, we observe that E219K adopts a highly stable conformation in which all the tridentate hydrogen-bonding interactions (K67(NZ)-S64(OG), K67(NZ)N152(OD1) and K67(NZ)-G220(O) mentioned above are broken". This is conclusion is very difficult to draw from Figure 5 alone. Unless the macrostates observed in the MSM can be shown (their structures) and could confirm the broken interactions, I really don't believe that the reader can come to the same conclusion as drawn by the authors here. I would recommend the authors to map the macrostates back to the coordinates and show them (what structure corresponds to what macrostate). After showing that, it makes sense to discuss what macrostate is being favored by what mutation. Taking conclusions from tiCA projections only is not recommended. I very strongly suggest that the authors revisit this entire section, adding more context so that the reader can draw conclusions from the data that is shown.

      We appreciate the reviewer’s concern. In the Markov state modeling section, our objective is to quantify the timescales (via mean first passage times) associated with the formation and disruption of the critical hydrogen bonds (K67(NZ)-S64(OG), K67(NZ)-N152(OD1), K67(NZ)-G220(O), Y150(N)A292(O), N287(ND2)-N314(OD1)) mentioned above. Representative structures illustrating these interactions are shown in Figures 3B and 4A. We agree that the main Figure 5 alone does not convey structural information. Accordingly, we provide Figure 5—figure supplements 12–16. Together, Figure 5B and Figure 5—figure supplements 12–16 map structures to metastable states, whereas Figures 3B and 4A supply atomistic detail of the interactions. Author response image 1 presents selected subplots from Figure 5— figure supplements 12–14. Together with the free-energy landscape in Figure 5A, these data indicate that E219K adopts a highly stable conformation in which all three K67-centered hydrogen bonds (K67(NZ)–S64(OG), K67(NZ)–N152(OD1), and K67(NZ)–G220(O)) are broken.

      Author response image 1.

      TICA plot illustrates the distribution of E219K with the colour indicating the K67(NZ)-S64(OG), K67(NZ)-N152(OD1) and K67(NZ)-G220(O) distance.

      (9) As a very minor issue, there are a few typos in the manuscript text. The authors might want to take some time to revisit their entire text. Examples in lines 70, 197, etc.

      Thank you for your comment. We have corrected these typos.

      Reviewer #3 (Recommendations for the authors):

      This manuscript aims to explore how mutations in the PDC-3 3 β-lactamase alter its ability to bind and catalyse reactions of antibiotic compounds. The topic is interesting, and the study uses MD simulations to provide hypotheses about how the size of the binding site is altered by mutations that change the conformation and flexibility of two loops that line the binding pocket.

      However, the study doesn't clearly describe the way the data is generated and potentially lacks statistical rigour, which makes it uncertain if the key results are significant. As such, it is difficult to judge if the conclusions made are supported by data.

      All necessary data-acquisition methods are described in the Methods section. The Markov state models have been validated by the ITS plot and the Chapman-Kolmogorov (CK) test (Figure 5—figure supplement 2–11) . The two-sample t-tests were also carried out for the volume and SASA (Table 2).

      The results section jumps straight to reporting RMSD and RMSF values; however, it is not clear what simulations are used to generate this information. Indeed, the main text does not mention the simulations themselves at all. The methods section mentions that 10 independent MD simulations were set up for each system, but no information is given as to how long these were run or the equilibration protocol used. Then it says that AB-MD simulations were run, but it is not clear what starting coordinates were used for this or how the 10 replicates were fed into these simulations. Most importantly, are the RMSD and RMSF calculations and later distance distribution information derived from the equilibrium MD runs or from the AB-MD simulations?

      Thank you for pointing this out. We have added “To investigate how the mutations in the Ω-loop affect PDC-3 dynamics, adaptive-bandit molecular dynamics (AB-MD) simulations were carried out for each system. 100 trajectories of 300 ns each (totaling 30 μs per system) were run.” to the Results and Discussion section. We didn’t run 10 independent MD simulations per system. We regret the typo in the Methods section that confused the reviewer. The sentence should have read – ‘All-atom MD simulations of wild-type PDC-3 and its variants were performed.’ Each system was equilibrated for 5 ns at 1 atmospheric pressure using Berendsen barostat. AB-MD simulations were initiated from these equilibrated structures. All analyses, apart from CpHMD, are based on the AB-MD trajectories.

      If these are taken from the equilibrium simulations, then it is critical that the reproducibility and statistical significance of the simulations is established. This can be done by calculating the RMSD and RMSF values independently for each replicate and determining the error bars. From this, the significance of differences between WT and mutant simulations can be determined. Without this, I have no data to judge if the main conclusions are supported or not. If these are derived from the AB-MD simulations, then I want to know how the independent simulations were combined and reweighted to generate overall RMSD, RMSF, and distance distributions. Unless I misunderstand the approach, the individual simulations no longer sample all regions of conformational space the same relative amount you would see in a standard MD simulation - specific conformational regions are intentionally run more to enhance sampling, then the overall conformational distributions cannot be obtained from these simulations without some form of reweighting scheme. But no such scheme is described. In addition, convergence of the data is required to ensure that the RMSD, RMSF, and distances have reached stable values. It is possible that I am misunderstanding the approach here. But in that case, I hope the authors can clarify the method and provide a means of ensuring that the data presented is converged. Many of the differences are clear by eye, but it is important to know they are not random differences between simulations and rather reflect differences between them.

      Thank you for raising this important point. In our AB-MD workflow, the adaptive bandit is used only for starting-structure selection (adaptive seeding). After each epoch, it chooses new starting snapshots from previously sampled conformations and launches the next runs. Each trajectory itself is standard, unbiased MD with no biasing potentials and no modification of the Hamiltonian. In other words, AB decides where we start, but does not alter the physics or sampling dynamics within an individual trajectory. In addition, our goal in this work is to compare variants under the same adaptive-bandit (AB) protocol, rather than to estimate equilibrium (Boltzmann) populations. Hence, we did not apply equilibrium reweighting to RMSD, RMSF, or distance distributions. However, MSM section provides reweighted reference results based on the MSM stationary distribution.

      In the response to reviews, the authors state that the "RMSF is a statistical quantity derived from averaging the time series of atomic displacements, resulting in a fixed value without an inherent error bar." But normally we would run multiple replicates and get an error bar from the different values in each. To dismiss the request for uncertainties and error bars seems to miss the point. I strongly agree with the prior reviewer that comparisons between RMSF or other values should be accompanied by uncertainties and estimates of statistical significance.

      Regarding the reviewers’ suggestion to present the data as a bar graph with error bars, we would like to note that RMSF is calculated as the time average of the fluctuations of each residue’s Cα atom over the entire simulation. As such, RMSF is a statistical quantity derived from averaging the time series of atomic displacements, resulting in a fixed value without an inherent error bar. We believe that our current presentation clearly and accurately reflects the local flexibility differences among the variants. Nearly all published studies report RMSF in this way, as indicated by the following examples:

      Figure 3a in DOI: https://doi.org/10.1021/jacsau.2c00077

      Figure 2 in DOI: https://doi.org/10.1021/acs.jcim.4c00089

      Supplementary Fig. 1, 2, 5, 9, 12, 20, 22, 24, and 26 in DOI: https://doi.org/10.1038/s41467-022-293313

      However, in response to the reviewers’ strong request, we present RMSF plots with error bars in our response letter. 

      Author response image 2.

      The root-mean-square fluctuation (RMSF) profiles of wild-type PDC-3 and its variants. Blue lines show the mean RMSF across 100 independent MD trajectories for each system; red translucent bands denote the standard deviation across trajectories. The Ω-loop (residues G183 to S226) is highlighted in yellow, and the R2-loop (residues L280 to Q310) is highlighted in blue.

      It was good to see that convergence of the constant-pH simulations was shown. While it can be challenging to get absolute pH values from the implicit solvent-based simulations, the differences between the systems are large and the trends appear significant. I was not clear how the starting coordinates were chosen for these simulations. Is the end point of the classical simulations, or is a representative snapshot chosen somehow?

      To ensure comparison, all systems used the X-ray crystal structure (PDB ID: 4HEF) with T79A substitution as the initial structure. The E219K and Y221A mutants were generated in silico using the ICM mutagenesis module. We have added the clarification in Methods section: “The starting structures were identical to those used for AB-MD.”

      Significant figures: Throughout the text and tables, the authors present data with more figures than are significant. 1071.81+-157.55 should be reported as 1100 +/ 160 or 1070 =- 160 . See the eLife guidelines for advice on this.

      Thank you for your suggestion. We have amended these now. 

      The manuscript is very long for the results presented, and I feel that a clearer story would come across if the authors shortened the text so that the main conclusions and results were not lost.

      We appreciate the suggestion. We examined the twenty most recent research articles published in eLife and found that they are either longer than or comparable in length to our manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      (1) The authors devote significant effort to characterizing the physical interaction between Bicc1 and Pkd2. However, the study does not examine or discuss how this interaction relates to Bicc1's well-established role in posttranscriptional regulation of Pkd2 mRNA stability and translation efficiency.

      The reviewer is correct that the present study has not addressed the downstream consequences of uthis interaction considering that Bicc1 is a posttranscriptional regulator of Pkd2 (and potentially Pkd1). We think that the complex of Bicc1/Pkd1/Pkd2 retains Bicc1 in the cytoplasm and thus restrict its activity in participating in posttranscriptional regulation (see Author response image 1). We, however, do not yet have data to support this and thus have not included this model in the manuscript. Yet, we have updated the discussion of the manuscript to further elaborate on the potential mechanism of the Bicc1/Pkd1/Pkd2 complex.

      We have updated the discussion to include a discussion on the potential consequences on posttranscriptional regulation by Bicc1.

      Author response image 1.

      Model of BICC1, PC1 and PC2 self-regulation. In this model Bicc1 acts as a positive regulator of PKD gene expression. In the presence of ‘sufficient’ amounts of PC1/PC2 complex, it is tethered to the complex and remains biologically inactive (Fig. 1A). However, once the levels of the PC1/PC2 complex are reduced, Bicc1 is now present in the cytoplasm to promote expression of the PKD proteins, thereby raising their levels (Fig. 4B), which then in turn will ‘shutdown’ Bicc1 activity by again tethering it to the plasma membrane.

      (2) Bicc1 inactivation appears to downregulate Pkd1 expression, yet it remains unclear whether Bicc1 regulates Pkd1 through direct interaction or by antagonizing miR-17, as observed in Pkd2 regulation. This should be further examined or discussed.

      This is a very interesting comment. Vishal Patel published that PKD1 is regulated by a mir-17 binding site in its 3’UTR (PMID: 35965273). We, however, have not evaluated whether BICC1 participates in this regulation. A definitive answer would require utilization of the mice described in above reference, which is beyond the scope of this manuscript. We, however, have revised the discussion to elaborate on this potential mechanism. 

      We have updated the discussion to include a statement on the potential direct regulation of Pkd1 mRNA by Bicc1.

      (3) The evidence supporting Bicc1 and ADPKD gene cooperativity, particularly with Pkd1, in mouse models is not entirely convincing, likely due to substantial variability and the aggressive nature of Bpk/Bpk mice. Increasing the number of animals or using a milder Bicc1 strain, such as jcpk heterozygotes, could help substantiate the genetic interaction.

      We have initially performed the analysis using our Bicc1 complete knockout, we previously reported on (PMID 20215348) focusing on compound heterozygotes. Yet, similar to the Pkd1/Pkd2 compound heterozygotes (PMID 12140187) no cyst development was observed when we sacrificed the mice as late as P21. Our strain is similar to the above mentioned jcpk, which is characterized by a short, abnormal transcript thought to result in a null allele (PMID: 12682776). We thank the reviewer for pointing us to the reference showing the heterozygous mice exhibit glomerular cysts in the adults (PMID: 7723240). This suggestion is an interesting idea we will investigate. In general, we agree with the reviewer that a better understanding of the contribution of Bicc1 to the adult PKD phenotype will be critical. To this end, we are currently generating a floxed allele of Bicc1 that will allow us to address the cooperativity in the adult kidney, when e.g. crossed to the Pkd1<sup>RC/RC</sup> mice. Yet, these experiments are beyond the timeframe for this revision. 

      No changes were made in the revised manuscript. 

      Reviewer #2 (Public review):

      (1) These results are potentially interesting, despite the limitation, also recognized by the authors, that BICC1 mutations seem exceedingly rare in PKD patients and may not "significantly contribute to the mutational load in ADPKD or ARPKD". The manuscript has several intrinsic limitations that must be addressed. 

      As mentioned above, the study was designed to explore whether there is an interaction between BICC1 and the PKD1/PKD2 and whether this interaction is functionally important. How this translates into the clinical relevance will require additional studies (and we have addressed this in the discussion of the manuscript).

      (2) The manuscript contains factual errors, imprecisions, and language ambiguities. This has the effect of making this reviewer wonder how thorough the research reported and analyses have been. 

      We respectfully disagree with the reviewer on the latter interpretation. The study was performed with rigor. We have carefully assessed the critiques raised by the reviewer. As presented below, most of the criticisms raised by the reviewer have been easily addressed in the revised version of the manuscript. Yet, none of the critiques seems to directly impact the overall interpretation of the data. 

      Reviewer #1 (Recommendations for the authors):

      (1) The manuscript requires further editing. For example, figure panels and legends are mismatched in Figure 1

      We have corrected the labeling of Figure 1. 

      (2) Y-axis units and values are inconsistent in Figures 4b-4g, Supplementary Figures S2e and S2f are not referenced in the text, genotypes are missing in Supplementary Figure S3f, and numerous typographical errors are present.

      In respect to the y-axis in Figure 4b-g, the scale is different for each of them, but that is intentional as one would lose the differences if they were all scaled identically. But we have now mentioned this in the figure legend to make the reader aware of it. In respect to the Supplemental Figure S2e,f, we included the panels in the description of the mutant BICC1 lines, but unfortunately forgot to reference them. This has now been done.

      We have updated the labeling of the Y-axis for the cystic indices adding “[%]” as the unit and updated the figure legend of Figure 4. We have included the genotypes in Supplementary Figure S3f. The Supplementary Figure S2e,f is now mentioned in the supplemental material (page 9, 2<sup>nd</sup> paragraph). 

      Reviewer #2 (Recommendations for the authors):

      (1) Previous data from mouse, Xenopus, and zebrafish suggest a crucial role for the RNAbinding protein Bicc1 in the pathogenesis of PKD, although BICC1 mutations in human PKD have not been previously reported." The cited sources (and others that were not cited) link Bicc1 mutations to renal cysts, similar to a report by Kraus (PMID: 21922595) that the authors cite later. However, a more direct link to PKD was reported by Lian and colleagues using whole Pkd1 mice (PMID: 20219263) and by Gamberi and colleagues using Pkd1 kidneys and human microarrays (PMID: 28406902). Although relevant, neither is cited here, and only the former is cited later in the manuscript.

      Thanks for pointing this out. We have added these three citations.

      We have added these three citations (PMID: 21922595, PMID: 20219263 and PMID: 28406902) in the indicated sentence.

      (2) In Figure 1B, the lanes do not seem to correspond among panels, particularly evident in the panel with myc-mBicc1. Hence, it is difficult to agree with the presented conclusions.

      We have corrected the labeling of the lanes in Figure 1b.

      (3) In the Figure 1 legend: "(g) Western blot analysis following co-IP experiments, using an anti-mouse Bicc1 or anti-goat PC2 antibody as bait, identified protein interactions between endogenous PC2 and BICC1 in UCL93 cells. Non-immune goat and mouse IgG were included as a negative control." There is no mention of panel H, although this reviewer can imagine what the authors meant. The capitalization differs in the figure and legend. More troublingly, in panel G, a non-defined star indicates a strong band present in both immune and non-immune control.

      We have corrected the figure legend of Figure 1 and clarified the non-specific band in the figure legend.

      (4) In Figure 4, the authors do not show the matched control for the Bicc1 Pkd1 interaction in panel d, nor do they show a scale bar in either a) or d). Thus, the phenotypic severity cannot be properly assessed.

      Thanks for pointing out the missing scale bars, which have now been added. In respect to the two kidneys shown in Figure 4d, the two kidneys shown are from littermates to illustrate the kidney size in agreement with the cumulative data shown in Figure 4e. Unfortunately, this litter did not have a wildtype control. As the data analysis in Figure 4e is based on littermates, mixing and matching kidneys of different litters does not seem appropriate. Thus, we have omitted showing a wildtype control in this panel. However, the size of the wildtype kidney can be seen in Figure 4a.

      We have added the scale bar to both panels and have updated the figure legend to emphasize that the kidneys shown are from littermates and that no wildtype littermate was present in this litter.

      (5) "Surprisingly, an 8-fold stronger interaction was observed between full-length PC1 and myc-mBicc1-ΔKH compared to mycmBicc1 or myc-mBicc1-ΔSAM." Assuming all the controls for protein folding and expression levels have been carried out and not shown/mentioned, this sentence seems to contradict the previous statement that Bicc1deltaSAM reduced the interaction with PC1 by 55%. Because the full length and SAM deletion have different interaction strengths, the latter sentence makes no sense.

      The reduction in the levels of myc-mBicc1-ΔSAM compared to wildtype mycmBicc1 in respect to PC1 binding was not significant. We have clarified this in the text.

      We have corrected the sentence and modified the Figure accordingly. 

      (6) Imprecise statements make a reader wonder how to interpret the data: "More than three independent experiments were analyzed." Stating the sample size or including it in the figure would save space and improve confidence in the data presented.

      We have stated the exact number of animals per conditions above each of the bars.

      (7) "Next, we performed a similar mouse study for Pkd1 by reducing the gene dose of Pkd1 postnatally in the collecting ducts using a Pkhd1-Cre as previously described40" What did the authors mean?

      The reference was included to cite the mouse strain, but realized that it can be mis-interpreted that the exact experiments has been performed previously. We have clarified this in the text.

      We have reworded the sentence to avoid misinterpretation. 

      (8) The authors examined the additive effects of knocking down Bicc1, Pkd1, and Pkd2 with morpholinos in Xenopus and, genetically, in mice. While the Bicc1[+/-] Pkd1 or 2[+/-] double heterozygote mice did not show phenotypes, the authors report that the Bicc1[-/-] Pkd1 or 2 [+/-] did instead show enlarged kidneys. What is the phenotype of a Bicc1[+/-] Pkd1 or 2 [-/-]? What we learn from the author's findings among the PKD population suggests that the latter situation would be potentially translationally relevant.

      The mouse experiments were designed to address a cooperativity between Bicc1 and either Pkd1 or Pkd2 and whether removal of one copy of Pkd1 or Pkd2 would further worsen the Bicc1 cystic kidney phenotype. Thus, the parental crosses were chosen to maximize the number of animals obtained for these genotypes. Unfortunately, these crosses did not yield the genotypes requested by the reviewer. To address the contribution of Bicc1 towards the PKD population, we will need to perform a different cross, where we eliminate Pkd1 or Pkd2 in a floxed background of Bicc1 postnatally in adult mice. While we are gearing up to perform such an experiment, this is timewise beyond the scope of the manuscript. In addition, please note that we have addressed the question about the translation towards the PKD population already in the discussion of the original submission (page 13/14, last/first paragraph).

      No changes have been made to the revised version of the manuscript.

      (9) How do the authors interpret the milder effects of the Bicc1[-/-] Pkd1[+/-] compared to Bicc1[-/-] Pkd2[+/-] relative to the respective protein-protein interactions?

      The milder effects are due to the nature of the crosses. While the Pkd2 mutant is a germline mutation, the Pkd1 mutant is a conditional allele eliminating Pkd1 only in the collecting ducts of the kidney. As such, we spare other nephron segments such as the proximal tubules, which also significantly contribute to the cyst load. As such these mouse data support the interaction between Pkd1 and Pkd2 with Bicc1, but do not allow us to directly compare the outcomes. While this was mentioned in the previous version of the manuscript, we have expanded on this in the revised version of the manuscript.

      We have expanded the results section in the revised version of the manuscript highlighting that the two different approaches cannot be directly compared.

      (10) How do the authors interpret that the strong Bicc1[Bpk] Pkd1 or Pkd2 double heterozygote mice did not have defects and "kidneys from Bicc1+/-:Pkd2+/- did not exhibit cysts (data not shown)", when the VEO PKD patients and - although not a genetic reduction - also the morpholino-treated Xenopus did?

      VEO PKD patients are characterized by a loss of function of PKD1 or PKD2 and – as we propose in this manuscript - that BICC1 further aggravates the phenotype. Yet, we do not address either in the mouse or Xenopus experiments whether BICC1 is a genetic modifier. We are simply addressing whether the two genes show a genetic interaction. In the mouse studies, we eliminate one copy of Pkd1 or Pkd2 in the background of a hypomorphic allele of Bicc1. Similarly, in the Xenopus experiments, we employ suboptimal doses of the morpholino oligomers, i.e., concentrations that did not yield a phenotypic change and then asked whether removing both together show cooperativity. It is important to state that this is based on a biological readout and not defined based on the amount of protein. While we have described this already in the original manuscript (page 7, first paragraph), we have amended our description of the Xenopus experiment to make this even clearer. 

      Finally, we agree with the reviewer that if we were to address whether Bicc1 is a modifier of the PKD phenotype in mouse, we would need to reduce Bicc1 function in a Pkd1 or Pkd2 mutants. Yet, we have recognized this already in the initial version of the manuscript in the discussion (page 14, first paragraph).

      We have expanded the results section when discussing the suboptimal amounts of the morpholino oligos (Page 6, 1<sup>st</sup> paragraph).

      (11) Unclear: "While variants in BICC1 are very rare, we could identify two patients with BICC1 variants harboring an additional PKD2 or PKD1 variant in trans, respectively." Shortly after, the authors state in apparent contradiction that "the patients had no other variants in any of other PKD genes or genes which phenocopy PKD including PKD1, PKD2, PKHD1, HNF1s, GANAB, IFT140, DZIP1L, CYS1, DNAJB11, ALG5, ALG8, ALG9, LRP5, NEK8, OFD1, or PMM2."

      The reviewer is correct. This should have been phrased differently. We have now added “Besides the variants reported below” to clarify this more adequately.

      The sentence was changed to start with “Besides the variants reported below, […].”

      (12) "The demonstrated interaction of BICC1, PC1, and PC2 now provides a molecular mechanism that can explain some of the phenotypic variability in these families." How do the authors reconcile this statement with their reported ultra-rare occurrence of the BICC1 mutations?

      As mentioned in the manuscript and also in response to the other two reviewers, Bicc1 has been shown to regulate Pkd2 gene expression in mice and frogs via an interaction with the miR-17 family of microRNAs. Moreover, the miR-17 family has been demonstrated to be critical in PKD (PMID: 30760828, PMID: 35965273, PMID: 31515477, PMID: 30760828). In fact, both other reviewers have pointed out that we should stress this more since Bicc1 is part of this regulatory pathway. Future experiments are needed to address whether Bicc1 contributes to the variability in ADPKD onset/severity. Yet, this is beyond the scope of this study. 

      Based on the comments of the two other reviewers we have further addressed the Bicc1/miR-17 interaction.

      (13) The manuscript should use correct genetic conventions of italicization and capitalization. This is an issue affecting the entire manuscript. Some exemplary instances are listed below.

      (a) "We also demonstrate that Pkd1 and Pkd2 modifies the cystic phenotype in Bicc1 mice in a dose-dependent manner and that Bicc1 functionally interacts with Pkd1, Pkd2 and Pkhd1 in the pronephros of Xenopus embryos." Genes? Proteins?

      The data presented in this section show that a hypomorphic allele of Bicc1 in mouse and a knockdown in Xenopus yields this. As both affect the proteins, the spelling should reflect the proteins.

      No changes have been made in the revised manuscript.

      (b) The sentence seems to use both the human and mouse genetic capitalization, although it refers to experiments in the mouse system “to define the Bicc1 interacting domains for PC2 (Fig. 2d,e). Full-length PC2 (PC2-HA) interacted with full-length myc-mBICC1.”

      We agree with the review that stating the species of the molecules used is critical, we have adapted a spelling of Bicc1, where BICC1 is the human homologue, mBicc1 is the mouse homologue and xBicc1 the Xenopus one.

      We have highlighted the species spelling in the methods section and labeled the species accordingly throughout the manuscript and figures. 

      (14) “Together these data supported our biochemical interaction data and demonstrated that BICC1 cooperated with PKD1 and PKD2.” Are the authors implying that these results in mice will translate to the human protein?

      We agree that we have not formally shown that the same applies to the human proteins. Thus, we have changed the spelling accordingly.

      We have revised the capitalization of the proteins. 

      (15) The text is often unclear, terse, or inconsistent.

      (a) “These results suggested that the interaction between PC1 and Bicc1 involves the SAM but not the KH/KHL domains (or the first 132 amino acids of Bicc1). It also suggests that the N-terminus could have an inhibitory effect on PC1-BICC1 association.” How do the authors define the N-terminus? The first 132 aa? KH/KHL domains?

      This was illustrated in the original Figure 2A. The DKH constructs lack the first 351 amino acids. 

      To make this more evident, we have specified this in the text as well.

      (b) Similarly, the authors state below, "Unlike PC1, PC2 interacted with mycmBICC1ΔSAM, but not myc-mBICC1-ΔKH suggesting that PC2 binding is dependent on the N-terminal domains but not the SAM domain." It is unclear if the authors refer to the KH/KHL domains or others. Whatever the reference to the N-terminal region, it should also be consistent with the section above.

      This is now specified in the text.

      (c) Unclear: "We have previously demonstrated that Pkd2 levels are reduced in a complete Bicc1 null mice,22 performing qRT-PCR of P4 kidneys (i.e. before the onset of a strong cystic phenotype), revealed that Bicc1, Pkd1 and Pkd2 were statistically significantly down9 regulated (Fig. 4h-j)".

      We have changed the text to clarify this. 

      (d) “Utilizing recombinant GST domains of PC1 and PC2, we demonstrated that BICC1 binds to both proteins in GST-pulldown assays (Fig. 1a, b)." GST-tagged domains? Fusions?

      We have changed the text to clarify this. 

      (e) "To study the interaction between BICC1, PKD1 and PKD2 we combined biochemical approaches, knockout studies in mice and Xenopus, genetic engineered human kidney cells" > genetically engineered.

      We have changed the text to clarify this.

      (f) Capitalization (e.g., see Figure S3, ref. the Bpk allele) and annotation (e.g., Gly821Glu and G821E) are inconsistent.

      We have homogenized the labeling of the capitalization and annotations throughout the manuscript. 

      (g) What do the authors mean by "homozygous evolutionarily well-conserved missense variant"?

      We have changed this is the revised version of the manuscript. 

      Reviewer #3 (Public review/Recommendations to the authors):

      (1) A further study in HUREC cells investigating the critical regulatory role of BICC1 and potential interaction with mir-17 may yet lead to a modifiable therapeutic target.

      (2) This study should ideally include experiments in HUREC material obtained from patients/families with BICC1 mutations and studying its effects on the PKD1/2 complex in primary cell lines.

      This is an excellent suggestion. We agree with the reviewer that it would have been interesting to analyze HUREC material from the affected patients. Unfortunately, besides DNA and the phenotypic analysis described in the manuscript neither human tissue nor primary patient-derived cells collected once the two patients with the BICC1 p.Ser240Pro variant passed away.

      No changes to the revised manuscript have been made to address this point.

      (3) Please remove repeated words in the following sentence in paragraph 2 of the introduction: "BICC1 encodes an evolutionarily conserved protein that is characterized by 3 K-homology (KH) and 2 KH-like (KHL) RNA-binding domains at the N-terminus and a SAM domain at the C-terminus, which are separated by a by a disordered intervening sequence (IVS).23-28".

      This has been changed.

    1. Author response:

      Reviewer #1 (Public review):

      The authors analysed large-scale brain-state dynamics while humans watched a short video. They sought to identify the role of thalamocortical interactions.

      Major concerns

      (1) Rationale for using the naturalistic stimulus

      In terms of brain state dynamics, previous studies have already reported large-scale neural dynamics by applying some data-driven analyses, like energy landscape analysis and Hidden Markov Model, to human fMRI/EEG data recorded during resting/task states. Considering such prior work, it'd be critical to provide sufficient biological rationales to perform a conceptually similar study in a naturalistic condition, i.e., not just "because no previous work has been done". The authors would have to clarify what type of neural mechanisms could be missed in conventional resting-state studies using, say, energy landscape analysis, but could be revealed in the naturalistic condition.

      We appreciate your insightful comments regarding the need for a biological rationale in our study. As you mentioned, there are similar studies, just like Meer et al. utilized Hidden Markov Models to identify various activation modes of brain networks that included subcortical regions[1], Song et al. linked brain states to narrative understandings and attentional dynamics[2, 3]. These studies could answer why we use naturalistic stimuli datasets. Moreover, there is evidence suggesting that the thalamus plays a crucial role in processing information in a more naturalistic context while pointing out the vital role in thalamocortical communications[4, 5]. So, we tended to bridge thalamic activity and cortical state transition using the energy landscape description.

      To address these gaps in conventional resting-state studies, we explored an alternative method—maximum entropy modeling based on the energy landscape. This allowed us to validate how the thalamus responds to cortical state transitions. To enhance clarity, we will update our introduction to emphasize the motivations behind our research and the significance of examining these neural mechanisms in a naturalistic setting.

      (2) Effects of the uniqueness of the visual stimulus and reproducibility

      One of the main drawbacks of the naturalistic condition is the unexpected effects of the stimuli. That is, this study looked into the data recorded from participants who were watching Sherlock, but what would happen to the results if we analyzed the brain activity data obtained from individuals who were watching different movies? To ensure the generalizability of the current findings, it would be necessary to demonstrate qualitative reproducibility of the current observations by analysing different datasets that employed different movie stimuli. In fact, it'd be possible to find such open datasets, like www.nature.com/articles/s41597-023-02458-8.

      We appreciate your concern regarding the reproducibility of our findings. The dataset from the "Sherlock" study is of high quality and has shown good generalizability in various research contexts. We acknowledge the importance of validating our results with different datasets to enhance the robustness of our conclusions. While we are open to exploring additional datasets, we intend to pursue this validation once we identify a suitable alternative. Currently, we are considering a comparison with the dataset from "Forrest Gump" as part of our initial plan.

      (3) Spatial accuracy of the "Thalamic circuit" definition

      One of the main claims of this study heavily relies on the accuracy of the localization of two different thalamic architectures: matrix and core. Given the conventional or relatively low spatial resolution of the fMRI data acquisition (3x3x3 mm^3), it appears to be critically essential to demonstrate that the current analysis accurately distinguished fMRI signals between the matrix and core parts of the thalamus for each individual.

      We acknowledge the importance of accurately localizing the different thalamic architectures, specifically the matrix and core regions. To address this, we downsampled the atlas of matrix and core cell populations from the previous study from a resolution of 2x2x2 mm<sup>3</sup> to 3x3x3 mm<sup>3</sup>, which aligns with our fMRI data acquisition. We would report the atlas as Supplementary Figures in our revision.

      (4) More detailed analysis of the thalamic circuits

      In addition, if such thalamic localisation is accurate enough, it would be greatly appreciated if the authors perform similar comparisons not only between the matrix and core architectures but also between different nuclei. For example, anterior, medial, and lateral groups (e.g., pulvinar group). Such an investigation would meet the expectations of readers who presume some microscopic circuit-level findings.

      We appreciate your suggestion regarding a more detailed analysis of thalamic circuits. We have touched upon this in the discussion section as a forward-looking consideration. However, we believe that performing nuclei segmentation with 3T fMRI may not be ideal due to well-documented concerns regarding signal-to-noise ratio and spatial resolution. That said, we are interested in exploring these nuclei-pathway connections to cortical areas in future studies with a proper 7T fMRI naturalistic dataset.

      (5) Rationale for different time window lengths

      The authors adopted two different time window lengths to examine the neural dynamics. First, they used a 21-TR window for signal normalisation. Then, they narrowed down the window length to 13-TR periods for the following statistical evaluation. Such a seemingly arbitrary choice of the shorter time window might be misunderstood as a measure to relax the threshold for the correction of multiple comparisons. Therefore, it'd be appreciated if the authors stuck to the original 21-TR time window and performed statistical evaluations based on the setting.

      Thank you for your valuable feedback regarding the choice of time window lengths. We aimed to maintain consistency in window lengths across our analyses. In light of your comments and suggestions from other reviewers, we plan to test our results using different time window lengths and report findings that generalize across these variations. Should the results differ significantly, we will discuss the implications of this variability in our revised manuscript.

      (6) Temporal resolution

      After identifying brain states with energy landscape analysis, this study investigated the brain state transitions by directly looking into the fMRI signal changes. This manner seems to implicitly assume that no significant state changes happen in one TR (=1.5sec), which needs sufficient validation. Otherwise, like previous studies, it'd be highly recommended to conduct different analyses (e.g., random-walk simulation) to address and circumvent this problem.

      Thank you for raising this important point regarding temporal resolution. Many fMRI studies, such as those examining event boundaries during movie watching, operate under similar assumptions concerning state changes within one TR. For example, Barnett et al. processed the dynamic functional connectivity (dFC) with a window of 20 TRs (24.4s). So, we do not think it is a limitation but is a common question related to fMRI scanning parameters. To strengthen our analysis of state transitions and ensure they are not merely coincidental, we plan to conduct random-walk simulations, as suggested, to validate our findings in accordance with methodologies used in previous research.

      Reviewer #2 (Public review):

      Summary:

      In this study, Liu et al. investigated cortical network dynamics during movie watching using an energy landscape analysis based on a maximum entropy model. They identified perception- and attention-oriented states as the dominant cortical states during movie watching and found that transitions between these states were associated with inter-subject synchronization of regional brain activity. They also showed that distinct thalamic compartments modulated distinct state transitions. They concluded that cortico-thalamo-cortical circuits are key regulators of cortical network dynamics.

      Strengths:

      A mechanistic understanding of cortical network dynamics is an important topic in both experimental and computational neuroscience, and this study represents a step forward in this direction by identifying key cortico-thalamo-cortical circuits. The analytical strategy employed in this study, particularly the LASSO-based analysis, is interesting and would be applicable to other data types, such as task- and resting-state fMRI.

      We thanks for this comment and encouragement.

      Weaknesses:

      Due to issues related to data preprocessing, support for the conclusions remains incomplete. I also believe that a more careful interpretation of the "energy" derived from the maximum entropy model would greatly clarify what the analysis actually revealed.

      Thank you for your valuable suggestions, and we apologize for any misunderstandings regarding the interpretation of the energy landscape in our study. To address this issue, we will include a dedicated paragraph in both the methods and results sections to clarify our use of the term "energy" derived from the maximum entropy model. This addition aims to eliminate any ambiguity and provide a clearer understanding of what our analysis reveals.

      (1) I think the method used for binarization of BOLD activity is problematic in multiple ways.

      a) Although the authors appear to avoid using global signal regression (page 4, lines 114-118), the proposed method effectively removes the global signal. According to the description on page 4, lines 117-122, the authors binarized network-wise ROI signals by comparing them with the cross-network BOLD signal (i.e., the global signal): at each time point, network-wise ROI signals above the cross-network signal were set to 1, and the rest were set to −1. If I understand the binarization procedure correctly, this approach forces the cross-network signal to be zero (up to some noise introduced by the binarization of network-wise signals), which is essentially equivalent to removing the global signal. Please clarify what the authors meant by stating that "this approach maintained a diverse range of binarized cortical states in data where the global signal was preserved" (page 4, lines 121-122).

      Thank you for highlighting the potential issue with our binarization method. We appreciate your insights regarding the comparison of network-wise ROI signals with the cross-network BOLD signal, as this may inadvertently remove the global signal. To address this, we will conduct a comparative analysis of results obtained from both our current approach and the original pipeline. If we decide to retain our current method, we will carefully reconsider the rationale and rephrase our descriptions to ensure clarity regarding the preservation of the global signal and the diversity of binarized cortical states.

      b) The authors might argue that they maintained a diverse range of cortical states by performing the binarization at each time point (rather than within each network). However, I believe this introduces another problem, because binarizing network-wise signals at each time point distorts the distribution of cortical states. For example, because the cross-network signal is effectively set to zero, the network cannot take certain states, such as all +1 or all −1. Similarly, this binarization biases the system toward states with similar numbers of +1s and −1s, rather than toward unbalanced states such as (+1, −1, −1, −1, −1, −1). These constraints and biases are not biological in origin but are simply artifacts of the binarization procedure. Importantly, the energy landscape and its derivatives (e.g., hard/easy transitions) are likely to be affected by these artifacts. I suggest that the authors try a more conventional binarization procedure (i.e., binarization within each network), which is more robust to such artifacts.

      Related to this point, I have a question regarding Figure S1, in which the authors plotted predicted versus empirical state probabilities. As argued above, some empirical state probabilities should be zero because of the binarization procedure. However, in Figure S1, I do not see data points corresponding to these states (i.e., there should be points on the y-axis). Did the authors plot only a subset of states in Figure S1? I believe that all states should be included. The correlation coefficient between empirical and predicted probabilities (and the accuracy) should also be calculated using all states.

      Thank you for your thoughtful examination of our data processing pipeline. We agree that a comparison between the conventional binarization method and our current approach is warranted, and we appreciate your suggestion. Upon reviewing Figure S1, we discovered that there was indeed an error related to the plotting style set to "log10." As you correctly pointed out, the data should reflect that the probabilities for states where all networks are either activated or deactivated are zero. We are very interested in exploring the state distributions obtained from both the original and current approaches, as your comments highlight important considerations. We sincerely appreciate your insightful feedback and will make sure to address these points thoroughly in our first revision.

      c) The current binarization procedure likely inflates non-neuronal noise and obscures the relationship between the true BOLD signal and its binarized representation. For example, consider two ROIs (A and B): both (+2%, +1%) and (+0.01%, −0.01%) in BOLD signal changes would be mapped to (+1, −1) after binarization. This suggests that qualitatively different signal magnitudes are treated identically. I believe that this issue could be alleviated if the authors were to binarize the signal within each network, rather than at each time point.

      Thank you for your important observation regarding the potential inflation of non-neuronal noise in our current binarization procedure. We recognize that this process could lead to qualitatively different signal magnitudes being treated similarly after binarization, as you illustrated with your example. While we acknowledge your point, we believe that conventional binarization pipelines may also encounter this issue, albeit by comparing signals to a network's temporal mean activity. To address this concern and maintain consistency with previous studies, we will discuss this limitation in our revised manuscript. Additionally, if deemed necessary, we will explore implementing a percentile-based threshold above the baseline to further refine our binarization approach. Your suggestion provides a valuable perspective, and we appreciate your insights.

      (2) As the authors state (page 5, lines 145-148), the "energy" described in the energy landscape is not biological energy but rather a statistical transformation of probability distributions derived from the Boltzmann distribution. If this is the case, I believe that Figure 2A is potentially misleading and should be removed. This type of schematic may give the false impression that cortical state dynamics are governed by the energy landscape derived from the maximum entropy model (which is not validated).

      Thank you for your valuable feedback regarding Figure 2A. We apologize for any confusion it may have created. While we recognize that similar figures are commonly used in literature involving energy landscapes (maximum entropy model), we agree that Figure 2A may mislead readers into thinking that cortical state dynamics are directly governed by the energy landscape derived from the maximum entropy model, which has not been validated. In light of your comments, we will remove Figure 2A and instead emphasize the analytical strategy presented in Figure 2B. Additionally, we will provide a simplified line graph as an illustrative example to clarify the concepts without the potential for misinterpretation.

      Reviewer #3 (Public review):

      Summary:

      In this study, Liu et al. analyze fMRI data collected during movie watching, applied an energy landscape method with pairwise maximum entropy models. They identify a set of brain states defined at the level of canonical functional networks and quantify how the brain transitions between these states. Transitions are classified as "easy" or "hard" based on changes in the inferred energy landscape, and the authors relate transition probabilities to inter-subject correlation. A major emphasis of the work is the role of the thalamus, which shows transition-linked activity changes and dynamic connectivity patterns, including differential involvement of parvalbumin- and calbindin-associated thalamic subdivisions.

      Strengths:

      The study is methodologically complex and technically sophisticated. It integrates advanced analytical methods into high-dimensional fMRI data. The application of energy landscape analysis to movie-watching data appears to be novel as well. The finding on the thalamus involved energy state transition and provides a strong linkage to several theories on thalamic control functions, which is a notable strength.

      Thanks for your comments on the novelty of our study.

      Weaknesses:

      The main weakness is the conceptual clarity and advances that this otherwise sophisticated set of analyses affords. A central conceptual ambiguity concerns the energy landscape framework itself. The authors note that the "energy" in this model is not biological energy but a statistical quantity derived from the Boltzmann distribution. After multiple reads, I still have major trouble mapping this measure onto any biological and cognitive operations. BOLD signal is a measure of oxygenation as a proxy of neural activity, and correlated BOLD (functional connectivity) is thought to measure the architecture of information communication of brain systems. The energy framework described in the current format is very difficult for most readers to map onto any neural or cognitive knowledge base on the structure and function of brain systems. Readers unfamiliar with maximum entropy models may easily misinterpret energy changes as reflecting metabolic cost, neural effort, or physiological variables, and it is just very unclear what that measure is supposed to reflect. The manuscript does not clearly articulate what conceptual and mechanistic advances the energy formalism provides beyond a mathematical and statistical report. In other words, beyond mathematical description, it is very hard for most readers to understand the process and function of what this framework is supposed to tell us in regards to functional connectivity, brain systems, and cognition. The brain is not a mathematical object; it is a biological organ with cognitive functions. The impact of this paper is severely limited until connections can be made.

      Thank you for your insightful and constructive comments regarding the conceptual clarity of our energy landscape framework. We appreciate your perspective on the challenges of mapping the statistical measure of "energy" derived from the Boltzmann distribution onto biological and cognitive operations. To address these concerns, we will revise our manuscript to clarify our expressions surrounding "energy" and emphasize its probabilistic nature. Additionally, we will incorporate a series of analyses that explicitly relate the features of the energy landscape to cognitive processes and key parameters, such as brain integration and functional connectivity. We believe these changes will help bridge the gap between our mathematical framework and its relevance to understanding brain systems and cognitive functions.

      Relatedly, the use of metaphors such as "valleys," "hills," and "routes" in multidimensional measures lacks grounding. Valleys and hills of what is not intuitive to understand. Based on my reading, these features correspond to local minima and barriers in a probability distribution over binarized network activation patterns, but similar to the first point, the manuscript does not clearly explain what it means conceptually, neurobiologically, or computationally for the brain to "move" through such a landscape. The brain is not computing these probabilities; they are measurement tools of "something". What is it? To advance beyond mathematical description, these measurements must be mapped onto neurobiological and cognitive information.

      Thank you for your valuable feedback. In our revisions, we would aim to link the concept of rapid transition routes in the energy landscape to cognitive processes, such as narrative understanding and related features. By exploring these connections, we hope to provide a clearer context for how our framework can enhance understanding of cognitive functions and their neural correlates.

      This conceptual ambiguity goes back to the Introduction. At the level of motivation, the purpose and deliverables of the study are not defined in the Introduction. The stated goal is "Transitions between distinct cortical brain states modulate the degree of shared neural processing under naturalistic conditions". I do not know if readers will have a clear answer to this question at the end. Is the claim that state transitions cause changes in inter-subject correlation, that they index moments of narrative alignment, or that they reflect changes in attentional or cognitive mode? This level of explanation is largely dissociated from the methods in their current form.

      Thank you for highlighting this important point regarding the conceptual clarity in our Introduction. We appreciate your feedback about the motivation and objectives of the study. To clarify the stated goal of investigating how transitions between distinct cortical brain states modulate shared neural processing under naturalistic conditions, we will revise the manuscript to explicitly define the specific claims we aim to address. We will ensure that these explanations are closely tied to the methods employed in our study, providing a clearer framework for our readers.

      Several methodological choices can use clarification. The use of a 21-TR window centered on transition offsets is unusually long relative to the temporal scale of fMRI dynamics and to the hypothesized rapidity of state transitions. On a related note, what is the temporal scale of state transition? Is it faster than 21 TRs?

      Thank you for your insightful questions regarding our methodological choices. Our focus on specific state transitions necessitated the use of a 21-TR window. While it’s true that other transitions may occur within this window, averaging across the same transitions at different times allows us to identify distinctive thalamic BOLD patterns that precede cortical state transitions. This methodology enables us to capture relevant dynamics while ensuring that we focus on the transitions of interest. We appreciate your feedback, and this clarification will be included in our revised manuscript. We would also add a figure that describe the dwell time of cortical states.

      The choice of movie-watching data is a strength. But, many of the analyses performed here, energy landscape estimation, clustering of states, could in principle be applied to resting-state data. The manuscript does not clearly articulate what is gained, mechanistically or cognitively, by using movie stimuli beyond the availability of inter-subject correlation.

      Thank you for your question, which closely aligns with a concern raised by Reviewer #1. Our core hypothesis posits that naturalistic stimuli yield a broader set of brain states compared to those observed during resting-state conditions. To support this assertion, we will clearly articulate the findings from previous studies that relate to this hypothesis. Additionally, if appropriate, we will provide a comparative analysis between our data and resting-state data to highlight the differences and emphasize the uniqueness of the brain states elicited by naturalistic stimuli.

      Because of the above issues, a broader concern throughout the results is the largely descriptive nature of the findings. For example, the LASSO analysis shows that certain state transitions predict ISC in a subset of regions, with respectable R² values. While statistically robust, the manuscript provides little beyond why these particular transitions should matter, what computations they might reflect, or how they relate to known cognitive operations during movie watching. Similar issues arise in the clustering analyses. Clustering high-dimensional fMRI-derived features will almost inevitably produce structure, whether during rest, task, or naturalistic viewing. What is missing is an explanation of why these specific clusters are meaningful in functional or mechanistic terms.

      Thank you for your questions. In our revisions, we will perform additional analyses aimed at linking state transitions to cognitive processes more explicitly. Regarding clustering, we will provide a thorough discussion in the revised manuscript.

      Finally, the treatment of the thalamus, while very exciting, could use a bit more anatomical and circuit-level specificity. The manuscript largely treats the thalamus as a unitary structure, despite decades of work demonstrating big functional and connectivity differences across thalamic nuclei. A whole-thalamus analysis without more detailed resolution is increasingly difficult to justify. The subsequent subdivision into PVALB- and CALB-associated regions partially addresses this, but these markers span multiple nuclei with overlapping projection patterns.

      This suggestion aligns with the feedback from Reviewer #1. We believe that performing nuclei segmentation with 3T fMRI may not be ideal due to well-documented concerns regarding signal-to-noise ratio and spatial resolution. Therefore, investigating core and matrix cell projections across different thalamic nuclei using 7T fMRI presents a promising avenue for further study.

      (1) Van Der Meer J N, Breakspear M, Chang L J, et al. Movie viewing elicits rich and reliable brain state dynamics [J]. Nature Communications, 2020, 11(1): 5004.

      (2) Song H, Park B Y, Park H, et al. Cognitive and Neural State Dynamics of Narrative Comprehension [J]. Journal of Neuroscience, 2021, 41(43): 8972-8990.

      (3) Song H, Shim W M, Rosenberg M D. Large-scale neural dynamics in a shared low-dimensional state space reflect cognitive and attentional dynamics [J]. Elife, 2023, 12.

      (4) Shine J M, Lewis L D, Garrett D D, et al. The impact of the human thalamus on brain-wide information processing [J]. Nature Reviews Neuroscience, 2023, 24(7): 416-430.

      (5) Yang M Y, Keller D, Dobolyi A, et al. The lateral thalamus: a bridge between multisensory processing and naturalistic behaviors [J]. Trends in Neurosciences, 2025, 48(1): 33-46.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1(Public review):

      In this study, Acosta-Bayona et al. aim to better understand how environmental conditions could have influenced specific gene functions that may have been selected for during the domestication of teosinte parviglumis into domesticated maize. The authors are particularly interested in identifying the initial phenotypic changes that led to the original divergence of these two subspecies. They selected heavy metal (HM) stress as the condition to investigate. While the justification for this choice remains speculative, paleoenvironmental data would add value; the authors hypothesize that volcanic activity near the region of origin could have played a role.

      The justification of choice to investigate the effects of heavy metal stress is not speculative. As mentioned now in the Abstract, the elucidation of the genome from the Palomero toluqueño maize landrace revealed heavy metal effects during domestication (Vielle-Calzada et al., Science 2009). Our aim was to test the hypothesis that heavy metal (HM) stress influenced the evolutionary transition of teosinte parviglumis to maize.

      (1) Although the paper presents some interesting findings, it is difficult to distinguish which observations are novel versus already known in the literature regarding maize HM stress responses. The rationale behind focusing on specific loci is often lacking. For example, a statistically significant region identified via LOD score on chromosome 5 contains over 50 genes, yet the authors focus on three known HM-related genes without discussing others in the region. It is unclear why ZmHMA1 was selected for mutagenesis over ZmHMA7 or ZmSKUs5.

      We appreciated the depth and value of this comment.

      Maize phenotypic responses to sublethal concentrations to heavy metals – copper (Cu) and cadmium (Cd) in particular - are well characterized and published, and in agreement with our results. In the first section of the Results (pgs 7 and 8), we added pertinent references to clearly show which observations are already known. By contrast, teosinte parviglumis responses are in all cases novel. To our knowledge this is the first study that analyzed in detail the phenotypic response of teosinte to sublethal concentrations of heavy metals, specifically Cu and Cd. We have now emphasized the novelty of these observations (pg 8).

      To address the fact that we only focused on three known HM-related genes without discussing others in the statistically significant region identified via LOD score on chr.5, we have added a full section that reads as follows (pgs. 11 to 13 of the new version):

      “Large-scale genomic and transcriptomic comparisons indicate that many HM response genes were positively selected across the maize genome.

      To expand the results well beyond the analysis of the three genes previously described, we performed a detailed analysis of genetic diversity across the 11.47 Mb genomic region comprised between Z_mSKUs5_ and ZmHMA1. This additional analysis reveals general tendencies in the quantity and nature of loci that were affected by positive selection during the teosinte parviglumis to maize transition in a region identified via LOD score on chr.5. We compared nucleotide variability by using 100 bp bins covering loci composed of two 30 Kb segments up and downstream of coding sequences, respectively, and the coding sequence itself, for 173 genes present within the genomic region comprised between ZmSKUs5 and ZmHMA (Figure S1 and Supplementary File 6). Two types of statistical tests (ANOVA and Wilcoxon) were applied to nucleotide variability comparisons using the entirety of each locus. The Benjamini-Hochber procedure allowed an estimation of the false discovery rate (FDR<0.05) to avoid type I errors (false positives). Although some individual loci appear as differently classified depending on the statistical test applied (22 out of 173 loci), the general differences in nucleotide variability are consistently maintained within the subregions described below. We found that 166 out of 173 loci show signatures of positive selection and are roughly organized in five independent subregions of variable length. The first six loci are consecutively ordered in a 402 Kb subregion that includes ZmSKUs5. A second group of 13 consecutive loci expands over a 1.44 Mb subregion that contains NRAMP ALUMINUM TRANSPORTER1, also involved in HM response through uptake of divalent ions. A third group of 17 consecutive loci expands over 1.28 Mb; eleven contain genes encoding for uncharacterized proteins. The fourth group is composed of 57 consecutive loci expanding over 3.22 Mb and contains genes encoding for DEFECTIVE KERNEL55, AUXIN RESPONSE FACTOR16, and peroxydases involved in responses to oxydative stress. The fifth group contains 12 consecutive loci expanding over 713 Kb and contains ZmHMA1. An additional segment of approximately 1.17 Mb and containing 25 consecutive loci that were positively selected expands away from the ZmSKUs5-ZmHMA1 segment; it also contains several genes encoding for peroxydases. Although multiple loci include genes that could be involved in abiotic stress and oxidative responses, these results suggest that multiple factors other than HM stress could have played a role in the evolutionary mechanisms that affected the genetic diversity of chr.5 during the teosinte parviglumis to maize transition.

      To further analyze the possibility that HM response could have played a role in maize emergence and subsequent domestication, we analyzed large scale transcriptomic data corresponding to independent experiments aiming at understanding the response of maize roots to HM stress. Six available transcriptomes were selected for in-depth analysis because they presented a fold change strictly higher than 1, and their results were supported by false discovery rates (FDR<0.05). These six transcriptomes (Table S5) included HM response datasets corresponding to growth conditions that not only incorporated Cu, but also lead (Pb) and chromium (Cr) that were not included in the substrate of our experiments. Transcriptional profiles were obtained from roots of plants at different stages: maize seedlings (Shen et al., 2012; Gao et al., 2015; Zhang et al., 2024a), three week old plantlets (Yang et al., 2023), and plants at V2 stage (Zhang et al., 2024b; Fengxia et al., 2025). A total of 120 genes shared by all six transcriptomes were found to be differentially expressed under HM stress conditions (66 upegulated and 54 downregulated; Figure S3), including ZmSKUs5, ZmHMA1 and ZmHMA7; 52 of them (43.3%) are located in maize loci showing less than 70% of the nucleotide variability found in teosinte parviglumis, suggesting that they were affected by positive selection (Yamasaki et al., 2005; Supplementary File 7). Of 18 mapping in chr.5, twelve are within the 82 cM that fractionates into multiple QTLs under selection during the parviglumis to maize transition. Interestingly, five additional loci containing HM response genes completely lack SNPs within their total length in both parviglumis and maize, and 19 additional loci lack SNPs in at least one 30 Kb segment or their coding region (Supplementary File 7), suggesting the frequent presence of ultraconserved genomic regions in many loci containing HM response genes. When this same analysis was conducted in a set of loci comprising 63 genes previously identified as differentially expressed in response to abiotic stress not directly related to HM responses (hypoxia; nutritional deficiency; soil alkalinity; drought; soil salinity), 18 loci (28.6%) showed less than 70% of the nucleotide variability found in teosinte parviglumis. Only one of them maps in chr.5 and none contained segments or coding regions lacking SNPs in parviglumis or maize. These results suggest that in contrast to other types of abiotic stress response genes, loci comprising a large set of genes that unambiguously respond to HM stress caused by chemical elements of diverse nature were affected by positive selection during the parviglumis to maize transition, irrespectively of their position in the genome.”

      The detailed analysis of genetic diversity across 11.47 Mb of chr.5 in the genomic region comprised between ZmSKUs5 and ZmHMA1 in presented as Supplementary File 6.

      The analysis of genetic diversity in loci encompassing heavy metal response genes shared by six transcriptomes and abiotic stress controls are described in Supplementary File 7.

      In the Discussion (pgs. 21 and 22), we added a paragraph section that reads as follows:

      “Although loss of genetic diversity is usually the result of human selection during domestication, it can also represent a consequence of natural selective pressures favoring fitness of specific teosinte parviglumis allelic variants better adapted to environmental changes and subsequently affected by human selection during the domestication process. This possibility is reflected by widely spread selective sweeps affecting a large portion of chr.5 that contains hundreds of genes showing signatures of positive selection. The analysis of 11.47 Mb covering the ZmHMA1ZmSKUs5 segment confirms the presence of large but discrete genomic subregions that were positively selected during the teosinte parviglumis to maize transition. Although several contain genes involved in HM response and oxidative stress, the diversity of gene functions does not necessarily favor abiotic stress over other factors that could be at the origin of selective forces affecting these regions. By contrast, a large scale transcriptomic survey indicates that genes consistently responding to HMs (Cu, Cd, Pb and Cr ) show signatures of positive selection at unusual high frequencies (43.3%) as compared to loci containing genes responding to other types of abiotic stress (28.6%). Our identification of HM response genes affected by positive selection is far from being exhaustive. Nevertheless, it agrees with the expected effects of a widespread selective sweep caused by environmental changes that influenced the parviglumis to maize transition at the genetic level. Of intriguing interest are 24 loci that partially or completely lack SNPs in both teosinte parviglumis and maize, suggesting possible genetic bottlenecks occurred before the teosinte to maize transition. Examples of other edaphological factors driving genetic divergence either in the teosintes or maize include local adaptation to phosphorus concentration in mexicana and parviglumis (Aguirre-Liguori et al. 2019), and fast maize adaptation to changing iron availability through the action of genes involved in its mobilization, uptake, and transport (Benke and Stich 2011). Our results reveal a teosinte parviglumis environmental plasticity that could be related to the function of HM response genes positively selected during the teosinte parviglumis to maize transition. Previous studies have demonstrated that transposable elements (TEs) contribute to activation of maize genes in response to abiotic stress, affecting up to 20% of the genes upregulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress (Makarevitch et al., 2015). It is therefore possible that the HM response of some specific genes that influenced maize emergence or domestication could be mediated by TEs influencing or driving their transcriptional regulation.”

      The mutagenic analysis of ZmHMA7 and ZmSKUs5 will be included in a different publication.

      (2) The idea that HM stress impacted gene function and influenced human selection during domestication is of interest. However, the data presented do not convincingly link environmental factors with human-driven selection or the paleoenvironmental context of the transition. While lower nucleotide diversity values in maize could suggest selective pressure, it is not sufficient to infer human selection and could be due to other evolutionary processes. It is also unclear whether the statistical analysis was robust enough to rule out bias from a narrow locus selection. Furthermore, the addition of paleoclimate records (Paleoenvironmental Data Sources as a starting point) or conducting ecological niche modeling or crop growth models incorporating climate and soil scenarios would strengthen the arguments.

      We think that the detailed analysis of genetic diversity across 11.46 Mb covering the ZmSKUs5 to ZmHMA1 genomic segment – and its statistical validation - provides a precise understanding of the selective sweep dimensions in chr.5.

      We do agree that lower nucleotide diversity values in maize are not sufficient to infer human selection. Because many HM response loci show unusually low nucleotide variability in teosinte parviglumis (see the results of the transcriptomic analysis presented above), we cannot discard the possibility that natural selection forces related to environmental changes could have affected native populations of teosinte parviglumis.

      To further explore the link between environmental factors, natural or human-driven selection, and the paleoenvironmental context of the parviglumis to maize transition, we revised paleoenvironmental and geological records and added results in two sections that read as follows (pgs. 17 to 20):

      “Paleoenvironmental studies reveal periods of climatic instability in the presumed region of maize emergence during the early Holocene.

      It is well accepted that temperature fluctuations, volcanism and anthropogenic impact shaped the distribution and abundance of plant species in the Transmexican Volcanic Belt (TMVB) during the last 14,000 years (Torrescano-Valle et al. 2019). The TMVB has produced close to 8000 volcanic structures (Ferrari et al., 2011), transforming the relief multiple times, and causing hydrographic and soil changes that actively modified the distribution and composition of plant communities in Central Mexico. Detailed paleoenvironmental data for the Pleistocene and Holocene is available for several lacustrine zones located within the 50 to 100 km range of the region currently considered the cradle of maize domestication (Matzuoka et al. 2002; Figure 5a). In Lake Zirahuén (102°44′ W; 19°26′ N and approximately 2075 meters above sea level; index [i] in Figure 5a), pollen, microcharcoal and magnetic susceptibility analyses of two sedimentary sequences reveals three periods of major ecological change during the early and middle Holocene.

      Between 9500 and 9000 calibrated years before present (cal yr BP), pine forests seem to have been associated with summer insolation increases. A second peak of forest change occurred at around 8200 cal yr BP, coinciding with cold oscillations documented in the North Atlantic. Finally, events occurred between 7500 and 7100 cal yr BP shows an abrupt change in the plant community related to humid Holocene climates and a presumed volcanic event (Lozano-García et al., 2013). The environmental history of the central Balsas watershed has also been documented by pollen, charcoal, and sedimentary analysis conducted in three lakes and a swamp of the Iguala valley (Piperno et al. 2007). Paleoecological records of lake Ixtacyola (8°20N, 99°35W and approximately 720 meters above sea level; index [ii] in Figure 5a) and lake Ixtapa (8°21N, 99°26W) indicate that an important increase in temperature and precipitation occurred between 13000 and 10000 cal yr BP. The pollen record of Ixtacyola showed that members of the genus Zea were already part of the vegetation coverage by 12900 to 13000 cal yr BP, suggesting that some teosintes – likely including parviglumis - were commonly found at elevation areas where they do not presently occur. Lake Almoloya (also named Chignahuapan; 19°05N, 99°20E and approximately 2575 meters above sea level; index [iii] in Figure 5a) in the upper Lerma basin is only 20 Km from the crater of the Nevado de Toluca that is responsible for creating the late Pleistocene Upper Toluca Pumice layer over which the Lerma basin is deposited. Pollen records indicate the presence of Zea species by 11080 to 10780 cal yr BP. As for other locations, an important period of climatic instability prevailed between 11500 and 8500 cal yr BP (Ludlow-Wiechers et al., 2005). Humidity fluctuations occurred until 8000 cal yr BP, with a stable temperate climate between 8500 and 5000 cal yr BP. Although pollen and diatom studies are often difficult to interpret at a regional scale, the overall results presented above suggest consistent periods of Zea plants present in periods of environmental and climatic instability that correlate with the history of volcanic activity during the early Holocene, as described in the next section.

      Temporal and geographical convergence between volcanic eruptions and maize emergence during the Holocene.

      Current evidence indicates that the emergence and domestication of maize initiated in Mesoamerica some time around 9,000 yr BP (Matsuoka et al. 2002). The current location of teosinte parviglumis populations that are phylogenetically most closely allied with maize are currently distributed in a region located between the Michoacan-Guanajuato Volcanic Field (MGVF) at their northwest, and the Nevado de Toluca and Popocatéptl volcanoes at their east and northeast (Figure 5a; Matsuoka et al. 2002). Precise records of field data indicate that ten accessions were collected in the Balsas river drainage near Teloloapan and Sierra de Huautla (Guerrero), at approximately 100 km south of the Nevado de Toluca crater. Three other accessions were collected near Tejupilco de Hidalgo and Zacazonapan (Estado de México), at approximately 50 to 60 km from the Nevado de Toluca crater (8762, JSG y LOS-161, and JSG-391). And four other accessions were located in Michoacan, at a location within the MGVF (accession 8763), or at mid-distance between the MGVF and the Nevado de Toluca crater (accessions JSG y LOS-130, 8761, and 8766).

      The most important source of HMs in ancient soils of Mesoamerica is TMBV-dependent volcanic activity through short- and long-term effects related to lava deposits, ores, hydrothermal flow, and ash (Torrescano-Valle et al. 2019). The Nevado de Toluca volcano produced one of the most powerful eruptions from central Mesoamerica in the Holocene, giving rise to the Upper Toluca Pumice deposit at 12621 to 12025 cal yr BP (Arce et al., 2003; Figure 5b). The pumice fallout blanketed the Lerma and Mexico basins with 40 cm of coarse ash (Bloomfield and Valastro 1977; Arce et al. 2003). A second eruption dated by 36Cl exposure occurred at 9700 cal yr BP (Arce et al. 2003; Figure 5b), and the most recent eruption occurred at 3580 to 3831 cal yr BP (Macías et al. 1997). During the early and middle Holocene, the Popocatéptl volcano produced at least four eruptions dated 13037-12060, 10775–9564, 8328-7591, and 6262-5318 cal yr BP (Siebe et al. 1997); three other important eruptions occurred during the late Holocene, between 2713 and 733 cal yr BP (Siebe and Macías, 2006). In addition, the MGFV is a monogenetic volcanic field for which 23 independent eruptions have been documented during the Holocene, 21 of them located towards the southern part of the field, in close proximity to the region harboring some of the teosinte parviglumis populations most closely related to maize. Three of these eruptions occurred in the early Holocene (El Huanillo 1130 to 9688 cal yr BP; La Taza 10649 to 10300 cal yr BP; Cerro Grande 10173 to 9502 cal yr BP; Figure 5b), and three others during the initial period of the middle Holocene, between 8400 and 7696 cal yr BP (La Mina, Los Caballos, and Cerro Amarillo; Figure 5b). On average, a new volcano forms every ~435 years in the MGFV (Macías and Arce, 2019). No less than 16 other eruptions occurred between 7159 cal yr BP and the present time (Figure 5b). Soils of volcanic origin (andosols) are currently distributed in regions north-west from the Nevado de Toluca and Popocatéptl craters, in close proximity with teosinte parviglumis populations most closely related to maize (Figure S5). Although modern distribution of teosinte populations may differ from their distribution around 9000 yr BP, and unknown populations more closely related to maize may yet to be discovered, this data indicates that the date and region where maize emerged is convergent with the dates and locations of several volcanic eruptions occurred during the Holocene in that same region.”

      (3) Despite the interest in examining HM stress in maize and the presence of a pleiotropic phenotype, the assessment of the impact of gene expression is limited. The authors rely on qPCR for two ZmHMA genes and the locus tb1, known to be associated with maize architecture. A transcriptomic analysis would be necessary to 1- strengthen the proposed connection and 2- identify other genes with linked QTLs, such as those in the short arm of chromosome 5.

      Real-time qPCR is an accurate and reliable approach to assess the expression of specific genes such as ZMHMA1 and Tb1, but we agree that our results do not allow to establish a direct regulatory link between the function of Tb1, the pleiotropic parviglumis phenotype under HM stress, and the function of ZmHMA1. We also concede that the large transcriptional analysis of HM response in maize (presented above) does not allow to elucidate a possible connection between these two genes. We have substantially downplayed our conclusion in this section by modifying the end of the section in pg. 17, that now reads:

      “These results do not allow to directly link the regulation of ZmHMA1 expression to the function of Tb1; however, they open an opportunity to further investigate the possibility that under HM stress, the formation of secondary ramifications in teosinte parviglumis could be repressed by transcription factors of the TCP family, including Tb1.”

      This is also emphasized in the Discussion (pg 21) as follows:

      “Under HM stress, we also show that Tb1 is overexpressed in the apical meristem of teosinte parviglumis, suggesting that formation of secondary ramifications is repressed by Tb1 function under HM stress, as in extant maize. At this stage we cannot discard the possibility that Tb1 upregulation in parviglumis reflects a more generalized response to abiotic stress; however, the expression ZmHMA1 is downregulated in W22 wild-type maize meristems in the presence of HMs but upregulated in teosinte parviglumis meristems, suggesting that a specific regulatory shift relating HM responses and ZmHMA1 function occurred during the teosinte parviglumis to maize transition.”

      On the other hand, the transcriptional analysis the identification of 52 additional HM response genes showing signatures of positive selection occurred during the parviglumis to maize transition; 12 of them map to chr.5 within the region having linked QTLs within the short arm of chr.5. So far, genes involved in HM response and oxidative stress represent the most prevalent class of genes identified within the genomic region showing pleiotropic effects on domestication and multiple linked QTLs in chr.5.

      Reviewer #2 (Public review):

      Summary:

      This work explores the phenotypic developmental traits associated with Cu and Cd responses in teosinte parviglumis, a species evolutionary related to extant maize crops. Cu and Cd could serve as a proxy for heavy metals present in the soils. The manuscript explores potential genetic loci associated with heavy metal responses and domestication identified in previous studies. This includes heavy metal transporters, which are unregulated during stress. To study that, the authors compare the plant architecture of maize defective in ZmHMA1 and speculate on its association with domestication.

      Strengths:

      Very few studies covered the responses of teosintes to heavy metal stress. The physiological function of ZmHMA1 in maize also gives some novelty in this study. The idea and speculation section is interesting and well-implemented.

      Weaknesses:

      The authors explored Cu/Cd stress but not a more comprehensive panel of heavy metals, making the implications of this study quite narrow. Some techniques used, such as end-point RT-PCR and qPCR, are substandard for the field. The phenotypic changes explored are not clearly connected with the potential genetic mechanisms associated with them, with the exception of nodal roots. If teosintes in response to heavy metal have phenotypic similarity with modern landraces of maize, then heavy metal stress might have been a confounding factor in the selection of maize and not a potential driving factor. Similar to the positive selection of ZmHMA1 and its phenotypic traits. In that sense, there is no clear hypothesis of what the authors are looking for in this study, and it is hard to make conclusions based on the provided results to understand its importance. The authors do not provide any clear data on the potential influence of heavy metals in the field during the domestication of maize. The potential role of Tb-1 is not very clear either.

      Thank you for these comments. We have now emphasized our hypothesis in the abstract and the last paragraph of the Introduction (pg. 6):

      “To test the hypothesis that heavy metal (HM) stress influenced the evolutionary transition of teosinte to maize, we exposed both subspecies to sublethal concentrations of copper and cadmium etc…”

      A comprehensive panel of heavy metals would not be more accurate in terms of simulating the composition of soils evolving across 9,000 years in the region where maize presumably emerged. Copper (Cu) and cadmium (Cu) correspond each to a different affinity group for proteins of the ZmHMA family. ZmHMA1 has preferential affinity for Cu and Ag (silver), whereas ZmHMA7 has preferential affinity to Cd, Zn (zinc), Co (cobalt), and Pb (lead). Since these P1b-ATPase transporters mediate the movement of divalent cations, their function remains consistent regardless of the specific metal tested, provided it belongs to the respective affinity group. By applying sublethal concentrations of Cd (16 mg/kg) and Cu (400 mg/kg), we caused a measurable physiological response while allowing plants to complete their life cycle, including the reproductive phase, facilitating a comprehensive analysis of metal stress adaptation. Whereas higher doses impair flowering or are lethal, lower Cu/Cd concentrations do not consistently show conventional phenotypic responses such as reduced plant growth (AbdElgawad et al. 2020; Atta et al., 2023)

      Based on comments by both reviewers, we present now a large transcriptional analysis that incorporates HM responses to lead (Pb) and chromium (Cr), in addition to Cu. Results show that many genes responding to Pb and Cr were also positively selected across the maize genome, suggesting that HM stress led to a ubiquitous rather than a specific evolutionary response to heavy metals (please see our response to Reviewer#1 and sections in pgs. 11 to 13) .

      Real-time qPCR is an accurate and reliable approach to assess the expression of specific genes such as ZMHMA1 and Tb1, but we agree that our results do not allow to establish a direct regulatory link between the function of Tb1, the pleiotropic parviglumis phenotype under HM stress, and the function of ZmHMA1. We also concede that the large transcriptional analysis of HM response in maize (presented above) does not allow to elucidate a possible connection between these two genes. Therefore, we have substantially downplayed our conclusion in this section by modifying the end of the section in pg. 17, that now reads:

      “These results do not allow to directly link the regulation of ZmHMA1 expression to the function of Tb1; however, they open an opportunity to further investigate the possibility that under HM stress, the formation of secondary ramifications in teosinte parviglumis could be repressed by transcription factors of the TCP family, including Tb1.”

      There are two phenotypic changes clearly connected with the genetic mechanisms involved in the parviglumis to maize transition: plant height and the number of seminal roots (not nodal roots). These changes have been now emphasized in the Abstract and the description of the results.

      Regarding the possibility for HM stress to represent a confounding factor in the selection of maize and not a driving factor, we expanded the genomic analysis of genetic diversity well beyond the analysis of the three genes under initial study, to cover a segment of 11.47 Mb comprised between ZmSKUs5 and ZmHMA1. We compared nucleotide variability by using 100 bp bins covering loci composed of two 30 Kb segments up and downstream of coding sequences, respectively, and the coding sequence itself, for 173 genes present within the genomic region comprised between ZmSKUs5 and ZmHMA (Figure S1 and Supplementary File 6). The full analysis is presented in a new section pgs. 11 and 12. We found that 166 out of 173 loci show signatures of positive selection and are roughly organized in five independent subregions of variable length. Four out of five subregions contain more than one HM or oxidative stress response gene within loci showing signatures of positive selection. Although multiple factors other than HM stress could have played a role in the evolutionary mechanisms that affected the genetic diversity of chr.5, large scale transcriptomic data corresponding to independent experiments aiming at understanding the response of maize roots to HM stress allowed the identification of 49 additional HM response genes within loci showing positive selection across the genome, a proportion (43.3%) far greater than the proportion of loci containing response genes to other types of abiotic stress not related to HMs (28.6%). These results are described in detail in pgs. 12 and 13 (Figure S3 and Supplementary File 7). These results provide strong evidence in favor of HM stress and not another factor driving positive selection.

      We now provide precise and pertinent paleoenvironmental data on the potential influence of heavy metals in the field. In sections pgs. 17 to 20 we review paleoenvironmental studies revealing periods of climatic instability in the presumed region of maize emergence during the early Holocene, and data indicating that the date and region where maize emerged is convergent with the dates and locations of several volcanic eruptions occurred during the early and middle Holocene in that same region. Please see responses to Reviewer#1 for details.

      We agree that our results do not allow to establish a direct regulatory link between the function of Tb1, the pleiotropic parviglumis phenotype under HM stress, and the function of ZmHMA1. We also concede that the large transcriptional analysis of HM response in maize (presented above) does not allow to elucidate a possible connection between these two genes. Therefore, we have substantially downplayed our conclusion in this section by modifying the end of the section in pg. 17, that now reads:

      “These results do not allow to directly link the regulation of ZmHMA1 expression to the function of Tb1; however, they open an opportunity to further investigate the possibility that under HM stress, the formation of secondary ramifications in teosinte parviglumis could be repressed by transcription factors of the TCP family, including Tb1.”

      This is also emphasized in the Discussion (pg 21) as follows:

      “Under HM stress, we also show that Tb1 is overexpressed in the apical meristem of teosinte parviglumis, suggesting that formation of secondary ramifications is repressed by Tb1 function under HM stress, as in extant maize. At this stage we cannot discard the possibility that Tb1 upregulation in parviglumis reflects a more generalized response to abiotic stress; however, the expression ZmHMA1 is downregulated in W22 wild-type maize meristems in the presence of HMs but upregulated in teosinte parviglumis meristems, suggesting that a specific regulatory shift relating HM responses and ZmHMA1 function occurred during the teosinte parviglumis to maize transition.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      While the dataset generated provides an interesting foundation for hypothesis testing on HM stress and domestication, the current data do not sufficiently support the conclusions of the manuscript.

      (1) The description of maize and teosinte architecture under HM stress is well presented.

      However, traits like shoot height, leaf size reduction, and biomass loss also occur under other environmental stresses such as drought and salinity. Additional evidence beyond shoot and root architecture would help validate the link between tb1 expression and specific ZmHMA genes under HM stress, or whether it reflects a more generalized stress response.

      We have already addressed in detail this point in the public response to Reviewer#1.

      (2) The nucleotide variability analysis is interesting, but I would have liked to see additional information to clarify the choice of the data selection and the strength of the conclusions with human selection.

      We have already addressed in detail this point in the public response to Reviewer#1.

      a) The choice of Tripsacum dactyloides as the outgroup to determine nucleotide variability seems to be distant, and I wonder whether other combinations with a closer outgroup or multiple outgroups were tried to provide a more accurate context.

      Nucleotide variability in Tripsacum dactyloides is used to graphically illustrate an external reference and not as an outgroup in the extended analysis of genetic diversity at the locus and genomic level. We did not used Tripsacum dactyloides as an outgroup in our statisticalm analysis. We could have indeed a closer teosinte subspecies as an outgroup, but at this stage no data warrants that environmentally-related selective pressures could have affected genetic diversite in other teosintes. This possibility in currently being investigated.

      b) Evolutionary differences not related to human influence could affect the results. The phrase "order of magnitude difference in π values" needs statistical validation (e.g., confidence intervals, p-values).

      We agree and have eliminated the sentence, as it is no longer relevant at the light of the detailed genomic analysis of genetic diversity prsented in Supplementary File 6.

      c) The comparison with ZmGLB1, a neutral control locus, suggests that domestication-related changes in nucleotide variability are specific to the three candidate genes. However, the concept of neutrality is complex, and while ZmGLB1 may be considered neutral in this case, the argument does not address the possibility of other factors, such as linked selection, that could influence variability in these genes. Referencing Hufford et al. is insufficient and would require a deeper argument.

      We also agree with this comment. We think that the influence and consequences of linked selection are now well documented for 11.46 Mb analyzed in chr.5 (pgs 11 and 12) in the main text and Supplementary File 6).

      (3) The statement: "Our evidence indicates that HM stress revealed a teosinte parviglumis environmental plasticity that is directly related to the function of specific HM response genes that were affected by domestication through human selection" is not supported by the presented data. The rationale for the specific Cd/Cu dosage used is unclear. A dose-response gradient would better demonstrate the nature and strength of the plastic response.

      Previous reports support the rationale for the specific HM dosage in this study; Cu/Cd dosage response gradients have been conducted in maize (AbdElgawad et al. 2020; Atta et al., 202), but since no studies have been conducted in teosinte, we reasoned that it was important to apply the same treatment to both subspecies. We have now emphasized this rationale by adding the following in pg XX: “Whereas higher doses impair flowering or are lethal, lower Cu/Cd concentrations do not consistently show conventional phenotypic responses such as reduced plant growth (AbdElgawad et al. 2020; Atta et al., 2023)”.

      We agree that the statement raised by the reviewer needed revision at the light of our results. We did revise the statement to accurately reflect our current evidence as follows: “Our results reveal a teosinte parviglumis environmental plasticity that is likely related to the function of HM response genes positively selected during the teosinte parviglumis to maize transition.”

      (4) In maize, TEs are known to influence gene expression under abiotic stress, including for tb1 (PMID: 25569788). Since the author appears to make a causative conclusion between ZmHMA1, TB1, and HM stress, I would have liked to see a whole-transcriptome analysis and not a curation of two genes to determine whether other factors, such as TEs, can have that would lead to similar outcomes.

      We agree that is definetely a possibility that we have not investigated at this stage. However, we added a pargraph to reflect this pertinent suggestion:

      “Previous studies have demonstrated that transposable elements (TEs) contribute to activation of maize genes in response to abiotic stress, affecting up to 20% of the genes upregulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress (Makarevitch et al., 2015). It is therefore possible that the HM response of some specific genes that influenced maize emergence or domestication could be mediated by TEs influencing or driving their transcriptional regulation.”

      (5) I would suggest that the authors carefully review the tables, figures, and the corresponding legends. For example :

      a) Table 2 is called before Table 1, I would therefore suggest changing the numbering to reflect the paragraph order.

      Thank you for your help, we did change the order of the Tables in the new version.

      b) In Table 2, it is not clear whether the P value applies to the mean difference between WT and the mutant zmhma1, either in the presence or the absence of heavy metals. In addition, the authors need to use the P-value to estimate the differences between WT in the absence vs presence of HM, and WT in the absence of HM versus the mutant in the absence of HM (idem for presence).

      We did address this issue in detail and added P-values and specific pairwise comparisons to that Table (now Table 1). Data are presented as mean ± standard deviation and were tested by a paired Student’s T-Test. When the effects were significant according to T-Test, the treatments were compared with the Welch two sample T-Test at P < 0.05.

      c) Table 1 and Table 2: Indicate what type of statistical test was used and the number of plants used for each experiment (n). Also, I recommend the use of scientific notation for the P-values.

      The statistical tests have now been indicated, scientific notation has been added to the P-values; the number of plants and biological replicates are indicated in the Methods section.

      d) Lines 202 and 204: I assume Table 1 should be called instead of Table 2.

      This error has been corrected.

      e) General: In the text, when significance is highlighted along with measurements, the p-value needs to be added.

      We have added the P-value along the measurement for all significant differences.

      f) In the text, it is also mentioned that "the expression of ZMHMA1 was significantly increased in the presence of HMs (Figure 3c)". We are looking here at an RT-PCR, which is qualitative and without a robust quantitative comparison and statistics, I cannot conclude this assessment based on the presented evidence. No statistical measure is indicated here.

      Panel 3c is not RT-PCR but a real-time qPCR, showing relative fold-change, normalized to actin, with a 3-technical triplicate per 3 biological replicates). We have added error bars (SD) and P-values represented by asterisks (calculated with Student's t statistic) to support significant differences (P<0.05 and P<0.01). ZmHMA1 expression was significantly increased in the presence of HMs only in teosinte; there was no significant difference in maize.

      g) Figure 3 should at least have the gene name in the figure to quickly understand the figure panel. The key conserved domains should also be identified.

      We agree and apologize for the omission. The gene names have been added adjacent to the structures.

      h) Sentence at lines 459-460 lacks words and punctuation.

      This unfortunate rror has also been corrected.

      i) Figure S1, the reference Lemmon and Doebley, 2024 should be Lemmon and Doebley, 2014 to harmonize with the text.

      The correct year is 2014. We have corrected this error.

      Reviewer #2 (Recommendations for the authors):

      (1) The narrative should be clearer, starting with a clearer hypothesis that is later sustained or not in the results, and then discussed in the idea and speculation section.

      Thank you for the comment. We have clarified the hypothesis, it is included in the abstract and the last paragraph of the Introduction. We hope it is now clear that the evidence presented supports our hypothesis

      (2) Focus more on traits that are relevant, for example, nodal and seminal roots.

      We modified the text to emphasize three relevant traits. In the case of teosinte under HM stress, absence of tillering and increase in the number of female inflorescences. In the case of the zmha1 mutant under HM stress, differences in the number of nodal roots, and differences in height.

      (3) RNA-seq in Cu/Cd stress could make the work much more useful and complete.

      As previously mentioned, we have incorporated a large scale transcriptional analysis on the basis of six transcriptomes statistically validated (Table S5). Please see sections pgs. 11 to 13 for details.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Lai and Doe address the integration of spatial information with temporal patterning and genes that specify cell fate. They identify the Forkhead transcription factor Fd4 as a lineage-restricted cell fate regulator that bridges transient spatial transcription factors to terminal selector genes in the developing Drosophila ventral nerve cord. The experimental evidence convincingly demonstrates that Fd4 is both necessary for lateborn NB7-1 neurons, but also sufficient to transform other neural stem cell lineages toward the NB7-1 identity. This work addresses an important question that will be of interest to developmental neurobiologists: How can cell identities defined by initial transient developmental cues be maintained in the progeny cells, even if the molecular mechanism remains to be investigated? In addition, the study proposes a broader concept of lineage identity genes that could be utilized in other lineages and regions in the Drosophila nervous system and in other species.

      Thanks for the accurate summary and positive comments!

      While the spatial factors patterning the neuroepithelium to define the neuroblast lineages in the Drosophila ventral nerve cord are known, these factors are sometimes absent or not required during neurogenesis. In the current work, Lai and Doe identified Fd4 in the NB7-1 lineage that bridges this gap and explains how NB7-1 neurons are specified after Engrailed (En) and Vnd cease their expression. They show that Fd4 is transiently co-expressed with En and Vnd and is present in all nascent NB7-1 progenies. They further demonstrate that Fd4 is required for later-born NB7-1 progenies and sufficient for the induction of NB7-1 markers (Eve and Dbx) while repressing markers of other lineages when force-expressed in neural progenitors, e.g., in the NB56 lineage and in the NB7-3 lineage. They also demonstrate that, when Fd4 is ectopically expressed in NB7-3 and NB5-6 lineages, this leads to the ectopic generation of dorsal muscle-innervating neurons. The inclusion of functional validation using axon projections demonstrates that the transformed neurons acquire appropriate NB7-1 characteristics beyond just molecular markers. Quantitative analyses are thorough and well-presented for all experiments.

      Thanks for the positive comments!

      (1) While Fd4 is required and sufficient for several later-born NB7-1 progeny features, a comparison between early-born (Hb/Eve) and later-born (Run/Eve) appears missing for pan-progenitor gain of Fd4 (with sca-Gal4; Figure 4) and for the NB7-3 lineage (Figure 6). Having a quantification for both could make it clearer whether Fd4 preferentially induces later-born neurons or is sufficient for NB7-1 features without temporal restriction.

      We quantified the percentage of Hb+ and Runt+ cells among Eve+ cells with sca-gal4, and the results are shown in Figure 4-figure supplement 1. We found that the proportion of early-born cells is slightly reduced but the proportion of later-born cells remain similar. Interestingly, we also found a subset of Eve+ cells with a mixed fate (Hb+Runt+) but the reason remains unclear.

      (2) Fd4 and Fd5 are shown to be partially redundant, as Fd4 loss of function alone does not alter the number of Eve+ and Dbx+ neurons. This information is critical and should be included in Figure 3.

      Because every hemisegment in an fd4 single mutant is normal, we just added it as the following text: “In fd4 mutants, we observe no change in the number of Eve+ neurons or Dbx+ neurons (n=40 hemisegments).”

      (3) Several observations suggest that lineage identity maintenance involves both Fd4dependent and Fd4-independent mechanisms. In particular, the fact that fd4-Gal4 reporter remains active in fd4/fd5 mutants even after Vnd and En disappear indicates that Fd4's own expression, a key feature of NB7-1 identity, is maintained independently of Fd4 protein. This raises questions about what proportion of lineage identity features require Fd4 versus other maintenance mechanisms, which deserves discussion.

      We agree, thanks for raising this point. We add the following text to the Discussion. “Interestingly, the fd4 fd5 mutant maintains expression of fd4:gal4, suggesting that the fd4/fd5 locus may have established a chromatin state that allows “permanent” expression in the absence of Vnd, En, and Fd4/Fd5 proteins.”

      (4) Similarly, while gain of Fd4 induces NB7-1 lineage markers and dorsal muscle innervation in NB5-6 and NB7-3 lineages, drivers for the two lineages remain active despite the loss of molecular markers, indicating some regulatory elements retain activity consistent with their original lineage identity. It is therefore important to understand the degree of functional conversion in the gain-of-function experiments. Sparse labeling of Fd4 overexpressing NB5-6 and NB7-3 progenies, as was done in Seroka and Doe (2019), would be an option.

      We agree it is interesting that the NB7-3 and NB5-6 drivers remain on following Fd4 misexpression. To explore this, we used sca-gal4 to overexpress Fd4 and observed that Lbe expression persisted while Eg was largely repressed (Author response image 1). The results show that Lbe and Eg respond differently to Fd4. A non-mutually exclusive possibility is that the continued expression of lbe-Gal4 UAS-GFP or eg-Gal4 UAS-GFP may be due to the lengthy perdurance of both Gal4 and GFP.

      Author response image 1.

      (5) The less-penetrant induction of Dbx+ neurons in NB5-6 with Fd4-overexpression is interesting. It might be worth the authors discussing whether it is an Fd4 feature or an NB56 feature by examining Dbx+ neuron number in NB7-3 with Fd4-overexpression.

      In the NB7-3 lineages misexpressing Fd4, only 5 lineages generated Dbx+ cells (0.1±0.4, n=64 hemisegments), suggesting that the low penetrance of Dbx+ induction is an intrinsic feature of Fd4 rather than lineage context. We have added this information in the results section.

      (6) It is logical to hypothesize that spatial factors specify early-born neurons directly, so only late-born neurons require Fd4, but it was not tested. The model would be strengthened by examining whether Fd4-Gal4-driven Vnd rescues the generation of laterborn neurons in fd4/fd5 mutants.

      When we used en-gal4 driver to express UAS-vnd in the fd4/fd5 mutant background, we found an average 7.4±2.2 Eve+ cells per hemisegment (n=36), significantly higher than fd4/fd5 mutant alone (3.9±0.8 cells, n=52, p=2.6x10<sup>-11</sup>) (Figure 3J). In addition, 0.2±0.5 Eve+ cells were ectopic Hb+ (excluding U1/U2), indicating that Vnd-En integration is sufficient to generate both early-born and late-born Eve+ cells in the fd4/fd5 mutants. We have added the results to the text.

      (7) It is mentioned that Fd5 is not sufficient for the NB7-1 lineage identity. The observation is intriguing in how similar regulators serve distinct roles, but the data are not shown. The analysis in Figure 4 should be performed for Fd5 as supplemental information.

      Thanks for the suggestion. Because the results are exactly the same as the wild type, we don’t think it is necessary to provide an additional images or analysis as supplemental information.

      Reviewer #2 (Public review):

      Via a detailed expression analysis, they find that Fd4 is selectively expressed in embryonic NB7-1 and newly born neurons within this lineage. They also undertake a comprehensive genetic analysis to provide evidence that fd4 is necessary and sufficient for the identity of NB7-1 progeny.

      Thanks for the accurate summary!

      The analysis is both careful and rigorous, and the findings are of interest to developmental neurobiologists interested in molecular mechanisms underlying the generation of neuronal diversity. Great care was taken to make the figures clear and accessible. This work takes great advantage of years of painstaking descriptive work that has mapped embryonic neuroblast lineages in Drosophila.

      Thanks for the positive comments!

      The argument that Fd4 is necessary for NB7-1 lineage identity is based on a Fd4/Fd5 double mutant. Loss of fd4 alone did not alter the number of NB7-1-derived Eve+ or Dbx+ neurons. The authors clearly demonstrate redundancy between fd4 and fd5, and the fact that the LOF analysis is based on a double mutant should be better woven through the text.The authors generated an Fd5 mutant. I assume that Fd5 single mutants do not display NB7-1 lineage defects, but this is not stated. The focus on Fd4 over Fd5 is based on its highly specific expression profile and the dramatic misexpression phenotypes. But the LOF analysis demonstrates redundancy, and the conclusions in the abstract and through the results should reflect the existence of Fd5 in the conclusions of this manuscript.

      We agree, and have added new text to clarify the single mutant phenotypes (there are none) and the double mutant phenotype (loss of NB7-1 molecular and morphological features. The following text is added to the manuscript: “Not surprisingly, we found that fd4 single mutants or fd5 single mutants had no phenotype (Eve+ neurons were all normal). Thus, to assess their roles, we generated a fd4 and fd5 double mutant. Because many Eve+ and Dbx+ cells are generated outside of NB7-1 lineage, it was also essential to identify the Eve+ or Dbx+ cells within NB7-1 lineage in wild type and fd4 mutant embryos. To achieve this, we replaced the open reading frame of fd4 with gal4 (called fd4-gal4) (see Methods); this stock simultaneously knocked out both fd4 and fd5 (called fd4/fd5 mutant hereafter) while specifically labeling the NB7-1 lineage. For the remainder of this paper we use the fd4/fd5 double mutant to assay for loss of function phenotypes.”

      It is notable that Fd4 overexpression can rewire motor circuits. This analysis adds another dimension to the changes in transcription factor expression and, importantly, demonstrates functional consequences. Could the authors test whether U4 and U5 motor axon targeting changes in the fd4/fd5 double mutant? To strengthen claims regarding the importance of fd4/fd5 for lineage identity, it would help to address terminal features of U motorneuron identity in the LOF condition.

      Thanks for raising this important point. We examined the axon targeting on body wall muscles in both wild type and in fd4/fd5 mutant background and added the results in Figure 3-figure supplement 2. We found that the axon targeting in the late-born neuron region (LL1) is significantly reduced, suggesting that the loss of late-born neurons in fd4/fd5 mutant leads to the absence of innervation of corresponding muscle targets.

      Reviewer #3 (Public review):

      The goal of the work is to establish the linkage between the spatial transcription factors (STFs) that function transiently to establish the identities of the individual NBs and the terminal selector genes (typically homeodomain genes) that appear in the newborn postmitotic neurons. How is the identity of the NB maintained and carried forward after the spatial genes have faded away? Focusing on a single neuroblast (NB 7-1), the authors present evidence that the fork-head transcription factor, fd4, provides a bridge linking the transient spatial cues that initially specified neuroblast identity with the terminal selector genes that establish and maintain the identity of the stem cell's progeny.

      Thanks for the positive comments!

      The study is systematic, concise, and takes full advantage of 40+ years of work on the molecular players that establish neuronal identities in the Drosophila CNS. In the embryonic VNC, fd4 is expressed only in the NB 7-1 and its lineage. They show that Fd4 appears in the NB while the latter is still expressing the Spatial Transcription Factors and continues after the expression of the latter fades out. Fd4 is maintained through the early life of the neuronal progeny but then declines as the neurons turn on their terminal selector genes. Hence, fd4 expression is compatible with it being a bridging factor between the two sets of genes.

      Thanks for the accurate summary!

      Experimental support for the "bridging" role of Fd4 comes from a set of loss-of-function and gain-of-function manipulations. The loss of function of Fd4, and the partially redundant gene Fd5, from lineage 7-1 does not aoect the size of the lineage, but terminal markers of late-born neuronal phenotypes, like Eve and Dbx, are reduced or missing. By contrast, ectopic expression of fd4, but not fd5, results in ectopic expression of the terminal markers eve and Dbx throughout diverse VNC lineages.

      Thanks for the accurate summary!

      A detailed test of fd4's expression was then carried out using lineages 7-3 and 5-6, two well-characterized lineages in Drosophila. Lineage 7-3 is much smaller than 7-1 and continues to be so when subjected to fd4 misexpression. However, under the influence of ectopic Fd4 expression, the lineage 7-3 neurons lost their expected serotonin and corazonin expression and showed Eve expression as well as motoneuron phenotypes that partially mimic the U motoneurons of lineage 7-1.

      Thanks for the positive comments!

      Ectopic expression of Fd4 also produced changes in the 5-6 lineage. Expression of apterous, a feature of lineage 5-6, was suppressed, and expression of the 7-1 marker, Eve, was evident. Dbx expression was also evident in the transformed 5-6 lineages, but extremely restricted as compared to a normal 7-1 lineage. Considering the partial redundancy of fd4 and fd5, it would have been interesting to express both genes in the 5-6 lineage. The anatomical changes that are exhibited by motoneurons in response to Fd4 expression confirm that these cells do, indeed, show a shift in their cellular identity.

      We appreciate the positive comments. We agree double misexpression of Fd4 and Fd5 might give a stronger phenotype (as the reviewer says) but the lack of this experiment does not change the conclusions that Fd4 can promote NB7-1 molecular and morphological aspects at the expense of NB5-6 molecular markers.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The title of Figure 4 may be intended to include the term "Widespread", not "Wild spread". (Though the expansion of the Eve and Dbx with Fd4 is quite remarkable…).

      Done!

      Reviewer #3 (Recommendations for the authors):

      (1) Line 138. Is part of the sentence missing? Did the authors mean to say "that fd5 is coexpressed with fd4 in NB7-1 and its .....".

      Done!

      (2) ln 237: In trying to explain the "U-like" phenotype of the transformed motoneurons in lineage 7-3, the authors speculate that "perhaps their late birth did not give them time to extend to the most distant dorsal muscles ". It is very difficult to convince a motoneuron to stop growing in the absence of a target! An alternate possibility is that since there is only one or two U neurons made instead of the normal five, the growing motoneuron has enough information to direct them to the dorsal domain, but they lack the specification that allows them to recognize a specific muscle target.

      We agree there are additional possibilities, and now update the text to say: “We observed that these transformed neurons did not innervate the dorsal muscles, perhaps their late birth did not give them time to extend to the most distant dorsal muscles, or they were incompletely specified.”

      (3) In the References, I think that the Anderson et al. reference should also include "BioRxiv" before the DOI.

      Done!

      (4) Figure 6A for wild-type 7-3 lineage. The corazonin expression appears to be expressed in EW2 as well as EW3. This should be explained.

      We agree it looks that way, due to the 3D rotation used; we now replace it with a more representative image. Note that our quantification always shows a single Cor+ neuron per hemisegment.

      (5) Figure 7: Issues of terminology. The designation of "longitudinal" for muscles is traditionally in reference to the body axis, such as the Dorsal Longitudinal Muscles (DLM) of the adult thorax. The "longitudinal" muscles in the figure are really "transverse" muscles. I also suggest using "axon" or "neurites" rather than "filament". For the middle and bottom parts of E and F, are these lateral and ventral views? They should be designated as such.

      Thanks, we agree and have made the changes, using Axon instead of Filament, and labeling the views (lateral and ventro-lateral).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Weaknesses:

      The technical approach is strong and the conceptual framing is compelling, but several aspects of the evidence remain incomplete. In particular, it is unclear whether the reported changes in connectivity truly capture causal influences, as the rank metrics remain correlational and show discrepancies with the manipulation results.

      We agree that our functional connectivity ranking analyses cannot establish causal influences. As discussed in the manuscript, besides learning-related activity changes, the functional connectivity may also be influenced by neuromodulatory systems and internal state fluctuations. In addition, the spatial scope of our recordings is still limited compared to the full network implicated in visual discrimination learning, which may bias the ranking estimates. In future, we aim to achieve broader region coverage and integrate multiple complementary analyses to address the causal contribution of each region.

      The absolute response onset latencies also appear slow for sensory-guided behavior in mice, and it is not clear whether this reflects the method used to define onset timing or factors such as task structure or internal state.

      We believe this may be primarily due to our conservative definition of onset timing. Specifically, we required the firing rate to exceed baseline (t-test, p < 0.05) for at least 3 consecutive 25-ms time windows. This might lead to later estimates than other studies, such as using the latency to the first spike after visual stimulus onset (Siegle et al., 2021) or the time to half-max response (Goldbach, Akitake, Leedy, & Histed, 2021).

      The estimation of response onset latency in our study may also be affected by potential internal state fluctuations of the mice. We used the time before visual stimulus onset as baseline firing, since firing rates in this period could be affected by trial history, we acknowledge this may increase the variability of the baseline, thus increase the difficulty to statistically detect the onset of response.

      Still, we believe these concerns do not affect the observation of the formation of compressed activity sequence in CR trials during learning.

      Furthermore, the small number of animals, combined with extensive repeated measures, raises questions about statistical independence and how multiple comparisons were controlled.

      We agree that a larger sample size would strengthen the robustness of the findings. However, as noted above, the current dataset has inherent limitations in both the number of recorded regions and the behavioral paradigm. Given the considerable effort required to achieve sufficient unit yields across all targeted regions, we wish to adjust the set of recorded regions, improve behavioral task design, and implement better analyses in future studies. This will allow us to both increase the number of animals and extract more precise insights into mesoscale dynamics during learning.

      The optogenetic experiments, while intended to test the functional relevance of rank increasing regions, leave it unclear how effectively the targeted circuits were silenced. Without direct evidence of reliable local inhibition, the behavioral effects or lack thereof are difficult to interpret.

      We appreciate this important point. Due to the design of the flexible electrodes and the implantation procedure, bilateral co-implantation of both electrodes and optical fibers was challenging, which prevented us from directly validating the inhibition effect in the same animals used for behavior. In hindsight, we could have conducted parallel validations using conventional electrodes, and we will incorporate such controls in future work to provide direct evidence of manipulation efficacy.

      Details on spike sorting are limited.

      We have provided more details on spike sorting in method section, including the exact parameters used in the automated sorting algorithm and the subsequent manual curation criteria.

      Reviewer #2 (Public review):

      Weaknesses:

      I had several major concerns:

      (1) The number of mice was small for the ephys recordings. Although the authors start with 7 mice in Figure 1, they then reduce to 5 in panel F. And in their main analysis, they minimize their analysis to 6/7 sessions from 3 mice only. I couldn't find a rationale for this reduction, but in the methods they do mention that 2 mice were used for fruitless training, which I found no mention in the results. Moreover, in the early case, all of the analysis is from 118 CR trials taken from 3 mice. In general, this is a rather low number of mice and trial numbers. I think it is quite essential to add more mice.

      We apologize for the confusion. As described in the Methods section, 7 mice (Figure 1B) were used for behavioral training without electrode array or optical fiber implants to establish learning curves, and an additional 5 mice underwent electrophysiological recordings (3 for visual-based decision-making learning and 2 for fruitless learning).

      As we noted in our response to Reviewer #1, the current dataset has inherent limitations in both the number of recorded regions and the behavioral paradigm. Given the considerable effort required to achieve high-quality unit yields across all targeted regions, we wish to adjust the set of recorded regions, improve behavioral task design, and implement better analyses in future studies. These improvements will enable us to collect data from a larger sample size and extract more precise insights into mesoscale dynamics during learning.

      (2) Movement analysis was not sufficient. Mice learning a go/no-go task establish a movement strategy that is developed throughout learning and is also biased towards Hit trials. There is an analysis of movement in Figure S4, but this is rather superficial. I was not even sure that the 3 mice in Figure S4 are the same 3 mice in the main figure. There should be also an analysis of movement as a function of time to see differences. Also for Hits and FAs. I give some more details below. In general, most of the results can be explained by the fact that as mice gain expertise, they move more (also in CR during specific times) which leads to more activation in frontal cortex and more coordination with visual areas. More needs to be done in terms of analysis, or at least a mention of this in the text.

      Due to the limitation in the experimental design and implementation, movement tracking was not performed during the electrophysiological recordings, and the 3 mice shown in Figure S4 (now S5) were from a separate group. We have carefully examined the temporal profiles of mouse movements and found it did not fully match the rank dynamics for all regions, and we have added these results and related discussion in the revised manuscript. However, we acknowledge the observed motion energy pattern could explain some of the functional connection dynamics, such as the decrease in face and pupil motion energy could explain the reduction in ranks for striatum.

      Without synchronized movement recordings in the main dataset, we cannot fully disentangle movement-related neural activity from task-related signals. We have made this limitation explicit in the revised manuscript and discuss it as a potential confound, along with possible approaches to address it in future work.

      (3) Most of the figures are over-detailed, and it is hard to understand the take-home message. Although the text is written succinctly and rather short, the figures are mostly overwhelming, especially Figures 4-7. For example, Figure 4 presents 24 brain plots! For rank input and output rank during early and late stim and response periods, for early and expert and their difference. All in the same colormap. No significance shown at all. The Δrank maps for all cases look essentially identical across conditions. The division into early and late time periods is not properly justified. But the main take home message is positive Δrank in OFC, V2M, V1 and negative Δrank in ThalMD and Str. In my opinion, one trio map is enough, and the rest could be bumped to the Supplementary section, if at all. In general, the figure in several cases do not convey the main take home messages. See more details below.

      We thank the reviewer for this valuable critique. The statistical significance corresponding to the brain plots (Figure 4 and Figure 5) was presented in Figure S3 and S5 (now Figure S5 and S7 in the revised manuscript), but we agree that the figure can be simplified to focus on the key results.

      In the revised manuscript, we have condensed these figures to focus on the most important comparisons to make the visual presentation more concise and the take-home message clearer.

      (4) The analysis is sometimes not intuitive enough. For example, the rank analysis of input and output rank seemed a bit over complex. Figure 3 was hard to follow (although a lot of effort was made by the authors to make it clearer). Was there any difference between the output and input analysis? Also, the time period seems redundant sometimes. Also, there are other network analysis that can be done which are a bit more intuitive. The use of rank within the 10 areas was not the most intuitive. Even a dimensionality reduction along with clustering can be used as an alternative. In my opinion, I don't think the authors should completely redo their analysis, but maybe mention the fact that other analyses exist

      We appreciate the reviewer’s comment. In brief, the input- and output-rank analyses yielded largely similar patterns across regions in CR trials, although some differences were observed in certain areas (e.g., striatum) in Hit trials, where the magnitude of rank change was not identical between input and output measures. We have condensed the figures to only show averaged rank results, and the colormap was updated to better covey the message.

      We did explore dimensionality reduction applied to the ranking data. However, the results were not intuitive as well and required additional interpretation, which did not bring more insights. Still, we acknowledge that other analysis approaches might provide complementary insights.

      Reviewer #3 (Public review):

      Weaknesses:

      The weakness is also related to the strength provided by the method. It is demonstrated in the original method that this approach in principle can track individual units for four months (Luan et al, 2017). The authors have not showed chronically tracked neurons across learning. Without demonstrating that and taking advantage of analyzing chronically tracked neurons, this approach is not different from acute recording across multiple days during learning. Many studies have achieved acute recording across learning using similar tasks. These studies have recorded units from a few brain areas or even across brain-wide areas.

      We appreciate the reviewer’s important point. We did attempt to track the same neurons across learning in this project. However, due to the limited number of electrodes implanted in each brain region, the number of chronically tracked neurons in each region was insufficient to support statistically robust analyses. Concentrating probes in fewer regions would allow us to obtain enough units tracked across learning in future studies to fully exploit the advantages of this method.

      Another weakness is that major results are based on analyses of functional connectivity that is calculated using the cross-correlation score of spiking activity (TSPE algorithm). Functional connection strengthen across areas is then ranked 1-10 based on relative strength. Without ground truth data, it is hard to judge the underlying caveats. I'd strongly advise the authors to use complementary methods to verify the functional connectivity and to evaluate the mesoscale change in subnetworks. Perhaps the authors can use one key information of anatomy, i.e. the cortex projects to the striatum, while the striatum does not directly affect other brain structures recorded in this manuscript

      We agree that the functional connectivity measured in this study relies on statistical correlations rather than direct anatomical connections. We plan to test the functional connection data with shorter cross-correlation delay criteria to see whether the results are consistent with anatomical connections and whether the original findings still hold.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The small number of mice, each contributing many sessions, complicates the  interpretation of the data. It is unclear how statistical analyses accounted for the small  sample size, repeated measures, and non-independence across sessions, or whether  multiple comparisons were adequately controlled.

      We realized the limitation from the small number of animal subjects, yet the difficulty to achieve sufficient unit yields across all regions in the same animal restricted our sample size. Though we agree that a larger sample size would strengthen the robustness of the findings, however, as noted below the current dataset has inherent limitations in both the scope of recorded regions and the behavioral paradigm.

      Given the considerable effort required to achieve sufficient unit yields across all targeted regions, we wish to adjust the set of recorded regions, improve behavioral task design, and implement better analyses in future studies. This will allow us to both increase the number of animals and extract more precise insights into mesoscale dynamics during learning.

      (2) The ranking approach, although intuitive for visualizing relative changes in  connectivity, is fundamentally descriptive and does not reflect the magnitude or  reliability of the connections. Converting raw measures into ordinal ranks may obscure  meaningful differences in strength and can inflate apparent effects when the underlying  signal is weak.

      We agree with this important point. As stated in the manuscript, our motivation in taking the ranking approach was that the differences in firing rates might bias cross-correlation between spike trains, making raw accounts of significant neuron pairs difficult to compare across conditions, but we acknowledge the ranking measures might obscure meaningful differences or inflate weak effects in the data.

      We added the limitations of ranking approach in the discussion section and emphasized the necessity in future studies for better analysis approaches that could provide more accurate assessment of functional connection dynamics without bias from firing rates.

      (3) The absolute response onset latencies also appear quite slow for sensory-guided  behavior in mice, and it remains unclear whether this reflects the method used to  determine onset timing or factors such as task design, sensorimotor demands, or  internal state. The approach for estimating onset latency by comparing firing rates in  short windows to baseline using a t-test raises concerns about robustness, as it may  be sensitive to trial-to-trial variability and yield spurious detections.

      We agree this may be primarily due to our conservative definition of onset timing. Specifically, we required the firing rate to exceed baseline (t-test, p < 0.05) for at least 3 consecutive 25-ms time windows. This might lead to later estimates than other studies, such as using the latency to the first spike after visual stimulus onset (Siegle et al., 2021) or the time to half-max response (Goldbach, Akitake, Leedy, & Histed, 2021).

      The estimation of response onset latency in our study may also be affected by potential internal state fluctuations of the mice. We used the time before visual stimulus onset as baseline firing, since firing rates in this period could be affected by trial history, we acknowledge this may increase the variability of the baseline, thus increase the difficulty to statistically detect the onset of response.

      Still, we believe these concerns do not affect the observation of the formation of compressed activity sequence in CR trials during learning.

      (4) Details on spike sorting are very limited. For example, defining single units only by  an interspike interval threshold above one millisecond may not sufficiently rule out  contamination or overlapping clusters. How exactly were neurons tracked across days  (Figure 7B)?

      We have added more details on spike sorting, including the processing steps and important parameters used in the automated sorting algorithm. Only the clusters well isolated in feature space were accepted in manual curation.

      We attempted to track the same neurons across learning in this project. However, due to the limited number of electrodes implanted in each brain region, the number of chronically tracked neurons in each region was insufficient to support statistically robust analyses.

      This is now stated more clearly in the discussion section.

      (5) The optogenetic experiments, while designed to test the functional relevance of  rank-increasing regions, also raise questions. The physiological impact of the inhibition  is not characterized, making it unclear how effectively the targeted circuits were  actually silenced. Without clearer evidence that the manipulations reliably altered local  activity, the interpretation of the observed or absent behavioral effects remains  uncertain.

      We appreciate this important point. Due to the design of the flexible electrodes and the implantation procedure, bilateral co-implantation of both electrodes and optical fibers was challenging, which prevented us from directly validating the inhibition effect in the same animals used for behavior. In hindsight, we could have conducted parallel validations using conventional electrodes, and we will incorporate such controls in future work to provide direct evidence of manipulation efficacy. 

      (6) The task itself is relatively simple, and the anatomical coverage does not include  midbrain or cerebellar regions, limiting how broadly the findings can be generalized to more flexible or ethologically relevant forms of decision-making.

      We appreciate this advice and have expanded the existing discussion to more explicitly state that the relatively simple task design and anatomical coverage might limit the generalizability of our findings.

      (7) The abstract would benefit from more consistent use of tense, as the current mix of  past and present can make the main findings harder to follow. In addition, terms like  "mesoscale network," "subnetwork," and "functional motif" are used interchangeably in  places; adopting clearer, consistent terminology would improve readability.

      We have changed several verbs in abstract to past form, and we now adopted a more consistent terminology by substituting “functional motif” as “subnetwork”. We still feel the use of

      “mesoscale network” and “subnetwork” could emphasize different aspects of the results according to the context, so these words are kept the same.

      (8) The discussion could better acknowledge that the observed network changes may  not reflect task-specific learning alone but could also arise from broader shifts in  arousal, attention, or motivation over repeated sessions.

      We have expanded the existing discussion to better acknowledge the possible effects from broader shifts in arousal, attention, or motivation over repeated sessions.

      (9) The figures would also benefit from clearer presentation, as several are dense and  not straightforward to interpret. For example, Figure S8 could be organized more  clearly to highlight the key comparisons and main message

      We have simplified the over-detailed brain plots in Figure 4-5, and the plots in Figure 6 and S8 (now S10 in the revised manuscript).

      (10) Finally, while the manuscript notes that data and code are available upon request,  it would strengthen the study's transparency and reproducibility to provide open access  through a public repository, in line with best practices in the field.

      The spiking data, behavior data and codes for the core analyses in the manuscript are now shared in pubic repository (Dryad). And we have changed the description in the Data Availability secition accordingly.

      Reviewer #2 (Recommendations for the authors):

      (A) Introduction:

      (1) "Previous studies have implicated multiple cortical and subcortical regions in visual  task learning and decision-making". No references here, and also in the next sentence.

      The references were in the following introduction and we have added those references here as well.

      We also added one review on cortical-subcortical neural correlates in goal-directed behavior (Cruz et al., 2023).

      (2) Intro: In general, the citation of previous literature is rather minimal, too minimal.  There is a lot of studies using large scale recordings during learning, not necessarily  visual tasks. An example for brain-wide learning study in subcortical areas is Sych et  al. 2022 (cell reports). And for wide-field imaging there are several papers from the  Helmchen lab and Komiyama labs, also for multi-area cortical imaging.

      We appreciate this advice. We included mainly visual task learning literature to keep a more focused scope around the regions and task we actually explored in this study. We fear if we expand the intro to include all the large-scale imaging/recording studies in learning field, the background part might become too broad.

      We have included (Sych, Fomins, Novelli, & Helmchen, 2022) for its relevance and importance in the field.

      (3) In the intro, there is only a mention of a recording of 10 brain regions, with no  mention of which areas, along with their relevance to learning. This is mentioned in the  results, but it will be good in the intro.

      The area names are now added in intro.

      (B) Results:

      (1) Were you able to track the same neurons across the learning profile? This is not  stated clearly.

      We did attempt to track the same neurons across learning in this project. However, due to the limited number of electrodes implanted in each brain region, the number of chronically tracked neurons in each region was insufficient to support statistically robust analyses.

      We now stated this more clearly in the discussion section.

      (2) Figure 1 starts with 7 mice, but only 5 mice are in the last panel. Later it goes down  to 3 mice. This should be explained in the results and justified.

      We apologize for the confusion. As described in the Methods section, 7 mice (Figure 1B) were used for behavioral training without electrode array or optical fiber implants to establish learning curves, and an additional 5 mice underwent electrophysiological recordings (3 for visual-based decision-making learning and 2 for fruitless learning).

      (3) I can't see the electrode tracks in Figure 1d. If they are flexible, how can you make  sure they did not bend during insertion? I couldn't find a description of this in the  methods also.

      The electrode shanks were ultra-thin (1-1.5 µm) and it was usually difficult to recover observable tracks or electrodes in section.

      The ultra-flexible probes could not penetrate brain on their own (since they are flexible), and had to be shuttled to position by tungsten wires through holes designed at the tip of array shanks. The tungsten wires were assembled to the electrode array before implantation; this was described in the section of electrode array fabrication and assembly. We also included the description about the retraction of the guiding tungsten wires in the surgery section to avoid confusion.

      As an further attempt to verify the accuracy of implantation depth, we also measured the repeatability of implantation in a group of mice and found a tendency for the arrays to end in slightly deeper location in cortex (142.1 ± 55.2 μm, n = 7 shanks), and slightly shallower location in subcortical structure (-122.6 ± 71.7 μm, n = 7 shanks). We added these results as new Figure S1 to accompany Figure 1.

      (4) In the spike rater in 1E, there seems to be ~20 cells in V2L, for example, but in 1F,  the number of neurons doesn't go below 40. What is the difference here? 

      We checked Figure 1F, the plotted dots do go below 40 to ~20. Perhaps the file that reviewer received wasn’t showing correctly?

      (5) The authors focus mainly on CR, but during learning, the number of CR trials is  rather low (because they are not experts). This can also be seen in the noisier traces  in Figure 2a. Do the authors account for that (for example by taking equal trials from  each group)? 

      We accounted this by reconstructing bootstrap-resampled datasets with only 5 trials for each session in both the early stage and the expert stage. The mean trace of the 500 datasets again showed overall decrease in CR trial firing rate during task learning, with highly similar temporal dynamics to the original data.

      The figure is now added to supplementary materials (as Figure S3 in the revised manuscript).

      (6) From Figure 2a, it is evident that Hit trials increase response when mice become  experts in all brain areas. The authors have decided to focus on the response onset  differences in CRs, but the Hit responses display a strong difference between naïve  and expert cases.

      Judged from the learning curve in this task the mice learned to inhibit its licking action when the No-Go stimuli appeared, which is the main reason we focused on these types of trials.

      The movement effects and potential licking artefacts in Hit trials also restricted our interpretation of these trials.

      (7) Figure 3 is still a bit cumbersome. I wasn't 100% convinced of why there is a need  to rank the connection matrix. I mean when you convert to rank, essentially there could  be a meaningful general reduction in correlation, for example during licking, and this  will be invisible in the ranking system. Maybe show in the supp non-ranked data, or  clarify this somehow

      We agree with this important point. As stated in the manuscript and response to Reviewer #1, our motivation in taking the ranking approach was that the differences in firing rates could bias cross-correlation between spike trains, making raw accounts of significant neuron pairs difficult to compare across conditions, but we acknowledge the ranking measures might obscure meaningful differences or inflate weak effects in the data.

      We added the limitations of ranking approach in the discussion section and emphasized the necessity in future studies for better analysis approaches that could provide more accurate assessment of functional connection dynamics without bias from firing rates.

      (8) Figure 4a x label is in manuscript, which is different than previous time labels,  which were seconds.

      We now changed all time labels from Figure 2 to milliseconds.

      (9) Figure 4 input and output rank look essentially the same.

      We have compressed the brain plots in Figures 4-5 to better convey the take-home message.

      (10) Also, what is the late and early stim period? Can you mark each period in panel A? Early stim period is confusing with early CR period. Same for early respons and late response.

      The definition of time periods was in figure legends. We now mark each period out to avoid confusion.

      (11) Looking at panel B, I don't see any differences between delta-rank in early stim,  late stim, early response, and late response. Same for panel c and output plots.

      The rankings were indeed relatively stable across time periods. The plots are now compressed and showed a mean rank value.

      (12) Panels B and C are just overwhelming and hard to grasp. Colors are similar both  to regular rank values and delta-rank. I don't see any differences between all  conditions (in general). In the text, the authors report only M2 to have an increase in  rank during the response period. Late or early response? The figure does not go well  with the text. Consider minimizing this plot and moving stuff to supplementary.

      The colormap are now changed to avoid confusion, and brain plots are now compressed.

      (13) In terms of a statistical test for Figure 4, a two-way ANOVA was done, but over  what? What are the statistics and p-values for the test? Is there a main effect of time  also? Is their a significant interaction? Was this done on all mice together? How many  mice? If I understand correctly, the post-hoc statistics are presented in the  supplementary, but from the main figure, you cannot know what is significant and what  is not.

      For these figures we were mainly concerned with the post-hoc statistics which described the changes in the rankings of each region across learning.

      We have changed the description to “t-test with Sidak correction” to avoid the confusion.

      (14) In the legend of Figure 4, it is reported that 610 expert CR trials from 6 sessions,  instead of 7 sessions. Why was that? Also, like the previous point, why only 3 mice?

      Behavior data of all the sessions used were shown in Figure S1. There were only 3 mice used for the learning group, the difficulty to achieve sufficient unit yields across all regions in the same animal restricted our sample size

      (15) Body movement analysis: was this done in a different cohort of mice? Only now  do I understand why there was a division into early and late stim periods. In supp 4,  there should be a trace of each body part in CR expert versus naïve. This should also  be done for Hit trials as a sanity check. I am not sure that the brightness difference  between consecutive frames is the best measure. Rather try to calculate frame-to frame correlation. In general, body movement analysis is super important and should  be carefully analyzed.

      Due to the limitation in the experimental design and implementation, movement tracking was not performed during the electrophysiological recordings, and the 3 mice shown in Figure S4 (now S5) were from a separate group. We have carefully examined the temporal profiles of mouse movements and found it did not fully match the rank dynamics for all regions, and we have added these results and related discussion in the revised manuscript. However, we acknowledge the observed motion energy pattern could explain some of the functional connection dynamics, such as the decrease in face and pupil motion energy could explain the reduction in ranks for striatum.

      Without synchronized movement recordings in the main dataset, we cannot fully disentangle movement-related neural activity from task-related signals. We have made this limitation explicit in the revised manuscript and discuss it as a potential confound, along with possible approaches to address it in future work.

      (16) For Hit trials, in the striatum, there is an increase in input rank around the  response period, and from Figure S6 it is clear that this is lick-related. Other than that,  the authors report other significant changes across learning and point out to Figure 5b,c. I couldn't see which areas and when it occurred.

      We did naturally expect the activity in striatum to be strongly related to movement.

      With Figure S6 (now S7) we wished to show that the observed rank increase for striatum could not simply be attributed to changes in time of lick initiation.

      As some readers may argue that during learning the mice might have learned to only intensely lick after response signal onset, causing the observed rise of input rank after response signal, we realigned the spikes in each trial to the time of the first lick, and a strong difference could still be observed between early training stage and expert training stage.

      We still cannot fully rule out the effects from more subtle movement changes, as the face motion energy did increase in early response period. This result and related discussion has been added to the results section of revised manuscript.

      (17) Figure 6, again, is rather hard to grasp. There are 16 panels, spread over 4 areas,  input and output, stim and response. What is the take home message of all this?  Visually, it's hard to differentiate between each panel. For me, it seems like all the  panels indicate that for all 4 areas, both in output and input, frontal areas increase in  rank. This take-home message can be visually conveyed in much less tedious ways.  This simpler approach is actually conveyed better in the text than in the figures  themselves. Also, the whole explanation on how this analysis was done, was not clear  from the text. If I understand it, you just divided and ranked the general input (or  output) into individual connections? If so, then this should be better explained.

      We appreciate this advice and we have compressed the figures to better convey the main message.The rankings for Figure 6 and Figure S8 (now Figure S9) was explained in the left panel of Figure 3C. Each non-zero element in the connection matrix was ranked to value from 1-10, with a value of 10 represented the 10% strongest non-zero elements in the matrix.

      We have updated the figure legends of Figure 3, and we have also updated the description in methods (Connection rank analyses) to give a clearer description of how the analyses were applied in subsequent figures.

      (18) Figure 7: Here, the authors perform a ROC analysis between go and no-go  stimuli. They balance between choice, but there is still an essential difference between  a hit and a FA in terms of movement and licks. That is maybe why there is a big  difference in selective units during the response period. For example, during a Hit trial  the mouse licks and gets a reward, resulting in more licking and excitement. In FAs,the mouse licks, but gets punished, which causes a reduction in additional licking and  movements. This could be a simple explanation why the ROC was good in the late  response period. Body movement analysis of Hit and FA should be done as in Figure  S4.

      We appreciate this insightful advice.

      Though we balanced the numbers of basic trial types, we couldn’t rule out the difference in the intrinsic movement amount difference in FA trials and Hit trials, which is likely the reason of large proportion of encoding neurons in response period.

      We have added this discussion both in result section and discussion section along with the necessity of more carefully designed behavior paradigm to disentangle task information.

      (19) The authors also find selective neurons before stimulus onset, and refer to trial  history effects. This can be directly checked, that is if neurons decode trial history.

      We attempted encoding analyses on trial history, but regrettably for our dataset we could not find enough trials to construct a dataset with fully balanced trial history, visual stimulus and behavior choice.

      (20) Figure 7e. What is the interpretation for these results? That areas which peaked  earlier had more input and output with other areas? So, these areas are initiating  hubs? Would be nice to see ACC vs Str traces from B superimposed on each other.  Having said this, the Str is the only area to show significant differences in the early  stim period. But is also has the latest peak time. This is a bit of a discrepancy.

      We appreciate this important point.

      The limitation in the anatomical coverage of brain regions restricted our interpretation about these findings. They could be initiating hubs or earlier receiver of the true initiating hubs that were not monitored in our study.

      The Str trace was in fact above the ACC trace, especially in the response period. This could be explained by the above advice 18: since we couldn’t rule out the difference in the intrinsic movement amount difference in FA trials and Hit trials, and considering striatum activity is strongly related to movement, the Str trace may reflect more in the motion related spike count difference between FA trials and Hit trials, instead of visual stimulus related difference.

      This further shows the necessity of more carefully designed behavior paradigm to disentangle task information.

      The striatum trace also in fact didn’t show a true double peak form as traces in other regions, it ramped up in the stimulus region and only peaked in response period. This description is now added to the results section.

      In the early stim period, the Striatum did show significant differences in average percent of encoding neurons, as the encoding neurons were stably high in expert stage. The striatum activity is more directly affected Still the percentage of neurons only reached peak in late stimulus period.

      (21) For the optogenetic silencing experiments, how many mice were trained for each  group? This is not mentioned in the results section but only in the legend of Figure 8. This part is rather convincing in terms of the necessity for OFC and V2M

      We have included the mice numbers in results section as well.

      (C) Discussion

      (1) There are several studies linking sensory areas to frontal networks that should be  mentioned, for example, Esmaeili et a,l 2022, Matteucci et al., 2022, Guo et a,l 2014,Gallero Salas et al, 2021, Jerry Chen et al, 2015. Sonja Hofer papers, maybe. Probably more.

      We appreciate this advice. We have now included one of the mentioned papers (Esmaeili et al., 2022) in the results section and discussion section for its direct characterization of the enhanced coupling between somatosensory region and frontal (motor) region during sensory learning.The other studies mentioned here seem to focus more on the differences in encoding properties between regions along specific cortical pathways, rather than functional connection or interregional activity correlation, and we feel they are not directly related to the observations discussed.

      (2) The reposted reorganization of brain-wide networks with shifts in time is best  described also in Sych et al. 2021.

      We regret we didn’t include this important research and we have now cited this in discussion section.

      (3) Regarding the discussion about more widespread stimulus encoding after learning,  the results indicate that the striatum emerges first in decoding abilities (Figure 7c left  panel), but this is not discussed at all.

      We briefly discussed this in the result section. We tend to attribute this to trial history signal in striatum, but since the structure of our data could not support a direct encoding analysis on trial history, we felt it might be inappropriate to over-interpret the results.

      (4) An important issue which is not discussed is the contribution of movement which  was shown to have a strong effect on brain-wide dynamics (Steinmetz et al 2019;  Musall et al 2019; Stringer et al 2019; Gilad et al 2018) The authors do have some movement analysis, but this is not enough. At least a discussion of the possible effects of movement on learning-related dynamics should be added.

      We have included these studies in discussion section accordingly. Since the movement analyses were done in a separate cohort of mice, we have made our limitation explicit in the revised manuscript and discuss it as a potential confound, along with possible approaches to address it in future work.

      (D) Methods

      (1) How was the light delivery of the optogenetic experiments done? Via fiber  implantation in the OFC? And for V2M? If the red laser was on the skull, how did it get  to the OFC?

      The fibers were placed on cortex surface for V2M group, and were implanted above OFC for OFC manipulation group. These were described in the viral injection part of the methods section.

      (2) No data given on how electrode tracking was done post hoc

      As noted in our response to the advice 3 in results section, the electrode shanks were ultra-thin (1-1.5 µm) and it was usually difficult to recover observable tracks or electrodes in section.

      As an attempt to verify the accuracy of implantation depth, we measured the repeatability of implantation in a group of mice and found a tendency for the arrays to end in slightly deeper location in cortex (142.1 ± 55.2 μm, n = 7 shanks), and slightly shallower location in subcortical structure (-122.6 ± 71.7 μm, n = 7 shanks). We added these results as new Figure S1 to accompany Figure 1.

      Reviewer #3 (Recommendations for the authors):

      (1) The manuscript uses decision-making in the title, abstract and introduction.  However, nothing is related to decision learning in the results section. Mice simply  learned to suppress licking in no-go trials. This type of task is typically used to study behavioral inhibition. And consistent with this, the authors mainly identified changes  related to network on no-go trials. I really think the title and main message is  misleading. It is better to rephrase it as visual discrimination learning. In the  introduction, the authors also reviewed multiple related studies that are based on  learning of visual discrimination tasks.

      We do view the Go/No-Go task as a specific genre of decision-making task, as there were literature that discussed this task as decision-making task under the framework of signal detection theory or updating of item values (Carandini & Churchland, 2013; Veling, Becker, Liu, Quandt, & Holland, 2022).

      We do acknowledge the essential differences between the Go/No-Go task and the tasks that require the animal to choose between alternatives, and since we have now realized some readers may not accept this task as a decision task, we have changed the title to visual discrimination task as advised.

      (2) Learning induced a faster onset on CR trials. As the no-go stimulus was not  presented to mice during early stages of training, this change might reflect the  perceptual learning of relevant visual stimulus after repeated presentation. This further  confirms my speculation, and the decision-making used in the title is misleading. 

      We have changed the title to visual discrimination task accordingly.

      (3) Figure 1E, show one hit trial. If the second 'no-go stimulus' is correct, that trial  might be a false alarm trial as mice licked briefly. I'd like to see whether continuous  licking can cause motion artifacts in recording. 

      We appreciate this important point. There were indeed licking artifacts with continuous licking in Hit trials, which was part of the reason we focused our analyses on CR trials. Opto-based lick detectors may help to reduce the artefacts in future studies.

      (4) What is the rationale for using a threshold of d' < 2 as the early-stage data and d'>3  as expert stage data?

      The thresholds were chosen as a result from trade-off based on practical needs to gather enough CR trials in early training stage, while maintaining a relatively low performance.

      Assume the mice showed lick response in 95% of Go stimulus trials, then d' < 2 corresponded to the performance level at which the mouse correctly rejected less than 63.9% of No-Go stimulus trials, and d' > 3 corresponded to the performance level at which the mouse correctly rejected more than 91.2% of No-Go stimulus trials.

      (5) Figure 2A, there is a change in baseline firing rates in V2M, MDTh, and Str. There  is no discussion. But what can cause this change? Recording instability, problem in  spiking sorting, or learning?

      It’s highly possible that the firing rates before visual stimulus onset is affected by previous reward history and task engagement states of the mice. Notably, though recorded simultaneously in same sessions, the changes in CR trials baseline firing rates in the V2M region were not observed in Hit trials.

      Thus, though we cannot completely rule out the possibility in recording instability, we see this as evidence of the effects on firing rates from changes in trial history or task engagement during learning.

      References:

      Carandini, M., & Churchland, A. K. (2013). Probing perceptual decisions in rodents. Nat Neurosci, 16(7), 824-831. doi:10.1038/nn.3410.

      Cruz, K. G., Leow, Y. N., Le, N. M., Adam, E., Huda, R., & Sur, M. (2023).Cortical-subcortical interactions in goal-directed behavior. Physiol Rev, 103(1), 347-389. doi:10.1152/physrev.00048.2021

      Esmaeili, V., Oryshchuk, A., Asri, R., Tamura, K., Foustoukos, G., Liu, Y., Guiet, R., Crochet, S., & Petersen, C. C. H. (2022). Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas. PLOS Biology, 20(5), e3001667. doi:10.1371/journal.pbio.3001667

      Goldbach, H. C., Akitake, B., Leedy, C. E., & Histed, M. H. (2021). Performance in even a simple perceptual task depends on mouse secondary visual areas. Elife, 10, e62156. doi:10.7554/eLife.62156.

      Siegle, J. H., Jia, X., Durand, S., Gale, S., Bennett, C., Graddis, N., Heller, G.,Ramirez, T. K., Choi, H., Luviano, J. A., Groblewski, P. A., Ahmed, R., Arkhipov, A., Bernard, A., Billeh, Y. N., Brown, D., Buice, M. A., Cain, N.,Caldejon, S., Casal, L., Cho, A., Chvilicek, M., Cox, T. C., Dai, K., Denman, D.J., de Vries, S. E. J., Dietzman, R., Esposito, L., Farrell, C., Feng, D., Galbraith, J., Garrett, M., Gelfand, E. C., Hancock, N., Harris, J. A., Howard, R., Hu, B.,Hytnen, R., Iyer, R., Jessett, E., Johnson, K., Kato, I., Kiggins, J., Lambert, S., Lecoq, J., Ledochowitsch, P., Lee, J. H., Leon, A., Li, Y., Liang, E., Long, F., Mace, K., Melchior, J., Millman, D., Mollenkopf, T., Nayan, C., Ng, L., Ngo, K., Nguyen, T., Nicovich, P. R., North, K., Ocker, G. K., Ollerenshaw, D., Oliver, M., Pachitariu, M., Perkins, J., Reding, M., Reid, D., Robertson, M., Ronellenfitch, K., Seid, S., Slaughterbeck, C., Stoecklin, M., Sullivan, D., Sutton, B., Swapp, J., Thompson, C., Turner, K., Wakeman, W., Whitesell, J. D., Williams, D., Williford, A., Young, R., Zeng, H., Naylor, S., Phillips, J. W., Reid, R. C., Mihalas, S., Olsen, S. R., & Koch, C. (2021). Survey of spiking in the mouse visual system reveals functional hierarchy. Nature, 592(7852), 86-92. doi:10.1038/s41586-020-03171-x

      Sych, Y., Fomins, A., Novelli, L., & Helmchen, F. (2022). Dynamic reorganization of the cortico-basal ganglia-thalamo-cortical network during task learning. Cell Rep, 40(12), 111394. doi:10.1016/j.celrep.2022.111394

      Veling, H., Becker, D., Liu, H., Quandt, J., & Holland, R. W. (2022). How go/no-go training changes behavior: A value-based decision-making perspective. Current Opinion in Behavioral Sciences, 47,101206.

      doi:https://doi.org/10.1016/j.cobeha.2022.101206.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      The authors' goal was to arrest PsV capsids on the extracellular matrix using cytochalasin D. The cohort was then released, and interaction with the cell surface, specifically with CD151, was assessed.

      The model that fragmented HS associated with released virions mediates the dominant mechanism of infectious entry has only been suggested by research from a single laboratory and has not been verified in the 10+ years since publication. The authors are basing this study on the assumption that this model is correct, and these data are referred to repeatedly as the accepted model despite much evidence to the contrary.

      We stated in the introduction on line 65/66 ´Two release mechanisms are discussed, that mutually are not exclusive´. This implies that we do not consider the shedding model as ‘the accepted model’. Furthermore, we do not state in the discussion neither that the shedding model is the preferred one. However, we referred to the shedding model in the discussion, because we find HS associated with transferred PsVs, which is in line with this model.

      The discussion in lines 65-71 concerning virion and HSPG affinity changes is greatly simplified. The structural changes in the capsid induced by HS interaction and the role of this priming for KLK8 and furin cleavage have been well researched. Multiple laboratories have independently documented this. If this study aims to verify the shedding model, additional data need to be provided.

      Our findings are compatible with both models, and we do not aim to verify the shedding model neither want to disprove the priming model. However, as we understand, the referee wishes more visibility of the priming model. Therefore, using inhibitors previously used in the field, we tested whether inhibition of KLK8 or furin reduces PsV translocation to the cell body (after CytD wash off). Leupeptin blocks transport, while Furin inhibitor I still allows some initial translocation. We incorporated this new data as Figure 2 (line 265): “…we would expect that inhibition of L1 processing during the CytD incubation prevents the recovery of PsV translocation from the ECM to the cell body (Figure 2A and D). To test for this possibility, as employed in earlier studies, the protease inhibitor leupeptin was used to inhibit proteases including KLK8 which is required for L1 cleavage (Cerqueira et al. 2015). Employing this inhibitor, the PCC between PsV-L1 and F-actin staining remains negative after CytD removal, showing that for translocation indeed the action of proteases is required (Figure 2B and D). In contrast, inhibition of L2 cleavage by a furin specific inhibitor has no effect on the PCC (Figure 2C and D). However, it should be noted that we occasionally observe PsVs not completely translocating but accumulating at the border of the F-actin stained area (for example see Figure 2C (60 min)). This results in an increase of the PCC almost equal to complete translocation, explaining why the PCC remains unaffected despite a furin inhibitory effect. Hence, furin inhibition may have some effect on translocation that, however, is undetected in this type of analysis.’

      Moreover, we have added a paragraph discussing how our data integrates into the established model of the HPV infection cascade (line 604): ‘HPV infection is the result of several steps, starting with the initial binding of virions via electrostatic and polar interactions (Dasgupta et al. 2011) to the primary attachment site HS (Richards et al. 2013), which induces capsid modification (Feng et al. 2024; Cerqueira et al. 2015) and HS cleavage (Surviladze et al. 2015), enabling the virion to be released from the ECM or the glycocalyx. Next, virions bind to the cell surface to a secondary receptor complex that forms over time, and become internalized via endocytosis, before they are trafficked to the nucleus (Ozbun and Campos 2021; Mikuličić et al. 2021). Regarding the transition from the primary attachment site to cell surface binding, as already outlined in the introduction, two models are discussed. In one model, proteases cleave the capsid proteins. After priming, the capsids are structurally modified and the virion can dissociate from its HS attachment site. It has been suggested that capsid priming is mediated by KLK8 (Cerqueira et al. 2015) and furin (Richards et al. 2006). In our system, KLK8 inhibition blocks PsV transport, while furin inhibition has some effect that, however, cannot be detected in this analysis (Figure 2) suggesting furin engagement at later steps in the infection cascade. This is in line with earlier in vitro studies on the role of cell surface furin (Surviladze et al. 2015; Day et al. 2008; Day and Schiller 2009). In any case, our results align with both models of ECM detachment: one involving HS cleavage (HS co-transfer) and another involving capsid modification (by e.g., KLK8).’

      The model should be fitted into established entry events,…

      Please see our reply above.

      or at minimum, these conflicting data, a subset of which is noted below, need to be acknowledged.

      (1) The Sapp lab (Richards et al., 2013) found that HSPG-mediated conformational changes in L1 and L2 allowed the release of the virus from primary binding and allowing secondary receptor engagements in the absence of HS shedding.

      (2) Becker et al. found that furin-precleaved capsids could infect cells independently of HSPG interaction, but this infection was still inhibited with cytochalasin D.

      (3) Other work from the Schelhaas lab showed that cytochalasin D inhibition of infection resulted in the accumulation of capsids in deep invaginations from the cell surface, not on the ECM

      (4) Selinka et al., 2007, showed that preventing HSPG-induced conformational changes in the capsid surface resulted in noninfectious uptake that was not prevented with cytochalasin D.

      (5) The well-described capsid processing events by KLK8 and furin need to be mechanistically linked to the proposed model. Does inhibition of either of these cleavages prevent engagement with CD151?

      The authors need to consider an explanation for these discrepancies.

      We do not see any discrepancies; our observations are compatible with aspects of both the shedding and the priming model. That PsVs carry HS-cleavage products doesn´t imply that HS cleavage is sufficient or required for infection, or that the priming model would be wrong. We do not view our data as being in conflict with the priming model. Most of the above-mentioned papers are now cited.

      Altogether, we acknowledge that the study gains importance by directly testing the priming model within our experimental system. We are thankful for the above comments and addressed this issue.

      Other issues:

      (1) Line 110-111. The statement about PsVs in the ECM being too far away from the cell surface to make physical contact with the cell surface entry receptors is confusing. ECM binding has not been shown to be an obligatory step for in vitro infection.

      Not obligatory, but strongly supportive (Bienkowska-Haba et al., Plos Path., 2018; Surviladze et al., J. Gen. Viro., 2015). As recently published by the Sapp lab (Bienkowska-Haba et al., Plos Path., 2018), ´Direct binding of HPV16 to primary keratinocytes yields very inefficient infection rates for unknown reasons.´ Moreover, the paper shows that HaCaT cell ECM binding of PsVs increases the infection of NHEK by 10-fold and of HFK by almost 50-fold.

      This idea is referred to again on lines 158-159 and 199. The claim (line 158) that PsV does not interact with the cell within an hour needs to be demonstrated experimentally and seems at odds with multiple laboratories' data. PsV has been shown to directly interact with HSPG on the cell surface in addition to the ECM. Why are these PsVs not detected?

      The reviewing editor speculated that HaCaT cells may be a model system in which the in vivo relevant binding to the ECM can be better studied as in non-polarized cell types. This is because binding to the ECM cannot be bypassed by direct cell surface binding. The observation that only few PsVs bind to the basal cell membrane indeed suggests restricted diffusional access of PsVs to binding receptors of the basal membrane. The reviewing editor asked for an experiment showing that more PsVs bind after cell detachment. We performed this experiment and indeed find more PsVs binding to the cell surface of detached cells. This point is very important for the understanding of the study and now we mention it in several sections of the manuscript, as outlined in the following.

      Line 125: ‘Many PsVs that bind to the ECM may locate distal from the cell surface and are thus unable to establish direct contact with entry receptors. However, they are capable of migrating by an actindependent transport along cell protrusions towards the cell body (Smith et al. 2008; Schelhaas et al. 2008). We aimed for blocking this transport in HaCaT cells, a cell line that is widely used as a cell culture model for HPV infection. HaCaT cells closely resemble primary keratinocytes in key aspects: they are not virally transformed and produce large amounts of ECM that facilitates infection (Bienkowska-Haba et al. 2018; Gilson et al. 2020). In addition, HaCaT cells exhibit cellular polarity that enforces binding of virus particles to the ECM, as the virions cannot bind to receptors/entry components, such as CD151, Itgα6 and HSPGs that co-distribute on the basolateral membrane of polarized keratinocytes (Sterk et al. 2000; Cowin et al. 2006; Mertens et al. 1996), making them inaccessible by diffusion.’

      Line 205: ‘During the CytD incubation, PsVs bind to HSPGs of the basolateral membrane for 5 h. Still, in the cell body area hardly any PsVs are present (0.14 PsV/µm<sup>2</sup>, Supplementary Figure 1B). In the control, the PsV density is several-fold larger (Supplementary Figure 1B). This is expected, as the PsVs bind to the ECM and translocate to the cell body. We wondered whether there are more binding sites at the basal membrane that remain inaccessible to PsVs by diffusion because of the insufficient space between glass-coverslip and basolateral membrane. For clarification, we incubated EDTA detached HaCaT cells in suspension with PsVs for 1 h at 4 °C, followed by re-attachment for 1 h. Under these conditions, we find a PsV density 12.4-fold larger than after 5 h of CytD incubation of adhered cells (Supplementary Figure 1B and D). However, it should be noted that these values cannot be directly compared. Aside from the different treatments, another difference lies in the size of the basal membrane, as re-attachment of cells is not complete after only 1 h (compare size of adhered membranes in Supplementary Figure 1A and C). Therefore, the imaged membranes are likely strongly ruffled, which results in the underestimation of the size of the adhered membrane. As a result, we overestimate the PsVs per µm<sup>2</sup> (please note that we cannot re-attach cells for longer times as we would then lose PsVs due to endocytosis). On the other hand, we would underestimate the PsV density at the basal membrane if after re-attachment we image in part also some apical membrane. In any case, the experiment suggests that PsVs bind more efficiently if membrane surface receptors are accessible by diffusion. This is in support of the above notion that the basal membrane may provide more entry receptors than one would expect from the low density of PsVs bound after 5 h CytD (Supplementary Figure 1B). This suggests that under our assay conditions, PsVs cannot easily bypass the translocation from the ECM to the cell body by diffusing directly to the basal membrane. Hence, the large majority of PsVs that enter the cell were previously bound to the ECM. Therefore, HaCaT cells serve as an ideal model for studying the transfer of ECM bound HPV particles to the cell surface, which is similar to in vivo infection of basal keratinocytes after binding to the basement membrane (Day and Schelhaas 2014; Kines et al. 2009; Schiller et al. 2010; Bienkowska-Haba et al. 2018).’

      Line 529: ‘Filopodia usage not only facilitates infection but also increases the likelihood of virions to reach their target cells during wound healing, namely the filopodia-rich basal dividing cells. In fact, several types of viruses exploit filopodia during virus entry (Chang et al. 2016), hinting at the possibility that for HPV and other types of viruses actin-driven virion transport may play a more important role than it is currently assumed. If this is the case, sub-confluent HaCaT cells, or even better single HaCaT cells, would be an ideal model system for the study of these very early infection steps that involve ECM attachment and subsequent filopodia-dependent transport. As shown in Supplementary Figure 1, HaCaT cells have many binding sites for the HPV16 PsVs. However, as they are polarized and the binding receptors are only at the basal membrane, they remain relatively inaccessible by diffusion. Therefore, the ECM binding that is also observed in vivo (Day and Schelhaas 2014) and subsequent transport via filopodia are used upon infection of HaCaT cells that locate at the periphery of cell patches. Here, PsVs bind to the ECM which strongly enhances infection of primary keratinocytes (Bienkowska-Haba et al. 2018). In contrast, HPV can readily bind to HSPGs on the cell surface of nonpolarized cells, and by this bypasses ECM mediated virus priming and the filopodia dependency. We propose that HaCaT cells are a valuable system for studying the very early events in HPV infection that allows for dissecting capsid interaction with ECM resident priming factors and cell surface receptors.’

      Finally, please note that in the previous version of the manuscript, we did not question that in many cellular systems PsVs interact with heparan sulfate proteoglycans (HSPGs) present on the cell surface, or both on the cell surface and the ECM. We stated on line 59 ´While in cell culture virions bind to HS of the cell surface and the ECM, it has been suggested that in vivo they bind predominantly to HS of the extracellular basement membrane (Day and Schelhaas, 2014; Kines et al., 2009; Schiller et al., 2010).´

      We hope that after adding the above explanations and the experiment requested by the reviewing editor it is now clear why only few PsVs bind directly (not via the ECM) to the cell surface. We appreciate the reviewer’s and the reviewing editor’s input that has significantly improved the manuscript.

      (2) The experiments shown in Figure 5 need to be better controlled. Why is there no HS staining of the cell surface at the early timepoints? This antibody has been shown to recognize N-sulfated glucosamine residues on HS and, therefore, detects HSPG on the ECM and cell surface.

      There is staining. However, as the staining at the periphery is stronger and images are shown at the same settings of brightness and contrast, the impression is given that the cell surface is not stained. We have added more images showing HS cell surface staining.

      (i) Supplementary Figure 4C shows an enlarged view of the CytD/0 min cell shown in Figure 6A. In the area stained by Itgα6, that marks the cell body, HS staining is present, although less abundant in comparison to the ECM.

      (ii) In Figure 8, CytD/30 min, a cell is shown with abundant HS in the cell body region (compare cyan and green LUT).

      (iii) In newly added Figure 3A, lower panel, another cell with HS in the cell body region is shown.

      Please note that the staining is highly variable. We indicate this by stating on Line 373: ‘The pattern of the HS staining (cyan LUT) and the overlap of HS with PsVs and Itgα6 are highly variable (Figure 6A).’

      Therefore, the conclusion that this confirms HS coating of PsV during release from the ECM (line 430431) is unfounded. How do the authors distinguish between "HS-coated virions" and HSPG-associated virions?

      The transient increase in the PCC at CytD/30 min can be interpreted as PsV/HS co-transport or as direct binding of PsVs to cell surface HSPGs. However, two arguments support co-transport.

      First, we find that CytD/PsVs increases the HS intensity (see newly added Figure 3, confirming old Figure 5 that is now Figure 6). We state on line 290 ‘… that without actin-dependent PsV translocation HS cleavage products are retained in the ECM, consistent with the hypothesis that cleaved HS remains associated with PsVs (Ozbun and Campos 2021).

      Second, the distance between HS and Itgα6 (the cell body marker) decreases over time after CytD removal, which suggests movement of HS to the cell body (Supplementary Figure 8D). We state on line 422: ‘The movement of HS towards the cell body after removal of CytD, which indirectly demonstrates that PsVs are coated with HS, is suggested by a shortening of the HS-Itgα6 distance over time (Supplementary Figure 8D).’

      It is difficult to comprehend how the addition of 50 vge/cell of PsV could cause such a global change in HS levels.

      Some areas are covered with confluent cells, to which hardly any PsVs are bound, because accessing their basolateral membrane is nearly impossible, and PsVs do not bind to the exposed apical membrane as well. We assume this is a major difference to cultures of unpolarized cells, where PsVs should distribute more or less equally over cells. This means that in our experiments the vge/cell is not a suitable parameter for relating the magnitude of an effect to a defined number of PsVs. In the ECM, the PsV density is very high, enabling one cell to collect, in theory, several hundred PsVs, much more than expected from the 50 vge/cell.

      We state on line 135: ‘Frequently, we observe patches of confluent cells which are common to HaCaT cells. Cells at the center of these patches are dismissed during imaging, because there are no anterogradely migrating PsVs at these cells. A second reason for our dismissal of these cells is that hardly any PsVs are bound to them, possibly because their basal membranes are inaccessible by diffusion. Instead, we focus on isolated HaCaT cells or cells at the periphery of cell patches. In these cells, we find more PsVs per cell than one would expect from the employed 50 viral genome equivalents (vge) per cell, indicating that PsVs are unequally distributed between the cells.’

      The claim that the HS levels are decreased in the non-cytochalasin-treated cells due to PsV-induced shedding needs to be demonstrated.

      We did not claim that PsVs induce shedding, we rather believe they retain shedded HS. Without PsVs, the shedded HS is washed off from the ECM. We have reproduced the observation made in old Figure 5 (now Figure 6) in the newly added Figure 3 that also shows that PsVs alone have no effect on the HS intensity, only when present together with CytD. We state on line 277: ‘As outlined above, during the 5 h incubation with CytD, proteases in the ECM are expected to cleave HS chains. These cleavage products should be able to diffuse out of the ECM, unless they remain associated with nontranslocating PsVs. In the control, PsV associated HS cleavage products would leave the ECM through PsV translocation…. Using an antibody that reacts with an epitope in native heparan sulfate chains, only after CytD and if PsVs are present, the level of HS staining is significantly increased (Figure 3B). As shown in Figure 3A, stronger HS staining at PsVs (open arrows) and as well in PsV free areas (closed arrows) was observed… Collectively, our findings indicate that without actin-dependent PsV translocation HS cleavage products are retained in the ECM, consistent with the hypothesis that cleaved HS remains associated with PsVs (Ozbun and Campos 2021).’

      If HS is actually shed, staining of the cell periphery could increase with the antibody 3G10, which detects the HS neoepitope created following heparinase cleavage.

      We have tested the antibody by which we obtain only a very weak staining (Supplementary Figure 2), not allowing to differentiate between an increase in the cell periphery and the cell body area. We still include the experiment as it suggests that CytD has no effect on HS processing. We state on line 286: ‘As additional control and shown in Supplementary Figure 2, we use an antibody that reacts with a HS neo-epitope generated by heparitinase-treated heparan sulfate chains (Yokoyama et al. 1999; for details see methods). This neo-epitope staining is independent of the presence of CytD and the incubation time, suggesting that CytD does not directly affect HS processing.’

      Reviewer #2 (Public review):

      Summary:

      Massenberg and colleagues aimed to understand how Human papillomavirus particles that bind to the extracellular matrix (ECM) transfer to the cell body for later uptake, entry, and infection. The binding to ECM is key for getting close to the virus's host cell (basal keratinocytes) after a wounding scenario for later infection in a mouse vaginal challenge model, indicating that this is an important question in the field.

      Strengths:

      The authors take on a conceptually interesting and potentially very important question to understand how initial infection occurs in vivo. The authors confirm previous work that actin-based processes contribute to virus transport to the cell body. The superresolution microscopy methods and data collection are state-of-the art and provide an interesting new way of analysing the interaction with host cell proteins on the cell surface in certain infection scenarios. The proposed hypothesis is interesting and, if substantiated, could significantly advance the field.

      Weaknesses:

      As a study design, the authors use infection of HaCaT keratinocytes, and follow virus localisation with and without inhibition of actin polymerisation by cytochalasin D (cytoD) to analyse transfer of virions from the ECM to the cell by filopodial structures using important cellular proteins for cell entry as markers.

      First, the data is mostly descriptive besides the use of cytoD, and does not test the main claim of their model, in which virions that are still bound to heparan sulfate proteoglycans are transferred by binding to tetraspanins along filopodia to the cell body.

      The study identifies a rapid translocation step from the ECM to CD151 assemblies. We have no data that demonstrates a physical interaction between PsVs and CD151. In the model figure, we draw CD151 as part of the secondary receptor complex. We are sorry for having raised the impression that PsVs would bind directly to CD151 and have modified the model Figure accordingly. In the new model figure (Figure 9), the first contact established is to a CD151 free receptor.

      Second, using cytoD is a rather broad treatment that not only affects actin retrograde flow, but also virus endocytosis and further vesicular transport in cells, including exocytosis. Inhibition of myosin II, e.g., by blebbistatin, would have been a better choice as it, for instance, does not interfere with endocytosis of the virus.

      As we focus on early events, we are not concerned about CytD blocking as well late steps in the infection cascade, like endocytosis. However, we agree that a comparison between CytD and blebbistatin would be very interesting. We added Figure 8, showing that blebbistatin only partially stops migration.

      Line 429: ‘Actin retrograde transport, which underlies the here observed virion transport, is the integrative result of three components (Smith et al. 2008; Schelhaas et al. 2008)…. As CytD broadly interferes with F-actin dependent processes, we investigated the effects upon inhibition of only one of the three components, namely the myosin II mediated retrograde movement towards the cell body. Instead of CytD, we employed in the 5 h preincubation the myosin II inhibitor blebbistatin. For the control (0 min), we show in Figure 8A one example of a cell with comparatively many PsVs at the periphery (as mentioned above, the PsV pattern is highly variable) to better illustrate the difference to the PsV pattern occasionally seen with blebbistatin. After blebbistatin treatment (0 min), PsVs are still distal to the cell body but less dispersed than after CytD treatment, seemingly as if translocation started but stopped in the midst of the pathway (Figure 8A, blebbistatin). The PCC between PsVs and HS, like after CytD (Figure 6C), is elevated after blebbistatin, albeit the effect is not significant (Figure 8C). The cell body PCC, is not at 30 min (CytD) but already at 0 min elevated (compare Figure 6D to Figure 8D), which can be explained by partial translocation. This is further supported by the fact that only 8% of PsVs are closely associated with HS (Figure 8E; blebbistatin, 0 min) compared to 15% after CytD treatment (Figure 6E; 0 min). Furthermore, after 0 min PsV incubation with blebbistatin we observe no effect on the HS intensity (compare Figure 8B to Figure 3B and Figure 6B). Hence, in contrast to CytD, blebbistatin does not trap the PsVs in the ECM where they associate with HS, but ongoing actin polymerization pushes actin filaments along with PsVs towards the cell body.’

      Third, the authors aim to study transfer from ECM to the cell body and the effects thereof. However, there are substantial, if not the majority of, viruses that bind to the cell body compared to ECM-bound viruses in close vicinity to the cells.

      Please see our detailed reply to referee #1 that has raised the same issue. In brief, we agree that in multiple cell culture systems viruses bind preferentially to the cell surface directly. However, in HaCaT cells, the majority of PsVs does not bind directly to the basal membrane but gets there after initial binding to the ECM. Thus, we believe our system appropriately models the physiologically relevant scenario of ECM-to-cell transfer, as also speculated by the reviewing editor that has suggested an experiment showing that more PsVs bind to detached cells (please see above).

      This is in part obscured by the small subcellular regions of interest that are imaged by STED microscopy, or by the use of plasma membrane sheets. As a consequence, the obtained data from time point experiments is skewed, and remains for the most part unconvincing due to the fact that the origin of virions in time and space cannot be taken into account. This is particularly important when interpreting association with HS, the tetraspanin CD151, and integral alpha 6, as the low degree of association could originate from cell-bound and ECM-transferred virions alike.

      As already stated above, we observe massive binding of PsVs to the ECM, in contrast to very few PsVs that diffuse beneath the basolateral membrane of the polarized HaCaT cells and do bind directly to the cell surface. In other cellular systems, cells may hardly secrete ECM, are not polarized, and therefore virions can easily bypass ECM binding. Therefore, it is reasonable to assume that in HaCaT cells the large majority of PsVs found on the cell body originates from the ECM.

      Fourth, the use of fixed images in a time course series also does not allow for understanding the issue of a potential contribution of cell membrane retraction upon cytoD treatment due to destabilisation of cortical actin. Or, of cell spreading upon cytoD washout.

      The newly added blebbistatin experiment suggests that the initial translocation is exclusively dependent on retrograde actin flow. However, we agree that we are not able to unravel more details regarding the different possible contributions to the movement. Importantly, the lack of PCC increase after CytD/leupeptin removal (Figure 2D) suggest there is not much cell spreading into the area of accumulated PsVs. Please see our more detailed reply to the same issue raised by the same referee in the recommendations for the authors.

      The microscopic analysis uses an extension of a plasma membrane stain as a marker for ECM-bound virions, which may introduce a bias and skew the analysis.

      The dye TMA-DPH stains exclusively cellular membranes and not the ECM. The stain is actually used to delineate the cell body from the ECM area (please see Figure 1).

      Fifth, while the use of randomisation during image analysis is highly recommended to establish significance (flipping), it should be done using only ROIs that have a similar density of objects for which correlations are being established.

      We agree that the way of how randomization is done is very important. Regarding the association of PsVs with CD151 and HS, we corrected for random background association, which is now explained in more detail in in the Figure legend of Supplementary Figure 7: “On flipped images, we often find values more than half of the values of the original images, demonstrating that many PsVs have a distance ≤ 80 nm to CD151 merely by chance (background association)… (C) Each time point in (A) and (B) obtained from flipped images is the average of three biological replicates. We use these altogether 24 data points, plotting the fraction of closely associated PsVs against the CD151 maxima density. The fraction increases with the maxima density, as the chance of random association increases with the maxima density. The fitted linear regression line describes the dependence of the background association from the maxima density. As a result, the background association (y) can be calculated for any maxima density (x) in original images with the equation y = 2.04x. Please note that the CytD/0 min may be overcorrected as we subtract background association with reference to the CD151 maxima density of the entire ROI (for an example ROI see Supplementary Figure 6A), although the local maxima density at distal PsVs is lower. On the other hand, PsVs at the cell border may have a larger local CD151 maxima density and consequently are undercorrected.’

      For instance, if one flips an image with half of the image showing the cell body, and half of the image ECM, it is clear that association with cell membrane structures will only be significant in the original.

      We are aware of this problem. For instance, it would produce ‘artificially’ low PCCs after flipping images of PsV/HS stainings (please see negative PCC value after flipping in Supplementary Figure 8). In this case, we do not use as argument that in flipped images the PCC is lower. Instead, we would argue that over time the PCC changes in the original images. We still provide the PCC values of flipped images, as additional information, showing that in most cases we obtain after flipping a PCC of zero, as expected

      Hence, we fully agree that careful controls in image analysis is required, and used the above-described method for the correction of background association when the fraction of closely associated PsVs is analyzed. We do not use a lower PCC value in flipped images as argument if not appropriate.

      I am rather convinced that using randomisation only on the plasma membrane ROIs will not establish any clear significance of the correlating signals.

      Figure 6D and 8D show the PCC specifically of the cell body (only of plasma membrane ROIs). In flipped images (not shown in the previous version for clarity), we obtain significantly lower PCCs (Supplementary Figure 8F/G and Supplementary Figure 10C/D. We propose that in this case it would be appropriate to use a lower PCC of flipped images as argument for specific association. Still, also in this experiment we argue with a change in the PCC over time, and not with a PCC of zero after flipping. As above, we still provide the PCC values of flipped images as additional information.

      Also, there should be a higher n for the measurements.

      One replicate is based on the average of 14-15 cells for each condition (more for figure 4). Hence, in a typical experiment (Control and CytD with 4 time points) about 120 cells are analyzed, which is a broad basis for the averages of one replicate.

      We realize that with three biological replicates we find significant effects only if we have strong effects or moderate effects with very low variance.

      Recommendations for the authors:

      Reviewing Editor:

      The focus on the events of HPV infection between ECM binding and keratinocyte-specific receptor binding is unique and interesting. However, I agree with the reviewers that some of the conclusions could use more experimental support, as detailed in their comments. The failure to detect direct binding of the PsV to HSPGs on the cell surface in in vitro assays contradicts much of the published literature. For example, others have found that HPV capsids bind cultured cell lines in suspension, i.e, in the absence of ECM. Do EDTA-suspended HaCaT cells bind PsV? Is the binding HSPG dependent? If the authors think that failure to detect direct cell binding of HaCaTs is an unusual feature of these cell lines or culture condition,s then it would be helpful to provide an explanation. However, it is worth noting that an in vitro system where the cells do not directly bind capsids through HSPG interactions would be a much better model for studying the stages of HPV infection that are the focus of this study, since there is no direct binding of keratinoctyes in vivo.

      We are thankful for this comment that had a strong influence on the revision. The suggested experiment has been incorporated as new Supplementary Figure 1. It shows that many more PsVs bind to the cell surface of cells in suspension than to adhered cells. As suggested by the reviewing editor, we explain now that HaCaT cells are a suitable model system for studying the in vivo transport from the ECM to the cell body that in these cells, due to their polarization, cannot be bypassed (for more details please see our replies above addressing these issues).

      Because conclusions drawn regarding HS interactions are largely based on experiments using a single HS mAb, it is important that the specificity of this mAb is described in more detail, either based on the literature or further experimentation.

      We provide now detailed information about the HS antibodies used in the study. We state on line 282 ‘Using an antibody that reacts with an epitope in native heparan sulfate chains…’ and on line 286 ‘we use an antibody that reacts with a HS neo-epitope generated by heparitinase-treated heparan sulfate chains…’ and in the methods section ‘For Heparan sulfate (HS) a mouse IgM monoclonal antibody (1:200) (amsbio, cat# 370255-S) was used that reacts with an epitope in native heparan sulfate chains and not with hyaluronate, chondroitin or DNA, and poorly with heparin (mAb 10E4 (David et al., 1992)). For HS neo-epitope (Yokoyama et al., 1999) detection, a mouse monoclonal antibody (1:200) (amsbio, cat#370260-S) was used that reacts only with heparitinase-treated heparan sulfate chains, proteoglycans, or tissue sections, and not with heparinase treated HSPGs. The antibody recognizes desaturated uronic acid residues (mAb 3G10 (David et al., 1992)).’

      Reviewer #1 (Recommendations for the authors):

      (1) The phrase "tight association" or similar is repeatedly used and is not acceptable for microscopic studies; use "close association", which has no affinity connotations.

      Has been changed as suggested by the referee.

      (2) Why are lysine-coated coverslips used for microscopy? HaCaT cells adhere tightly to untreated glass, and this coating could affect the distribution of ECM and extracellular PsV.

      We believe a tight association of the basal cell membrane to its substrate, as in vivo, where the basal membrane is tightly adhered to other cells, is important in these experiments. In weakly adherent cells more PsVs may bind to the cell surface, bypassing the transport step. Hence, although HaCaT cells may not require the coat and would be able to adhere to glass, the association may not be tight enough to mimic in vivo conditions.

      (3) What is the reason to use detection of the pseudogenome for some of the experiments instead of L1 detection throughout? The process of EdU detection is sufficiently denaturing to affect some protein epitopes. The introduction of this potential artifact doesn't seem warranted for capsid detection experiments.

      The L1 and the Itgα6 antibody are from the same species, wherefore we have used in Figures 4 and 6 click-labeling of the reporter plasmid. We do not disagree with the notion of the referee, that EdU detection may denature the epitope of some proteins. For instance, we have observed a different staining pattern for CD151; for Itgα6 and HS we saw no obvious difference in the staining patterns. In double staining experiments using L1 antibody and click-labeling, both staining patterns overlapped very well, indicating that click-labeling is suitable to visualize PsVs.

      (4) What concentration of TMA-DPH was used?

      TMA-DPH is a poorly water-soluble dye that becomes strongly fluorescent upon insertion into a membrane. Because of its poor water solubility, a precise concentration cannot be given. We added 50 µl of a saturated TMA-DPH solution in PBS to 1 ml of PBS in the imaging chamber. We state this now in the methods section.

      (5) Line 419: This statement is misleading. Although PsV interaction with HSPG on the ECM is crucial for infectious transfer to cells, the majority of the PsV binding on the ECM has been attributed to interaction with laminin 332. Treatment of PsV with heparin causes sequestration to the ECM.

      We are sorry for the confusion and have removed the misleading statement.

      (6) Some reference choices are poor:

      Line 54: Ozbun and Campos, this is not the correct reference

      In the review we cited, in the introduction it is stated that PsVs establish infection via a break in the epithelial barrier? However, we have replaced this reference by a review that focuses more on epithelial wounding: ‘Ozbun, Michelle A. (2019): Extracellular events impacting human papillomavirus infections: Epithelial wounding to cell signaling involved in virus entry. In Papillomavirus research (Amsterdam, Netherlands) 7, pp. 188–192. DOI: 10.1016/j.pvr.2019.04.009.’

      Line 2012: Doorbar et al., this is not the correct reference.

      Thank you for pointing this out (..we assume the referee refers to line 104 and not line 2012). We have noticed this error during revision. As it is difficult to get a specialized review on this topic, we now cite Ozbun and Campus, 2021 that states PsVs are ‘structurally and immunologically indistinguishable from lesion- and tissue-derived HPVs.’

      Minor issues:

      (1) It is difficult to appreciate the ECM and cell surface binding pattern from the provided images, which do not even contain an entire cell. We need to see a few representative field views with the ECM delineated with laminin 332 staining, as HS antibodies stain both the ECM and cell surface.

      We now provide overview images in Supplementary Figure 4. The only experiment requiring a clear delineation between ECM and cell surface is the experiment of Figure 4. Here, we do not use the HS as a reference staining because it stains both the ECM and the cell surface.

      (2) For Figure 1E, the cells were only infected for 24 hours. The half-time for infectious internalization of HaCaT cells was shown to be 8 hours for cell-associated PsV and closer to 20 hours for PsV that was associated with the ECM prior to cell association (Becker et al., 2018). Why was such a short infection time chosen?

      During assay establishment it has been observed that after 24 h the luciferase activity is optimal.

      (3) Figure 5, the staining of uninfected cells +/- cyto treatment needs to be included.

      Now visible in new Figure 3.

      I am confused by lines 54-57. It seems as if the authors are claiming that HSPGs are not present on the ECM. This sentence, as written, is misleading.

      We agree, and state now on line 58 ‘Here, virions bind to the linear polysaccharide heparan sulfate (HS) that is present in the extracellular matrix (ECM) but as well on the plasma membrane surface. HS is attached to proteins forming so called heparan sulfate proteoglycans (HSPGs).’

      Reviewer #2 (Recommendations for the authors):

      There are further issues that are not pertaining to the study design that I find important.

      (1) It remains speculative whether the virions that are transferred from the ECM are actually structurally modified.

      The newly added Figure 2, showing that leupeptin blocks infection in our assay, suggests that virions indeed are primed.

      (2) The origin of HS correlated with virions on the cell body after transfer is also not clear: does the virus associate with cell surface HS, or does it bring HS from the ECM? Simply staining HS against Nsulfated moieties does not allow such conclusions.

      This issue has been already raised in the public review to which we replied above. In brief, we agree that the transient increase of the PCC between PsVs and HS in the cell body region can be also explained by PsVs coming from the ECM without HS and binding to cell surface HS, or from PsVs binding directly (not via the ECM) to cell surface HSPGs. However, there are two more arguments indicating that PsVs are coated with HS. Please see our detailed reply above.

      (3) Figure 1: There are few, if any, filopodia in untreated cells. It would be good to quantify their abundance to substantiate that resting HaCat cells are indeed a good model for filopodial transport bs. membrane retraction / spreading. In HaCat ECM, the virus also binds to laminin-332 for a good part. Would this not also confound the analysis?

      At first glance, the number of filopodia appears to be too low to account for such an efficient transport. However, please note that the formation of filopodia is very dynamic, and that they can form and disappear within minutes (see below). We also often observe many PsVs aligned at one filopodium. Moreover, not every cell periphery exhibits large accumulations of PsVs. Therefore, we believe it is in principle possible that filopodia are largely responsible for the transport. We cannot exclude that we overestimate the transport rate due to partial cell spreading after CytD removal, which, however, we consider as rather unlikely as in Figure 2 we observe no increase in the PCC when leupeptin was present during the CytD incubation. Under these conditions, PsVs do not translocate but cells could spread, and this would increase he PCC between PsVs and F-actin if cells would spread into the area of accumulated PsVs.

      We now state on line 304: ‘This suggests that the half-time of PsV translocation from the periphery to the cell body is about 15 min. In fact, the half-time maybe longer, as we cannot exclude that cell spreading after CytD removal contributes to less PsVs measured in the cell periphery.’ and on line 477 ‘As mentioned above, the half-time could be longer if cell spreading is in part responsible for the translocation of PsVs onto the cell body. However, we assume that this is rather unlikely, as cell spreading would increase the PCC between PsVs and F-actin under a condition where filopodia mediated transport is blocked but not cell spreading, which is not the case (Figure 2B and D, CytD/leupeptin).’

      (4) Figure 2: This would benefit from live cell analysis. There are considerable amounts of virions on the cell body, which partially contradicts statements from Figure 1.

      Does the referee refer to the images shown in Figure 4 (old Figure 2)? Please note that at CytD/0 min there are hardly any PsVs in the cell body region, the fluorescence (magenta LUT) is autofluorescence (this is explained in the results section). Only at later time points PsVs are in the cell body region.

      The fast transfer to the cell body after cyto D washout is based on the assumption that filopodia formation and transport along them (and not membrane extension) occur quickly. Is this reasonable?

      We are no experts on filopodia, but one finds references suggesting that they grow at rates of several µm per minutes and have lifetimes between a few seconds and several minutes. Hence, within the 15 min we determine for the transport, cells may need a few minutes to recover from CytD, a few minutes to form filopodia that reach out into the ECM, and a few minutes for the transport itself. However, we agree that we cannot exclude membrane extension contributing to our observed transport, although we consider this as rather unlikely (see above).

      (5) Figure 3: The rationale of claiming the existence of 'endocytic structures' needs to be better explained and quantified in the according supplementary figure.

      We now state in the legend ‘We propose that the agglomerated CD151 maxima close to PsVs feature the characteristics of endocytic structures, as CD151 has been shown to co-internalize with PsVs (Scheffer et al. 2013), and as these structures invaginate into the cell, like PsV filled tubular organelles previously described by electron microscopy (Schelhaas et al. 2012).’ For a proper quantification of these highly variable structures a much larger sample would be required.

      The formation of virus-filled tubules upon cytoD treatment has been previously reported. Are these viruses that come from the cell body or from the ECM?

      With the new data and explanations that have been added to the manuscript, it should be clear that it is reasonable to assume that they come largely from the ECM.

      (6) Figure 4: How are the subcellular ROIs chosen? Is there not a bias by not studying a full cell?

      We now explain better how we chose cells for analysis. We state on line 138 ‘Instead, we focus on isolated HaCaT cells or cells at the periphery of cell patches. In these cells, we find more PsVs per cell than one would expect from the employed 50 viral genome equivalents (vge) per cell, as PsVs are unequally distributed between the cells. Moreover, these PsVs usually are not homogenously distributed around the cell but concentrate at one region. We investigate the translocation of PsVs from these regions, defining ROIs for analysis that cover PsVs at the periphery and the cell body (see Supplementary Figures 6A and 8A).’

      (7) Figure 5/6: The data needs a better analysis on correlation by using randomisation as explained above.

      Please see our reply to the same point of the public review raised by the same referee.

      (8) Figure 7: This model involves CD151 being a mediator in transfer, but this has not been functionally shown. There are HaCaT CD151 KO cells available (from the Sonnenberg lab), it would be good to use those to test the model and whether transfer indeed involves CD151.

      As already stated above, we are sorry for having raised the impression that PsVs bind directly to CD151. The model Figure has been modified. Please see our reply above.

      (9) The manuscript would benefit from a number of experiments addressing the most crucial issues:

      (a) As mentioned before, the use of blebbistatin, which blocks myosin II function and arrests actin retrograde flow within seconds of addition, would be a good inhibitor to control for transfer in at least some of the most crucial experiments.

      In Figure 8 we have tested blebbistatin. Please see our reply above.

      (b) Live cell analysis would allow for monitoring of whether membrane retraction upon cytoD treatment would have to be taken into account for the analysis of the data. The same is true for the cytoD washouts, upon which most cells exhibit pronounced membrane spreading. The latter is important to support filopodial transport rather than membrane ruffling and spreading, leading to the clearance of extracellular virions from the ECM.

      We agree that this would be desirable. As replied above, we now discuss the issue of possible membrane spreading and reason why we consider it as rather unlikely.

      (c) To rid oneself of the issue of plasma membrane-bound virions as a confounding factor, one could use cells treated by sodium chlorate, which leads to undersulfation of HS on the cell surface, and seed them onto ECM with functional HSPGs. This would then indeed establish that the HS and virus are transferred together.

      We agree that this would be a smart experiment. As the main focus of our study is not clarifying whether PsVs are coated with HS or not, we gave other experiments priority.

      (10) The manuscript is, while carefully and thoughtfully worded on the issue of microscopy analysis, for a good part, extrapolating too strongly from the authors' data and unsubstantiated assumptions to conclude on their model. It would be good if the authors would support their claims with previous or their own experimental work. Just two examples of several: the assumption that cell-bound virions are negligible should be substantiated, as the literature would indicate otherwise.

      We determined the PsV density in adhered, CytD treated cells, and find around 0.14 per µm<sup>2</sup> (Supplementary figure 1B), which is 4 to 5-fold less when compared to the PsV density quantified in an area covering the cell body and the periphery (Figure 1B, see line 174 for PsVs/µm<sup>2</sup> values). Quantifying the PsV density only in the periphery would yield a severalfold larger difference. However, due to the limited resolution of the microscope we would strongly underestimate the PsV density in the accumulations. We prefer not to discuss this in detail, as exact numbers are difficult to obtain.

      Line 129: Cyto D should not inhibit the enzymes modifying HS or proteins (including virions). This is true, but cytoD may limit their secretion and abundance.

      We show in Figure 3 that CytD does not reduce HS staining (e.g., by limiting HS secretion, as suggested by the referee), suggesting that it rather does not limit secretion.

      We thank the referee´s and the reviewing editor for their helpful comments!

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors aimed to examine how the covariation between cognition (represented by a g-factor based on 12 features of 11 cognitive tasks) and mental health (represented by 133 diverse features) is reflected in MR-based neural markers of cognition, as measured through multimodal neuroimaging (structural, rsfMRI, and diffusion MR). To integrate multiple neuroimaging phenotypes across MRI modalities, they used a so-called stacking approach, which employs two levels of machine learning. First, they built a predictive model from each neuroimaging phenotype to predict a target variable. Next, in the stacking level, they used predicted values (i.e., cognition predicted from each neuroimaging phenotype) from the first level as features to predict the target variable. To quantify the contribution of the neural indicators of cognition explaining the relationship between cognition and mental health, they conducted commonality analyses. Results showed that when they stacked neuroimaging phenotypes within dwMRI, rsMRI, and sMRI, they captured 25.5%, 29.8%, and 31.6% of the predictive relationship between cognition and mental health, respectively. By stacking all 72 neuroimaging phenotypes across three MRI modalities, they enhanced the explanation to 48%. Age and sex shared substantial overlapping variance with both mental health and neuroimaging in explaining cognition, accounting for 43% of the variance in the cognition-mental health relationship.

      Strengths:

      (1) A big study population (UK Biobank with 14000 subjects).

      (2) The description of the methods (including Figure 1) is helpful in understanding the approach.

      (3) This revised manuscript is much improved compared to the previous version.

      Weaknesses:

      (1) Although the background and reason for the study are better described in this version of the manuscript, the relevance of the question is, in my opinion, still questionable. The authors aimed to determine whether neural markers of cognition explain the covariance between cognition and mental health and which of the 72 MRI-based features contribute to explaining most of the covariance. I would like to invite the authors to make a stronger case for the relevance, keeping the clinical and scientific relevance in mind (what would you explain to the clinician, what would you explain to the people with lived experience, and how can this knowledge contribute to innovation in mental health care?).

      Thank you for this insightful observation. We agree that establishing the real-world significance of fundamental research is paramount, and we have revised our manuscript to better articulate this relevance.

      For clinicians, our work (a) corroborates the link between cognition and mental health, confirming the transdiagnostic role of cognition, and (b) demonstrates that current neuroimaging tools can capture the neurobiology underlying this relationship. These findings offer several implications for clinical practice. First, they support the development of interventions aimed at enhancing cognitive functioning as a pathway to improving mental health. Second, our work introduces neuroimaging as a potential tool for assessing the neurobiological basis of the cognition–mental health connection. With further research, clinicians may be able to use neuroimaging to track cognitive changes at the neural level, which could help monitor treatment efficacy for interventions (e.g., stimulant medications for ADHD) designed to boost cognitive functioning.

      Following your suggestions, we have expanded the Discussion (Line 684) to include future directions and clinical perspectives on the findings.

      Line 684: “Neuroimaging offers a unique window into the biological mechanisms underlying cognition–mental health overlap – insights unattainable from behavioural data alone. Our findings validate brain-based neural markers as a core unit of analysis for cognitive functioning, advancing mental health research through the lens of cognition. Beyond this conceptual contribution, the study has clinical implications. First, by demonstrating a transdiagnostic link between cognition and mental health, we support interventions that enhance cognition as a pathway to improving mental health. Second, we show neuroimaging as an effective tool for assessing the neurobiological basis of this link. Quantifying neuroimaging’s capacity to capture this relationship is essential for future research integrating imaging with cognitive testing to monitor treatment-related neural changes. Such work could enable personalised interventions, using neuroimaging to track cognitive changes and treatment efficacy (e.g., stimulant medications for ADHD) aimed at boosting cognitive functioning.”

      (2) The discussion on the interpretation of the positive and negative PLRS loadings is not very convincing, and the findings are partly counterintuitive. For example (1) how to explain that distress has a positive loading and anxiety/trauma has a negative loading?; (2) how to explain that mental health features like wellbeing and happiness load in the same direction as psychosis and anxiety/trauma? From both a clinical and a neuroscientific perspective, this is hard to interpret.

      Thank you for pointing this out. We appreciate your concern regarding the interpretation of positive and negative PLSR loadings. To clarify:

      (1) The directions of PLSR loadings are broadly consistent with univariate correlations, suggesting that the somewhat counterintuitive relationships mentioned are shown even when we apply simply univariate correlations. PLSR extends beyond univariate approaches by modelling multivariate relationships across features and outcomes. It constructs new components – linear combinations of predictors – that simultaneously explain variance in the predictors and their covariance with the response.

      (2) The positive loading of distress likely reflects cohort-specific questionnaire design in the UK Biobank, where feeling of distress was tied to seeking medical help. Individuals with higher cognition and socioeconomic status may be more likely to seek professional support, which explains the counterintuitive direction.

      (3) The negative loadings of wellbeing and happiness may also reflect cohort-specific effects, such as older age, and align with prior work linking excessive optimism to poorer reasoning and cognitive performance. This suggests that realism or pessimism may sometimes be associated with better cognition, particularly in older adults.

      These points are discussed in detail in the manuscript (Lines 493–545). We have emphasised that some of these findings may be cohort-specific and cited supporting literature, as seen below.

      (1) How to explain that distress has a positive loading and anxiety/trauma has a negative loading?

      Line 493: “The directions of PLSR loadings were broadly consistent with univariate correlations. PLSR extends beyond univariate approaches by modelling multivariate relationships across features and outcomes. Consistently, both univariate correlations and factor loadings derived from the PLSR model indicated that scores for mental distress, alcohol and cannabis use, and self-harm behaviours related positively, and the scores for anxiety, neurological and mental health diagnoses, unusual or psychotic experiences, happiness and subjective well-being, and negative traumatic events related negatively to the g-factor. Positive PLSR loadings of features related to mental distress may indicate greater susceptibility to or exaggerated perception of stressful events, psychological overexcitability, and predisposition to rumination in people with higher cognition [72]. On the other hand, these findings may be specific to the UK Biobank cohort and the way the questions for this mental health category were constructed. In particular, to evaluate mental distress, the UK Biobank questionnaire asked whether an individual sought or received medical help for or suffered from mental distress. In this regard, the estimate for mental distress may be more indicative of whether an individual experiencing mental distress had an opportunity or aspiration to visit a doctor and seek professional help [73]. Thus, people with better cognitive abilities and also with a higher socioeconomic status may indeed be more likely to seek professional help.”

      Line 529: “Consistent with previous studies, we showed that anxiety and negative traumatic experiences were inversely associated with cognitive abilities [90–93]. Anxiety may be linked to poorer cognitive performance via reduced working memory capacity, increased focus on negative thoughts, and attentional bias to threatening stimuli that hinder the allocation of cognitive resources to a current task [94–96]. Individuals with PTSD consistently showed impaired verbal and working memory, visual attention, inhibitory function, task switching, cognitive flexibility, and cognitive control [97–100]. Exposure to traumatic events that did not reach the PTSD threshold was also linked to impaired cognition. For example, childhood trauma is associated with worse performance in processing speed, attention, and executive function tasks in adulthood, and age at a first traumatic event is predictive of the rate of executive function decline in midlife [101,102]. In the UK Biobank cohort, adverse life events have been linked to lower cognitive flexibility, partially via depression level [103].”

      (2) How to explain that mental health features like wellbeing and happiness load in the same direction as psychosis and anxiety/trauma?

      Line 545: “Finally, both negative PLSR loadings and corresponding univariate correlations for features related to happiness and subjective well-being may be specific to the study cohort, as these findings do not agree with some previous research [107–109]. On the other hand, our results agree with the study linking excessive optimism or optimistic thinking to lower cognitive performance in memory, verbal fluency, fluid intelligence, and numerical reasoning tasks, and suggesting that pessimism or realism indicates better cognition [110]. The concept of realism/optimism as indicators of cognition is a plausible explanation for a negative association between the gfactor and friendship satisfaction, as well as a negative PLSR loading of feelings that life is meaningful, especially in older adults who tend to reflect more on the meaning of life [111]. The latter is supported by the study showing a negative association between cognitive function and the search for the meaning of life and a change in the pattern of this relationship after the age of 60 [112]. Finally, a UK Biobank study found a positive association of happiness with speed and visuospatial memory but a negative relationship with reasoning ability [113].”

      (3) The analysis plan has not been preregistered (e.g. at OSF).

      Note: the computational aspects of the methods fall beyond my expertise.

      Thank you for pointing this out. We acknowledge that the analysis plan was not preregistered, as our approach was primarily data‑driven rather than hypothesis‑driven. We essentially applied the machine learning approach to quantify the strength of the cognition-mental health relationship in relation to neuroimaging. To ensure transparency and reproducibility, we have made all analysis code and intermediate outputs publicly available on our GitHub repository (https://github.com/HAM-lab-Otago-University/UKBiobank/) within the constraints of UK Biobank’s ethical policy and provided a detailed description of each methodological step in the Supplementary Materials.

      Reviewer #2 (Public review):

      Summary:

      The goal of this manuscript was to examine whether neural indicators explain the relationship between cognition and mental health. The authors achieved this aim by showing that the combination of MRI markers better predicted the cognition-mental health covariation.

      Strengths:

      The evidence supporting the conclusions is compelling. There is a large sample (UK biobank data) and a clear description of advanced analyses.

      Weaknesses:

      In the previous version of the paper, it was not completely clear what it means to look at the overlap between cognition and mental health. The authors have addressed this in the current version.

      Thank you for your positive feedback and for recognizing the strengths of our work. We appreciate your comments and are happy that the revisions addressed your concerns.

    1. Author response:

      A more in-depth explanation of marker panel applications is needed. Specifically, how should users interpret gene panels where individual genes show only moderate or low expression levels, but the combination provides high specificity? Providing a concrete example, along with guidelines for interpreting such combinatorial signatures, would enhance the practical utility of the method.

      We appreciate the need to explain and demonstrate how to use the novel combinatorial gene marker sets that CellCover generates. To be clear, individual genes expressed at low levels and in small numbers of cells, in general, have high specificity (the ability to mark cells of a particular type without erroneously marking other cells as this type) and are often used in combinations by CellCover to achieve a panel of genes with high sensitivity (the ability to mark all cells of a particular type). Low or sparsely expressed genes of this type may represent poorly measured genes (i.e. zero inflation known to occur in single-cell data, where genes are measured as zero in cells which actually express the gene) or may represent genes which are truly expressed only in a subset of the annotated class. Because CellCover can borrow strength across genes, it can harness the true information in either class of genes, even if affected by zero inflation. Further investigation of structure within the cell class (and across other cell classes) using the CellCover gene marker panel, as well as other genes, is necessary to clarify this issue in any particular analysis. In the manuscript, we evaluate the expression of individual genes within and across classes in this manner to understand deeper structure in Figures 1A, S6 and S8.

      To demonstrate how CellCover selects individual genes with high specificity and low sensitivity, but which are complementary to one another, in order to achieve high collective sensitivity, here we consider a hypothetical dataset of many cells where we focus on one cell class that contains 100 cells composed of four subtypes.

      - Subtype A: cells 1–20

      - Subtype B: cells 21–30

      - Subtype C: cells 31–50

      - Subtype D: cells 51–100

      To illustrate how CellCover evaluates marker gene panels, in this example, the genes under instigation have very different weights (i.e. the ratio of a gene’s expression in the cell class of interest versus its expression in other cells). Suppose we have two candidate marker panels:

      Panel 1 (coarse markers).

      - Gene A: covers cells 1–30 (weight = 0.4)

      - Gene B: covers cells 30–60 (weight = 0.3)

      - Gene C: covers cells 60–100 (weight = 0.2)

      Each gene in this panel covers a relatively large portion of the population (> 30%), but their weights are comparatively high, indicating limited specificity to the focal cell type. Although the panel {A,B,C} attains full coverage, its markers are coarse and nonspecific.

      Panel 2 (fine-grained, combinatorial markers).

      - Gene A’: covers cells 1–20 (weight = 0.05)

      - Gene B’: covers cells 20–30 (weight = 0.10)

      - Gene C’: covers cells 30–50 (weight = 0.05)

      - Gene D’: covers cells 50–100 (weight = 0.10)

      Each marker is expressed in a smaller fraction of the population (individually low sensitivity), but the weights are substantially lower, reflecting strong subtype specificity. Importantly, these genes are complementary: their union covers all 100 cells (high combinatorial sensitivity), even though no single gene spans more than 20–50% of the cells.

      Under a strict covering requirement (e.g., α \= 0, requiring 100% coverage, i.e. perfect sensitiity), both panels satisfy the constraint. However, CellCover selects the second panel because its total weight (specificity) is smaller. This preference reflects the design of the objective function: the method favors markers that are highly cell-type-specific, even if they individually cover only a subset of the population, as long as their complements yield full coverage. As a result, CellCover can reveal refined subtype structure within what appears to be a single cell population.

      Interpretation guidelines. We explicitly note that CellCover marker panels should be interpreted as combinatorial signatures:

      - Individual genes may show localized, subtype-restricted expression.

      - The union of their expression defines the target cell type.

      - Low-weight genes are more specific; CellCover therefore prioritizes them whenever they provide complementary coverage.

      - The resulting panel may highlight latent heterogeneity or subpopulations within the cell type that express different subsets of the markers.

      In addition to these technical guidelines for interpreting gene panels, throughout the manuscript we use the transfer of CellCover marker gene panels to related datasets to assess the biological function of the gene sets. We propose this as a general tool in the examination of gene lists and have implemented methods to visualize the expression of any gene list (including gene lists uploaded by users) using the Projection Tool within NeMO Anlaytics.

      Further quantification of CellCover’s sensitivity in detecting rare cell subtypes or states would strengthen the evaluation of its performance. Additionally, it would be helpful to assess how CellCover performs under noisy conditions, such as low cell numbers or read depths, which are common challenges in scRNA-seq datasets.

      While CellCover is a method to define marker gene panels for cell classes that are already defined in a dataset, its performance on rare cell classes, small numbers of cells and low read depths is still a relevant issue. The analyses in the paper can speak to some of these concerns: The Telley dataset, which we use throughout the manuscript, used FlashTag labeling of cells prior to sequencing in order to ascertain the time since terminal division for each cell. This unique metadata linked to each cell’s expression data enabled many of the analyses we performed in the paper, but also limited the number of cells that were sequenced. For this reason, the number of cells in this dataset (total cells = 2756) is much lower than that seen in the vast majority of other single-cell sequencing studies, including those we use for the transfer of marker gene sets defined by CellCover in the Telley data. As a result, the cell classes for which we define marker gene panels in the paper contain relatively small numbers of cells. This is especially true in the 12-class analysis in Figures 4 and 5 where CellCover successfully defines gene panels for all 12 classes which transfer well to other datasets. Total cells per class range from 134 to 301. Figure S6 shows that the discriminative power of the 12 gene panels varied widely, with the most highly discriminative panel being from the E12.1H condition with only 189 cells).

      In addition, we note that the behavior of CellCover on rare (or any) cell classes can be characterized deterministically under mild condition. For a fixed cell class and a required covering rate of 1, a depth-k covering gene panel exists if and only if every cell in the class expresses at least k genes. Under this condition, CellCover is guaranteed to find a covering panel of depth-k. Importantly, this guarantee does not impose any restriction on the panel size. Consequently, the compactness of the resulting panel reflects intrinsic properties of the data rather than algorithmic limitations: a small panel indicates that a subset of genes is robustly and consistently expressed across most cells in the class, even if the class itself is rare, whereas a large panel suggests highly heterogeneous expression patterns, where different genes are expressed in different cells. In this sense, the feasibility and structure of a covering panel are determined by the biological and technical characteristics of the dataset (e.g., read depth, expression sparsity, and the specificty of gene expression in the defined cell classes), rather than by the performance of CellCover itself.

      It is intriguing and novel that CellCover analysis of the dataset from Telley et al. suggests cell-type-specific expression of ribosomal, mitochondrial, or tRNA genes. These findings would be significantly strengthened by additional validation. For example, the reported radial glia-specific expression of Rps18-ps3 and Rps10-ps1, as well as the postmitotic neuron-specific expression of mt-Tv and mt-Nd4l, should be corroborated using independent scRNA-seq or spatial transcriptomic datasets of the developing neocortex. Alternatively, these expression patterns could be directly examined through immunostaining or single-molecule FISH analysis.

      The main problem with such analysis is that most studies have omitted the expression of these genes (especially mitochondrial genes that are primarily viewed as QC metrics) from their datasets. We encourage researchers to retain the expression of these transcripts in their data so that their biological functions can be explored. Where available, the expression of these genes can be visualized in NeMO Analytics in the mouse where the enrichment of Rps18-ps3 expression in radial glia can be seen in the Di Bella 2021 dataset and in the human where the expression of mt-Tv can be seen in neurons in the Polioudakis 2019, Darmanis 2015, Camp 2015, and Liu 2016 datasets.

      Taking a broader perspective, a growing body of foundational work in developmental neurobiology supports the observation that mitochondrial state and metabolic programs undergo systematic changes during neuronal differentiation, consistent with our CellCover findings. For example, Khacho 2016 demonstrated that mitochondrial dynamics are essential regulators of neuronal fate commitment and that the maturation of the mitochondrial network is essential for the transition from the progenitor metabolic state to the neuronal state. Iwata 2020 further highlight cell type specific mitochondrial dynamics by showing that daughter cells with highly fragmented mitochondria tend to become neurons.

      The observation that outer radial glia (oRG) markers are expressed in neural progenitors before the emergence of gliogenic progenitors in primates and humans is compelling. This could be further supported by examining the temporal and spatial expression patterns of early oRG-specific markers versus gliogenic progenitor markers in recent human spatial transcriptomic datasets - such as the one published by Xuyu et al. (PMID: 40369074) or Wang et al. (PMID: 39779846).

      We have added the scRNA-seq data from Wang et al., as well as data from the Nano et al. 2025 meta-atlas to the NeMO Analytics data collection. oRG markers from Liu et al 2023 can now be visualized across the Wang, Nano and many more human in vivo datasets. In the Nano data, these oRG markers can be seen increasing in expression in the human neocortex from GW7-12, leading into peak neurogenesis and prior to gliogenesis. Although with lower age resolution, the peaking of oRG markers in the 2nd trimester (dring peak neurogenesis) and their precipitous drop in the 3rd trimester (during peak gliogenesis) can also be seen in the Wang data. At NeMO Analytics individual marker genes of oRGs can also visualized in these datasets.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      MPRAs are a high-throughput and powerful tool for assaying the regulatory potential of genomic sequences. However, linking MPRA-nominated regulatory sequences to their endogenous target genes and identifying the more specific functional regions within these sequences can be challenging. MPRAs that tile a genomic region, and saturation mutagenesis-based MPRAs, can help to address these challenges. In this work, Tulloch et al. describe a streamlined MPRA system for the identification and investigation of the regulatory elements surrounding a gene of interest with high resolution. The use of BACs covering a locus of interest to generate MPRA libraries allows for an unbiased and high-coverage assessment of a particular region. Follow-up degenerate MPRAs, where each nucleotide in the nominated sequences is systematically mutated, can then point to key motifs driving their regulatory activity. The authors present this MPRA platform as straightforward, easily customizable, and less time- and resource-intensive than traditional MPRA designs. They demonstrate the utility of their design in the context of the developing mouse retina, where they first use the LS-MPRA to identify active regulatory elements for select retinal genes, followed by d-MPRA, which allowed them to dissect the functional regions within those elements and nominate important regulatory motifs. These assays were able to recapitulate some previously known cis-regulatory modules (CRMs), as well as identify some new potential regulatory regions. Follow-up experiments assessing co-localization of the gene of interest with the CRM-linked GFP reporter in the target cells, and CUT&RUN assays to confirm transcription factor binding to nominated motifs, provided support linking these CRMs to the genes of interest. Overall, this method appears flexible and could be an easy-to-implement tool for other investigators aiming to study their locus of interest with high resolution.

      Strengths:

      (1) The method of fragmenting BACs allows for high, overlapping coverage of the region of interest.

      (2) The d-MPRA method was an efficient way to identify key functional transcription factor motifs and nominate specific transcription factor-driven regulatory pathways that could be studied further.

      (3) Additional assays like co-expression analyses using the endogenous gene promoter, and use of the Notch inhibitor in the case of Olig2, helped correlate the activity of the CRMs to the expression of the gene of interest, and distinguish false positives from the initial MPRA.

      (4) The use of these assays across different time points, tissues, and even species demonstrated that they can be used across many contexts to identify both common and divergent regulatory mechanisms for the same gene.

      Weaknesses:

      The LS-MPRA assay most strongly identified promoters, which are not usually novel regulatory elements you would try to discover, and the signal-to-noise ratio for more TSS-distal, non-promoter regulatory elements was usually high, making it difficult to discriminate lower activity CRMs, like enhancers, from the background. For example, NR2 and NR3 in Figure 3 have very minimal activity peaks (NR3 seems non-existent). The ex vivo data in Figure 2 are similarly noisy. Is there a particular metric or calculation that was or could be used to quantitatively or statistically call a peak above the background? The authors mention in the discussion some adjustments that could reduce the noise, such as increased sequencing depth, which I think is needed to make these initial LS-MPRA results and the benchmarking of this assay more convincing and impactful.

      Much of the statistical and quantitative data asked for by the Reviewers have been provided in the Revision. However, it is important to note that the types of statistics using peak callers asked for regarding candidate choice will be of limited value. If one is testing a library in a single cell type in vitro, and/or running genome-wide assays, these statistics could aid in the choice of candidates. However, here we are electroporating a complex and dynamic set of cells, with each cell type constituting what can be very different frequencies (e.g. Olig2-expressing cells are <2.4% of cells). This fact alone will give different apparent signal to noise values. In addition, at least for Olig2 and Ngn2, their expression is very transient, suggesting dynamic regulation by what is likely multiple positive and negative CRMs. An additional confound is that the level of expression of each gene that one might test is variable. All of these variables render a statistical prediction of candidates to be less valuable than one might hope, and might lead one to miss those CRMs of interest, particularly those in a small subset of cells. Instead, we suggest that one use one’s own level of interest and knowledge in choosing CRM candidates. We provide several examples of experimental, rather than purely statistical, approaches that might help in one’s choice of candidates. We used a functional read-out of CRM activity (Notch perturbation), carried out in the context of the entire LS-MPRA library, as one method. Co-expression in single cells of candidate regulators identified by the d-MPRA is another. One can of course use chromatin structure and sequence conservation, as used in many studies of regulatory regions, as other ways to narrow down candidates. The d-MPRA predictions also can be viewed in light of previous genetic studies, i.e. mutations in TFs that effect the cell type of interest or the regulation of the gene of interest, as we were able to do here for CRMs predicted to be regulated by Otx2.

      Reviewer #2 (Public review):

      Summary:

      In this study, Tulloch et al. developed two modified massively parallel reporter assays (MPRAs) and applied them to identify cis-regulatory modules (CRMs) - genomic regions that activate gene expression, controlling retinal gene expression. These CRMs usually function at specific developmental stages and in distinct cell types to orchestrate retinal development. Studying them provides insights into how retinal progenitor cells give rise to various retinal cell types.

      The first assay, named locus-specific MPRA (LS-MPRA), tests all genomic regions within 150-300 kb of the gene of interest, rather than relying on previously predicted candidate regulatory elements. This approach reduces potential bias introduced during candidate selection, lowers the cost of synthesizing a library of candidate sequences, and simplifies library preparation. The LS-MPRA libraries were electroporated into mouse retinas in vivo or ex vivo. To benchmark the method, the authors first applied LS-MPRA near stably expressed retinal genes (e.g., Rho, Cabp5, Grm6, and Vsx2), and successfully identified both known and novel CRMs. They then used LS-MPRA to identify CRMs in embryonic mouse retinas, near Olig2 and Ngn2, genes expressed in subsets of retinal progenitor cells. Similar experiments were conducted in chick retinas and postnatal mouse retinas, revealing some CRMs with conserved activity across species and developmental stages.

      Although the study identified CRMs with robust reporter activity in Olig2+ or Ngn2+ cells, the data do not provide sufficient evidence to support the claims that these CRMs regulate Olig2 or Ngn2, rather than other nearby genes, in a cell-type-specific manner. For example, the authors propose that three regions (NR1/2/3) regulate Olig2 specifically in retinal progenitor cells based on: (1) the three regions are close to Olig2, (2) increased Olig2 expression and NR1/2/3 activity upon Notch inhibition, and (3) reporter activity observed in Olig2+ cells (though also present in many Olig2- cells). While these are promising findings, they do not directly support the claims.

      The second assay, called degenerate MPRA (d-MPRA), introduces random point mutations into CRMs via error-prone PCR to assess the impact of sequence variations on regulatory activity. This approach was used on NR1/2/3 to identify mutations that alter CRM activity, potentially by influencing transcription factor binding. The authors inferred candidate transcription factors, such as Mybl1 and Otx2, through motif analysis, co-expression with Olig2 (based on single-cell RNA-seq), and CUR&RUN profiling. While some transcription factors identified in this way overlapped with the d-MPRA results, others did not. This raises questions about how well d-MPRA complements other methods for identifying transcriptional regulators.

      Strengths:

      (1) The study introduces two technically robust MPRA protocols that offer advantages over standard methods, such as avoiding reliance on predefined candidate regions, reducing cost and labor, and minimizing selection bias.

      (2) The identified regulatory elements and transcription factors contribute to our understanding of gene regulation in retinal development and may have translational potential for cell-type-specific gene delivery into developing retinas.

      Weaknesses:

      (1) The claims for gene-specific and cell type-specific CRMs would benefit from further validation using complementary approaches, such as CRISPR interference or Prime editing.

      The methods that we developed were meant to provide candidates for regulatory elements for a gene of interest. These candidates could be used to further understand the regulation of a gene, a complex and difficult task, especially for dynamically regulated genes in the context of development. These candidates could also, or instead, be used to drive gene expression specifically in a target cell of interest for applications such as gene therapy or perturbations that need this type of specificity. In the first case, to use the candidates to understand the regulation of a gene, one would need to validate the candidates using the types of methods typically employed for this purpose, most rigorously in the in vivo genomic context. We did not pursue this level of validation as it would encompass a great deal of work outside the scope of the current study. However, by initially testing loci which have been studied by several groups (as cited in the manuscript, Rho, Grm6, Vsx2, and Cabp5), we were able to show that LS-MPRA can identify known CRMs. In the cases of Rho and Vsx2, previous data have shown the CRMs to be relevant in the genomic context in vivo. In addition, two Vsx2 CRM’s identified by LS-MPRA are located at -37 Kb and -17Kb, and the Grm6 CRM identified by LS-MPRA is at -8Kb. These are the same CRM locations identified previously using classical methods. These data show that the method is capable of identifying distal elements. When one has only one or a few loci of interest, i.e. one does not need to use genome-wide approaches, LS-MPRA is accurate enough to be worth the relatively small effort to identify potential CRMs, even those at some distance from the TSS. However, it is apparent that our methods are not perfect and that the LS-MPRA does not pick up all CRMs. We do not know of a method that has been shown to do so.

      Reviewer #3 (Public review):

      Summary:

      Use of reporter assays to understand the regulatory mechanisms controlling gene expression moves beyond simple correlations of cis-regulatory sequence accessibility, evolutionary sequence conservation, and epigenetic status with gene expression, instead quantifying regulatory sequence activity for individual elements. Tulloch et al., provide a systematic characterization of two new reporter assay techniques (LS-MPRA and d-MPRA) to comprehensively identify cis-regulatory sequences contained within genomic loci of interest during retinal development. The authors then apply LS-MPRA and d-MPRA to identify putative cis-regulatory sequences controlling Olig2 and Ngn2 expression, including potential regulatory motifs that known retinal transcription factors may bind. Transcription factor binding to regulatory sequences is then assessed via CUT&RUN. The broader utility of the techniques is then highlighted by performing the assays across development, across species, and across tissues.

      Strengths:

      (1) The authors validate the reporter assays on retinal loci for which the regulatory sequences are known (Rho, Vsx2, Grm6, Cabp5) mostly confirming known regulatory sequence activity but highlighting either limitations of the current technology or discrepancies of previous reporter assays and known biology. The techniques are then applied to loci of interest (Olig2 and Ngn2) to better understand the regulatory sequences driving expression of these transcription factors across retinal development within subsets of retinal progenitor cells, identifying novel regulatory sequences through comprehensive profiling of the region.

      (2) LS-MPRA provides broad coverage of loci of interest.

      (3) d-MPRA identifies sequence features that are important for cis-regulatory sequence activity.

      (4) The authors take into account transcript and protein stability when determining the correlation of putative enhancer sequence activity with target gene expression.

      Weaknesses:

      (1) In its current form, the many important controls that are standard for other MPRA experiments are not shown or not performed, limiting the interpretations of the utility of the techniques. This includes limited controls for basal-promoter activity, limited information about sequence saturation and reproducibility of individual fragments across different barcode sequences, limitations in cloning and assay delivery, and sequencing requirements. Additional quantitative metrics, including locus coverage and number of barcodes/fragments, would be beneficial throughout the manuscript.

      We thank the reviewer for these comments and have provided detailed responses to the additional analyses in the subsequent Recommendations section.

      (2) There are no statistical metrics for calling a region/sequence 'active'. This is especially important given that NR3 for Olig2 seems to have a small 'peak' and has non-significant activity in Figure 4.

      See comments about peak calling in our response to Reviewer #1.

      (3) The authors present correlational data for identified cis-regulatory sequences with target gene expression. Additionally, the significance of transcription factor binding to the putative regulatory sequences is not currently tested, only correlated based on previous single-cell RNA-sequencing data. While putative regulatory sequences with potential mechanisms of regulation are identified/proposed, the lack of validation (and discrepancies with previous literature) makes it hard to decipher the utility of the techniques.

      See comments about further validation in our response to Reviewer #2.

      (4) While the interpretations that Olig2 mRNA/protein expression is dynamically regulated improved the proportions of cells that co-expressed CRM-regulated GFP and Olig2, alternate explanations (some noted) are just as likely. First, the electroporation isn't specific to Olig2+ progenitors. Also, the tested, short CRM fragments may have activating signals outside of Olig2 neurogenic cells because chromatin conformation, histone modifications, and DNA methylation are not present on plasmids to precisely control plasmid activity. Alternatively, repressive elements that control Olig2 expression are not contained in the reporter vectors.

      The electroporation of Olig2 minus and plus cells is an excellent way to determine if a CRM is active in all cells, or only a specific subset, and we therefore consider this the best way to answer the question of specificity. We agree that we were unable to show that all CRM active cells were indeed Olig2-expressing cells. As noted by the Reviewer, we went to some lengths to quantify RNA and protein co-expression, including of endogenous Olig2 protein and RNA. Even with the endogenous RNA and protein, there was a mismatch wherein one infrequently saw the two together in the same cell, which could be predicted from the short half-lives of these molecules. Regarding chromatin, etc., we are intrigued by the proper regulation that we have observed for CRMs that we have previously discovered by plasmid electroporation (e.g. Kim et al. 2008, Matsuda and Cepko, 2004, Wang et al. 2014, Emerson et al. 2013). It is indeed interesting that plasmids can recapitulate proper regulation, without the proper genomic context or chromatin modifications. We have expanded our discussion of these points in the Discussion.

      (5) It is unclear as to why the d-MPRA uses a different barcoding strategy, placing a second copy of the cis-regulatory sequence in the 3' UTR. As acknowledged by the author, this will change the transcript stability by changing the 3' UTR sequence. Because of this, comparisons of sequence activity between the LS-MPRA and d-MPRA should not be performed as the experiments are not equivalent.

      We had provided a rationale for the different strategies of barcoding in the original submission, and believe it is at the discretion of the experimenter to utilize either strategy for their specific purposes. We agree that comparing activity between different techniques would not be appropriate. The analysis of mutated CRMs using d-MPRA does not utilize data from the LS-MPRA, but is an analysis of relative activity among all mutated d-MPRA constructs.

      (6) Furthermore, details of the mutational burden in d-MPRA experiments are not provided, limiting the interpretations of these results.

      We have provided detailed responses to the additional analyses in the subsequent Recommendations section and included details of the mutational burden in Supplemental Document A.

      (7) Many figures are IGV screenshots that suffer from low resolution. Many figures could be consolidated.

      We have increased the resolution of all IGV genome tracks, but believe the content within all figures remains appropriate.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Suggestions for improving the clarity of the results in the figures:

      (1) The pie charts used the show the percentage of overlapping cells in the colocalization analyses were not especially intuitive to read, and although the percentages and any statistical significance were often written in the text, it would've been helpful to have them written in the figures. I would suggest displaying the results in stacked bar plots, possibly like the one shown in Figure 6A, to demonstrate the data more clearly.

      We thank the reviewer for the suggestions. Though adding the percentages directly to the pie charts would make the relevant panels too confusing to interpret, we added supplemental tables (Tables S5-S9) with the percentages displayed in all pie charts for readers interested in the precise quantifications.

      (2) The scRNA-seq UMAPs showing co-expression of Olig2 with the TFS of interest - it is very hard to see the cells that co-express. I would recommend either having a window zoomed in on the Olig2-expressing cell population to be able to see the co-expression more clearly visually, and/or including a graph demonstrating the percentages of co-expressing cells. These numbers were written in the text, but would be useful to see in the figure.

      The resolution of the scRNA-Seq plot has been improved for the visualization of co-expressing cells, which were also brought forward in all UMAP plots to improve clarity. Because of the higher quality images, insets should no longer be necessary. We have also included percentages of co-expression in the figures (Figs. 8 and 8S) and thank the reviewer for the suggestion.

      Other minor suggestions/corrections:

      (3) Figures 6B and 10S are missing the overlap quantification (in bar or pie charts) like in the other figures.

      The quantification for the image in 6B (i.e., GFP fluorescence and GFP RNA) is displayed in 6D for the four Olig2 CRM plasmid constructs. In Fig. 10S, the experiments in early chick ventral neural tube delivered constructs to a very limited number of cells, and quantification of cells would not necessarily represent an accurate number of cells with CRM activity. We therefore decided to show only representative images of CRM activity in this population of cells rather than present a biased count or increase the number of experiments/samples to obtain a robust quantification.

      (4) On the second-to-last line of page 10, in the sentence "The d-MPRA approach provided a robust, high resolution method for functionally relevant TF binding sites....", I think you're missing a word between "for" and "functionally". For example, it might be "for identifying..." or "for nominating...".

      We have revised the sentence accordingly.

      Reviewer #2 (Recommendations for the authors):

      Minor suggestions:

      (1) Please indicate which mouse reference genome (e.g., mm10) was used in plots such as Figure 2.

      We have added text to the relevant sections in the Results (the reference genome was already mentioned in Methods).

      (2) In Figures 2 and 2S, the CRMs discussed in the text are not labeled or highlighted, making it unclear which regions are being referenced.

      We have labeled peaks with roman numerals in both the figures, legends, and text for clarity and thank the reviewer for the suggestion.

      (3) Consider listing the genomic coordinates for the CRMs mentioned in the text, as this information would be especially useful for readers interested in exploring these regions further.

      This information was included in Table 2S in the original submission, with all relevant coordinates provided therein.

      (4) The d-MPRA plots (e.g., Figure 7C-E) do not clearly show the effects of different nucleotide substitutions. A more informative visualization style can be found in Kircher et al (PMID: 31395865, Fig. 1D) or Deng et al (PMID: 38781390, Fig. 5F).

      The precise nucleotide substitutions would be informative to visualize the effects of specific changes. However, we were more interested in how any nucleotide substitution influenced the CRM activity to hone in on relevant TFBS. We therefore believe the current visualization is the most appropriate to accomplish this. However, for some types of future applications, a more informative visualization as noted would be a valuable addition.

      (5) It would be extremely helpful to the community if the LS-MPRA data were uploaded to the UCSC genome browser and made accessible via a link.

      We have uploaded all LS-MPRA genome tracks to a Track Hub in the UCSC genome browser and provided the appropriate link to access the Hub (https://github.com/cattapre/ALAS00) in the methods section.

      Reviewer #3 (Recommendations for the authors):

      (1) The authors should address the following metrics to showcase the utility of the techniques:

      We thank the reviewer for requesting the detailed metrics outlined below. We have addressed all inquiries and included the majority of metrics in the resubmission.

      (a) Library size

      This should be shown for each library that is generated. It is acknowledged that the complete size of the library is limited by sequencing, and the comprehensiveness of the library will change every time the library is re-prepped. However, metrics of this are not currently provided in a robust manner for each library. "Libraries of at least 7x10^6 and as many as 9x10^7 fragments are made" - vague - how was library complexity established since this seems to be an estimation, how many reads were utilized to estimate library complexity?

      We created a new supplemental table (Table S3) that displays the complexity based on sequencing rather than the estimated complexity based on the serial dilutions prior to 3D culture (which was used for the estimates listed in the results). We updated the complexity range in the text as well and thank the reviewer for the suggestion.

      Does library size scale proportionally to the BACs of different sizes?

      The fragmentation of different BACs with differing sizes does not necessarily alter the size of the library. Library size is primarily determined by the library creation pipeline, with the size selection step of the fragmented BAC and the cloning step that inserts adapter-ligated fragments into the barcoded expression vector being the primary determinants of complexity of plasmid libraries.

      (b) Sequence saturation

      Can the authors please provide evidence that the libraries have been sequenced to saturation or estimates of the degree of under-sequencing? How many reads does it take to discover a new barcode associated with a new regulatory sequence?

      We have provided library characteristics for this in Table S3 and have also generated Sequence Saturation Curves for each association library in Supplemental Document A.

      (c) Barcode saturation

      How many barcodes are present for each fragment in the libraries? Are most fragments only covered by 1 barcode? The barcoding strategy doesn't prevent the same barcode from being assigned to multiple different fragments, as barcodes are random. What is the incidence of barcode collisions?

      We have provided library characteristics for this in Table S3 and have also generated Barcode Saturation Curves for each association library in Supplemental Document A.

      Additionally, we tested whether the omission of barcode collisions would affect the output of our LS-MPRA. We reanalyzed one barcode abundance library (one replicate following 12h Notch inhibitor) and filtered the barcodes so that only unique barcodes were analyzed. We were able to replicate all previously identified peaks. Though it is not necessary to filter out barcode collisions, there may be an improvement in signal-to-noise if the sequencing depth of libraries was sufficient (see Supplemental Document B).

      (d) Normalization

      As performed, fragment activity is normalized by RNA expression compared to the presence of fragments in the library. While this is done for small libraries, for large libraries, this may not be appropriate. For large libraries, every sequence in the library will not be delivered to each cell, and many fragments contained in the library may not be electroporated at all. Ideally, the authors would have sequenced both the RNA and DNA from the electroporations to i) identify the fragment distribution of the library that was successfully electroporated and ii) provide an internal normalization factor across replicate samples. This is especially important if the libraries were ever re-prepped, as the jack-potting or asymmetries in fragment recovery can occur every time the library is re-derived.

      We agree with the reviewer’s comments about the variability in fragments delivered experimentally, though we also believe the normalization of the libraries is still appropriate. We never needed to re-prep the libraries as there was sufficient material for many more experiments than were performed. However, should one ever need to re-prep an LS-MPRA library, all experimental sequencing should be normalized to the respective sequenced association library to account for biased distributions, as the reviewer mentions.

      In the absence of these metrics (this would likely require the authors to repeat all experiments and is acknowledged to be outside the scope of revisions), the authors should provide information on the percentage of the library that is profiled in the RNA for each library.

      We have provided RNA profiles of all abundance libraries in Table S4. The overall fraction of fragments represented in the RNA pools was lower than that observed in other published MPRAs. This difference is expected given that most MPRA studies preselect fragments based on chromatin accessibility, transcription factor binding, sequence conservation, or bioinformatically predicted CRMs, thereby enriching for regulatory elements with high activity potential. Our locus-specific MPRA libraries, by contrast, include all fragments across the targeted genomic region, many of which are likely to be inactive in the tested context. Consequently, only a smaller proportion of fragments show measurable RNA expression.

      (e) Fragment sizes

      Please provide a density plot or something similar showcasing the size distribution of the libraries generated. Is there any correlation between sequence activity and the size of fragments?

      We have generated size distribution plots and correlations between fragment size and activity of all libraries and have included them in Supplemental Document A.

      (2) Questions about the statistical validity of results:

      (a) What threshold is utilized for calling a sequence as active? This is important as NR3 does not seem to be an element that has significant activity.

      See comments about peak calling in prior responses.

      (b) A Fisher's exact test using cells from single-cell RNA-sequencing as replicate samples is inappropriate as the cells are i) not from replicate experiments and ii) potentially in different cell states. The proportions of cells across replicate scRNA-seq datasets would be more appropriate.

      We thank the reviewer for raising this important point. While we agree that individual cells do not substitute for biological replicates, we believe Fisher’s exact test remains appropriate for testing whether gene expression is associated with Olig2 expression within a single scRNA-seq dataset. The test assesses co-occurrence at the level of individual cells, which is valid under the assumption that each cell represents an independent sampling of transcriptional states, even when it is possible that cells are in different states. We use this method as an exploratory tool to identify candidate genes associated with Olig2 expression in this dataset, and in the future, this could also be further validated by comparing the proportions of cells across replicate datasets, as the reviewer mentions.

      (3) Discussion of the reporter/Olig2/Ngn2 RNA/protein disconnect needs to be expanded. Some simpler explanations for the presence of GFP in Olig2- and Ngn2- cells, as well as the presence of Olig2 or Ngn2 in GFP- cells, is that (i) these putative CRMs are being introduced to cells in plasmids, taking them out of their native genomic context where they may be inaccessible or repressed and allowing them to drive reporter expression even if their candidate target gene is not endogenously expressed, (ii) these putative CRMs may regulate genes besides just Olig2 or Ngn2, and (iii) Olig2 and Ngn2 are regulated by far more regulatory elements than the 3 or 4 being tested in each reporter assay, so their expression likely does not rely solely on the activity of the few putative CRMs tested.

      We have added these points in an expanded discussion in the text.

      (4) Problems with figures: Low resolution of many IGV genome tracks, pink 'co-expression' dots are completely indiscernible. Numbers should be listed with the pie charts. BFP expression should be shown since this is being quantified, especially since electroporation efficiency can change across age and/or tissue samples.

      We have reconfigured the IGV tracks so that they are higher resolution and have included supplemental tables for the numbers pertaining to the pie charts. For electroporation controls (BFP and RFP), BFP expression is shown in Figs 5S, 6, and 10S and the RFP electroporation control is shown in Fig. 11. Though BFP is sometimes used as a qualifier in the denominator of some of the quantification, displaying its expression, particularly in combination with three other signals that are already included in most images, provides limited utility.

      (5) More information is required to understand the utility of the d-MPRA. Detailed quantification of the number of mutations/fragments needs to be ascertained. When multiple mutations are present, how are the authors controlling for which mutation is affecting activity? What is the coverage of the loci of interest for mutational burden (ie, is every base pair mutated in at least one fragment?). For mutations that increase the activity of the element, are there specific sequence features that increase activity (new motifs generated)?

      The d-MPRA platform is a high-throughput assay that seeks to identity putative sub-regions within CRMs nominated by the LS-MPRA, or any other assay. It relies on deep mutational coverage to determine positive and negative regulatory sub-regions of the CRMs. While many reads have multiple mutations, they are broadly co-occurring across the entire fragment (see Supplemental Document A) so as not to create a false linkage between the sites. Every individual site is mutated many times with roughly even coverage across each fragment (see Supplemental Document A), thus allowing us to assess the requirement of each base in contributing to a putative CRM’s activity. Comparing d-MPRA plots using bulk fragments or fragments with singleton mutations (Supplemental Document A) yielded almost identical plots for two libraries, and a similar analysis of the third library. Any differences between analysis of fragments with one or more mutations is likely a result of either sequencing depth or the requirement of multiple bases for binding or CRM activation. Follow-up experiments investigating intra-CRM interactions would elucidate such variability. Whether new motifs are generated for any specific substitution is an interesting question, which could be followed up for a CRM of interest. The d-MPRA data that we provide would provide the starting point for such follow-up experiments.

      (6) Transcription factors as regulators of CRM-activity.

      It is appreciated that the authors validated the binding of transcription factors to NR2. However, this correlative analysis should be further tested in follow-up experiments to highlight novel biology using systems already in place. Potential experiments that could be performed include the following (reagents in hand, or performed in a manner similar to experiments performed by the lab in previous publications):

      (a) over-expression of TF using LS-MPRA library.

      (b) over-expression of TF using d-MPRA library, showing that mutations in the putative TF binding site disrupt activity compared to non-mutated sequences.

      (c) performing TF over-expression using target CRMs, including sequences where the TF binding site is mutated (similar to a small MPRA).

      (d) the quantification of target gene expression when i) TF is over-expressed, ii) CRM is activated using CRISPRa, or iii) CRM is inhibited using CRISPRi.

      These are all valid follow-up experiments. Please see prior responses we have provided regarding further validation.

      Minor points

      (1) Please acknowledge that some distal regulatory sequences may be contained outside of the BAC regions. Also, the authors should emphasize the point that the assay is NOT cell-type-specific or specific to regulatory sequences for the gene of interest, but ALL regulatory sequences contained within the locus. The discussion of this with respect to Ift122 and Rpl32 is somewhat confusing.

      We have added a sentence in the Discussion addressing possible CRMs outside the BAC coverage. We believe it is implicitly understood that the assay only screens regulatory activity in the BAC, and believe we have addressed this in the manuscript.

      If one wishes to use a candidate CRM to drive gene expression in a targeted cell type, one needs to establish specificity. In particular, specificity needs to be established in the context of the vector that is being used. Non-integrated vs integrated vectors, different types of viral vectors with their own confounding regulatory sequences, different types of plasmids and methods of delivery, and copy number can all affect specificity. We provided a double in situ hybridization method for the examination of specificity for some of the novel candidate CRMs. It was quite difficult in the case of Olig2 and Ngn2 as their RNAs and proteins are unstable. We would need to provide further evidence should we wish to use these candidate CRMs for directing expression specifically in Olig2- or Ngn2-expressing cells. We suggest that an investigator can choose the vector and method for establishing specificity depending upon the goals of the application.

      (2) I am curious as to why low-resolution, pseudo-bulked single-nucleus ATAC was utilized instead of more comprehensive retina ATAC samples at similar time-points (for example, as available in Al Diri et al., 2017 (E14, E17, P0, P3, P7, P10) samples are all available.

      The use of pseudo-bulked single-nucleus ATAC-seq data provided a convenient and consistent comparison to our LS-MPRA results. We agree that incorporating higher-resolution datasets such as those from Al Diri et al. would be valuable for future analyses aimed at linking CRM activity with broader chromatin accessibility dynamics.

    1. Author response:

      eLife Assessment

      This study provides valuable mechanistic insight into the mutually exclusive distributions of the histone variant H2A.Z and DNA methylation by testing two hypotheses: (i) that DNA methylation destabilizes H2A.Z nucleosomes, thereby preventing H2A.Z retention, and (ii) that DNA methylation suppresses H2A.Z deposition by ATP-dependent chromatin remodeling complexes. Through a series of well-designed and carefully executed experiments, findings are presented in support of both hypotheses. However, the evidence in support of either hypothesis is incomplete, so that the proposed mechanisms underlying the enrichment of H2A.Z on unmethylated DNA remain somewhat speculative.

      We would like to thank the editor and reviewers for their critical assessments of our manuscript. While we do acknowledge the limitations of our work, we believe that our results provide important mechanistic insights into the long-standing question of how H2A.Z is preferentially enriched in hypomethylated genomic DNA regions. First, our structural and biochemical data suggest that DNA methylation increases the openness and physical accessibility of H2A.Z, albeit the effect is relatively subtle and is sequence-dependent. Second, using Xenopus egg extracts and synthetic DNA templates, we provide the first clear and direct evidence that DNA methylation-sensitive H2A.Z deposition is due to the H2A.Z chaperone SRCAP-C, corroborated by our discovery that SRCAP-C binding to DNA is suppressed by DNA methylation. Although the molecular details by which DNA methylation inhibits binding of SRCAP-C is an important area of future study, in our current manuscript, we do provide evidence that directly links the presence of SRCAP-C to the establishment of the DNA methylation/H2A.Z antagonism in a physiological system. Thanks to criticisms by the reviewers, we realized that we did not clearly state in our Abstract that the impact of DNA methylation on intrinsic H2A.Z nucleosome stability is relatively subtle, although we did explain these observations and limitations in the main text. In our revised manuscript, we are willing to edit the text to better clarify the criticisms raised by the reviewers.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors considered the mechanism underlying previous observations that H2A.Z is preferentially excluded from methylated DNA regions. They considered two non-mutually exclusive mechanisms. First, they tested the hypothesis that nucleosomes containing both methylated DNA and H2A.Z might be intrinsically unstable due to their structural features. Second, they explored the possibility that DNA methylation might impede SRCAP-C from efficiently depositing H2A.Z onto these DNA methylated regions.

      Their structural analyses revealed subtle differences between H2A.Z-containing nucleosomes assembled on methylated versus unmethylated DNA. To test the second hypothesis, the authors allowed H2A.Z assembly on sperm chromatin in Xenopus egg extracts and mapped both H2A.Z localization and DNA methylation in this transcriptionally inactive system. They compared these data with corresponding maps from a transcriptionally active Xenopus fibroblast cell line. This comparison confirmed the preferential deposition or enrichment of H2A.Z on unmethylated DNA regions, an effect that was much more pronounced in the fibroblast genome than in sperm chromatin. Furthermore, nucleosome assembly on methylated versus unmethylated DNA, along with SRCAP-C depletion from Xenopus egg extracts, provided a means to test whether SRCAP-C contributes to the preferential loading of H2A.Z onto unmethylated DNA.

      Strengths:

      The strength and originality of this work lie in its focused attempt to dissect the unexplained observation that H2A.Z is excluded from methylated genomic regions.

      Weaknesses:

      The study has two weaknesses. First, although the authors identify specific structural effects of DNA methylation on H2A.Z-containing nucleosomes, they do not provide evidence demonstrating that these structural differences lead to altered histone dynamics or nucleosome instability. Second, building on the elegant work of Berta and colleagues (cited in the manuscript), the authors implicate SRCAP-C in the selective deposition of H2A.Z at unmethylated regions. Yet the role of SRCAP-C appears only partial, and the study does not address how the structural or molecular consequences of DNA methylation prevent efficient H2A.Z deposition. Finally, additional plausible mechanisms beyond the two scenarios the authors considered are not investigated or discussed in the manuscript.

      Although we acknowledge the limitations of our study and are willing to expand our discussion to more thoroughly discuss these points, we believe our manuscript provides several important mechanistic insights which this reviewer may not have fully appreciated.

      Our first conclusion that H2A.Z nucleosomes on methylated DNA are more open and accessible compared to their unmethylated counterparts is supported by both our cryo-EM study and the restriction enzyme accessibility assay. Although the physical effect of DNA methylation is relatively subtle and is likely sequence dependent, as we clearly noted within the manuscript, the difference does exist and is valuable information for the chromatin field at large to consider.

      The second major conclusion of our manuscript is that SRCAP-C exhibits preferential binding to unmethylated DNA over methylated DNA, and that SRCAP-C represents the major mechanism that can explain the biased deposition of H2A.Z to unmethylated DNA in Xenopus egg extracts. Furthermore, our experiments using Xenopus egg extract clearly demonstrated that H2A.Z is deposited by both DNA-methylation sensitive and insensitive mechanisms. Depletion of SRCAP-C almost completely eliminated the levels of DNA-methylation-sensitive H2A.Z deposition and reduced the total level of H2A.Z on chromatin to less than half of that seen in non-depleted extract. This result demonstrated that DNA methylation-sensitive H2A.Z loading is primarily regulated by SRCAP-C, at least in our experimental context where transcription, replication, and other epigenetic modifications are not involved. It is likely that additional mechanisms do further contribute, implicated by our sequencing experiments, particularly at regions with active transcription, and we have noted these possibilities and the rationale for their existence in the Discussion.

      Our study also suggests that a SRCAP-independent, DNA methylation-insensitive mechanism of H2A.Z loading exists, which we suspect to be mediated by Tip60-C. In line with this possibility, our data suggest that Tip60-C binds DNA in a DNA methylation-insensitive manner in Xenopus egg extract. Since antibodies to deplete Tip60-C from Xenopus egg extract are currently unavailable, we were unable to directly test that hypothesis and decided not to include Tip60-C into our final model as we lacked experimental evidence for its role. However, whether or not Tip60-C is the complex responsible for the DNA methylation-insensitive pathway does not influence our final conclusion that SRCAP-C plays a major role in DNA methylation-sensitive H2A.Z loading. We are planning to edit our manuscript to more comprehensively discuss these points.

      Please note that while Berta et al reported that DNA methylation increases at H2A.Z loci in tumors defective in SRCAP-C, they selected those regions based off where H2A.Z is typically enriched within normal tissues (Berta et al., 2021). They did not show data indicating whether H2A.Z is still retained specifically at those analyzed loci upon mutation of SRCAP-C subunits. Thus, although we greatly admire their work and are pleased that many of our findings align with theirs, their paper did not directly address whether SRCAP-C itself differentiates between DNA methylation status nor the impact that has on H2A.Z and DNA methylation colocalization. In contrast, our Xenopus egg extract system, where de novo methylation is undetectable (Nishiyama et al., 2013; Wassing et al., 2024) offers a unique opportunity to examine the direct impact of DNA methylation on H2A.Z deposition using controlled synthetic DNA substrates. Corroborated with our demonstration that DNA binding of SRCAP-C is suppressed by DNA methylation, we believe that our manuscript provides a specific mechanism that can explain the preferential deposition of H2A.Z at hypomethylated genomic regions.

      Reviewer #2 (Public review):

      This manuscript aims to elucidate the mechanistic basis for the long-standing observation that DNA methylation and the histone variant H2A.Z occupy mutually exclusive genomic regions. The authors test two hypotheses: (i) that DNA methylation intrinsically destabilizes H2A.Z nucleosomes, thereby preventing H2A.Z retention, and (ii) that DNA methylation suppresses H2A.Z deposition by ATP-dependent chromatin-remodelling complexes. However, neither hypothesis is rigorously addressed. There are experimental caveats, issues with data interpretation, and conclusions that are not supported by the data. Substantial revision and additional experiments, including controls, would be required before mechanistic conclusions can be drawn. Major concerns are as follows:

      We appreciate the critical assessment of our manuscript by this reviewer. Although we acknowledge the limitations of our study and will revise the manuscript to better describe them, we would like to respectfully argue against the statement that our "conclusions […] are not supported by the data".

      (1) The cryo-EM structure of methylated H2A.Z nucleosomes is insufficiently resolved to address the central mechanistic question: where the methylated CpGs are located relative to DNA-histone contact points and how these modifications influence H2A.Z nucleosome structure. The structure provides no mechanistic insights into methylation-induced destabilization.

      The fact that the DNA resolution in the methylated structure was not high enough to resolve the positions of methylated CpGs despite a high overall resolution of 2.78 Å implies that 1) the Sat2R-P DNA was not as stably registered as the 601L sequence, requiring us to create two alternative Sat2R-P atomic models to account for the variable positioning in our samples, and 2) that the presence of DNA methylation increases that positional variability. We understand that one may prefer to see highly resolved density around each methylation mark, but we do believe that our inability to accomplish that is actually a feature rather than a weakness and has important biological implications. The decrease in local DNA resolution on the methylated Sat2R-P structure compared to its unmethylated counterpart is meaningful and suggests to us that DNA methylation weakens overall DNA wrapping and positioning on the nucleosome, supported by the increased flexibility seen at the linker DNA ends as well as an increase in the population of highly shifted nucleosomes amongst the methylated particles. Additionally, one major view in the DNA methylation/nucleosome stability field is that the presence of DNA methylation can make DNA stiffer and harder to bend, causing opening and destabilization of nucleosomes (Ngo et al., 2016). The increased opening of linker DNA ends and accessibility of methylated H2A.Z nucleosomes in our hands also aligns with such an idea, again suggesting decreased histone-DNA contact stability on methylated DNA substrates. We plan to revise the writing in our manuscript to better reflect these ideas.

      The experimental system also lacks physiological relevance. The template DNA sequence is artificial, despite the existence of well-characterised native genomic sequences for which DNA methylation is known to inhibit H2A.Z incorporation. Alternatively, there are a number of studies examining the effect of DNA methylation on nucleosome structure, stability, DNA unwrapping, and positioning. Choosing one of these DNA sequences would have at least allowed a direct comparison with a canonical nucleosome. Indeed, a major omission is the absence of a cryo-EM structure of a canonical nucleosome assembled on the same DNA template - this is essential to assess whether the observed effects are H2A.Z-specific.

      The reviewer raises a fair question about whether canonical H2A would experience the same DNA methylation-dependent structural effects. We had considered solving the H2A structures, however, ultimately decided against it for a few reasons. First, there already exists crystal structures of canonical H2A nucleosomes using a DNA sequence highly similar to our Sat2R-P with and without the presence of DNA methylation (PDB: 5CPI and 5CPJ). The authors of this study did not see any physical differences present in their structures (Osakabe et al., 2015). Additionally, we had included canonical H2A conditions within our restriction enzyme accessibility assay and did not see a significant impact of DNA methylation on those samples (Fig 3). Because of the previous report and our own negative data, we expected that only limited additional insights would be obtained from the canonical H2A structures and decided not to pursue that analysis.

      One of the primary reasons we chose the Sat2R-P sequence was, as noted above, that there already was a published study examining how DNA methylation affects nucleosome structure using a variant of this sequence which we could compare to our results, as the reviewer has suggested. We did have to modify the sequence, namely by making it palindromic, in order to increase the final achievable resolution. We viewed the Sat2R-P sequence as an attractive candidate because it is physiologically relevant; the initial sequence was taken directly from human satellite II. Several modifications were made for technical reasons, including making the sequence palindromic as described above and also ensuring that each CpG is recognizable by a methylation-sensitive restriction enzyme so that we could be certain about the degree of methylation on our substrates. These practical concerns outweighed the necessity of maintaining a strict physiological sequence to us. However, we still believe the final Sat2R-P more closely mimics physiological sequences than Widom 601. Additionally, human satellite II is a highly abundant sequence in the human genome that is known to undergo large methylation changes on the onset of many disorders, like cancer, as well as during aging. Thus, there are interesting biological questions surrounding how the methylation state of this particular sequence affects chromatin structure. Furthermore, it has been reported that satellite II is devoid of H2A.Z (Capurso et al., 2012). Beyond those reasons, the satellite II sequence is generally interesting to our lab because we have been studying genes involved in ICF syndrome, where hypomethylation of satellite II sequences forms one of the hallmarks of this disorder (Funabiki et al., 2023; Jenness et al., 2018; Wassing et al., 2024). We understand that sequence context plays a large role in nucleosome wrapping and stability. This is why we strived to test multiple sequences in each of our assays. We do agree that it would be interesting to use DNA sequences where H2A.Z binding has already been described to be affected in a DNA methylation-dependent manner, forming an exciting future study to pursue.

      Furthermore, the DNA template is methylated at numerous random CpG sites. The authors' argument that only the global methylation level is relevant is inconsistent with the literature, which clearly demonstrates that methylation effects on canonical nucleosomes are position-dependent. Not all CpG sites contribute equally to nucleosome stability or unwrapping, and this critical factor is not considered.

      We did not argue that only the global methylation level is relevant. We also would appreciate it if the reviewer could provide specific references that "clearly demonstrates that methylation effects on canonical nucleosomes are position-dependent". We are aware of a series of studies conducted by Chongli Yuan's group, including one testing the effect of placing methylated CpGs at different positions along the Widom 601 sequence. In that study (Jimenez-Useche et al., 2013), they did find that positioning of mCpGs has differential impacts on the salt resistance of the nucleosomes, with 5 tandem mCpG copies at the dyad causing the most dramatic nucleosome opening whereas having mCpGs only at the DNA major grooves, but not elsewhere, increased nucleosome stability. However, they did also find that methylation of the original Widom 601 sequence also caused destabilization, albeit to a lesser degree, and another study by the same group (Jimenez-Useche et al., 2014) also found that CpG methylation decreased nucleosome-forming ability for all tested variants of the Widom 601 sequence, regardless of CpG density or positioning.

      Other studies monitored how distribution of methylated CpGs correlates with nucleosome positioning (Collings et al., 2013; Davey et al., 1997; Davey et al., 2004). However, these studies assessed the sequence-dependent effects specifically on nucleosome assembly during in vitro salt dialysis, which is a different physical process than the one our manuscript focuses on, especially when considering the fact that H2A.Z is deposited onto preassembled H2A-nucleosome. Our cryo-EM analysis examines the structural changes induced by DNA methylation on already formed nucleosomes rather than the process of formation. Thus, probing accessibility changes using a restriction enzyme was the more appropriate biochemical assay to verify our structures.

      We do very much agree that DNA context can influence nucleosome stability under different conditions. A study of molecular dynamics simulations concluded that the "combination of overall DNA geometrical and shape properties upon methylation" makes nucleosomes resistant to unwrapping (Li et al., 2022), while another modeling study suggests that DNA methylation impacts nucleosome stability in a manner dependent on DNA sequence, where "[s]trong binding is weakened and weak binding is strengthened" (Minary and Levitt, 2014). While G/C-dinucleotides are preferentially placed at major groove-inward positions in the nucleosomes in vivo (Chodavarapu et al., 2010; Segal et al., 2006) and G/C-rich segments are excluded from major groove-outward positions in Widom 601-like nucleosomes (Chua et al., 2012), methylated CpG dinucleotides are preferably, if not exclusively, located at major groove-outward positions in vivo. Mechanisms behind this biased mCpG positioning on the nucleosome remain speculative, likely caused by a combination of multiple factors, but the fact that we did not observe clear structural impacts using the Widom 601L sequence, where mCpGs are located at the major groove-outward and -inward positions ((Chua et al., 2012) and our structure), deserves a space for discussion. On the other hand, positioning of mCpG on satellite II-derived sequences that we used in this study was based on a physiological sequence, and thus it may not be appropriate to say that those CpGs are placed at multiple "random" positions. Although we decided not to discuss the position of 5mC on our Sat2R nucleosome structure due to ambiguous base assignments, neither of our two atomic models is consistent with an idea that DNA methylation repositions the CpG to the outward major grooves. As the potential contribution of how DNA methylation affects the nucleosome structure via modulating DNA stiffness has been extensively studied (Choy et al., 2010; Li et al., 2022; Ngo et al., 2016; Perez et al., 2012), we believe that it is appropriate to consider overall DNA properties along the whole DNA sequence, though we are willing to discuss potential positional effects in the revised manuscript.

      Perhaps one of the most important points that we did not emphasize enough in our original manuscript was that in contrast to the subtle intrinsic effect of DNA methylation that was DNA sequence dependent, we observed SRCAP-dependent preferential H2A.Z deposition to unmethylated DNA over methylated DNA in both 601 and satellite II DNAs. In the revised manuscript, we will make the value of comparative studies on 601 and satellite II in two distinct mechanisms.

      Finally, and most importantly, the reported increase in accessibility of the methylated H2A.Z nucleosome is negligible compared with the much larger intrinsic DNA accessibility of the unmethylated H2A.Z nucleosome. These data do not support the authors' hypothesis and contradict the manuscript's conclusions. Claims that methylated H2A.Z nucleosomes are "more open and accessible" must therefore be removed, and the title is misleading, given that no meaningful impact of DNA methylation on H2A.Z nucleosome stability is demonstrated.

      We respectfully disagree with this reviewer's criticism. We investigated the potential impact of DNA methylation on nucleosome stability to the best of our abilities through complementary assays and reported our observations. The effect of DNA methylation is smaller than the difference between H2A.Z and H2A, but we were able to see an effect. It is also not uncommon for small differences to have functional impacts in biological systems. We agree that further testing is required to determine whether this subtle effect is functionally important, and it remains the subject of future research due to the many technical challenges associated with addressing said question. We would like to note that 18 years have passed since Daniel Zilberman first reported the antagonistic relationship between H2AZ and DNA methylation (Zilberman et al., 2008) but very few studies have since directly tested specific mechanistic hypotheses. We believe that our study lays the groundwork for exciting future investigation that better elucidates the pathways that contribute to this antagonism and will have meaningful impacts on the field in general. However, thanks to the reviewer's criticism, we realized that we did not clearly state in the Abstract the relatively subtle effect of DNA methylation on the intrinsic H2A.Z nucleosome stability. Therefore, we will accordingly revise the Abstract to make this point clearer.

      (2) The cryo-EM structures of methylated and unmethylated 601L H2A.Z nucleosomes show no detectable differences. As presented, this negative result adds little value. If anything, it reinforces the point that the positional context of CpG methylation is critical, which the manuscript does not consider.

      We believe the inclusion and factual reporting of negative data is important for the scientific community as one of the major issues currently in biology research is biased omission of negative data. We considered eLife as a venue to publish this work for this reason. We understand that the reviewer believes our 601L structures may detract from the overall message of our manuscript. We believe this data rather emphasizes the importance of DNA sequence context, something that the reviewer also rightfully notes. It is standard practice in the nucleosome field to use the Widom 601 sequence, along with its variants. Our experience has shown that use of an artificially strong positioning sequence may mask weaker physical effects that could play a physiological role. Thus, we were careful to validate all further assays with multiple DNA sequences and believed it important to report these sequence-dependent effects on nucleosome structure.

      (3) Very little H3 signal coincides with H2A.Z at TSSs in sperm pronuclei, yet this is neither explained nor discussed (Supplementary Figure 10D). The authors need to clarify this.

      Our H3 signal, which represents the global nucleosome population, is more broadly distributed across the genome than H2A.Z, which is known to localize at specific genomic sites. Since both histone types were sequenced to similar read depths, H3 peaks are generally shallower than H2A.Z and peak heights cannot be directly compared (i.e. they should be represented in separate appropriate data ranges).

      (4) In my view, the most conceptually important finding is that H2A.Z-associated reads in sperm pronuclei show ~43% CpG methylation. This directly contradicts the model of strict mutual exclusivity and suggests that the antagonism is context-dependent. Similarly, the finding that the depletion of SRCAP reduces H2A.Z deposition only on unmethylated templates is also very intriguing. Collectively, these result warrants further investigation (see below).

      (5) Given that H2A.Z is located at diverse genomic elements (e.g., enhancers, repressed gene bodies, promoters), the manuscript requires a more rigorous genomic annotation comparing H2A.Z occupancy in sperm pronuclei versus XTC-2 cells. The authors should stratify H2A.Z-DNA methylation relationships across promoters, 5′UTRs, exons, gene bodies, enhancers, etc., as described in Supplementary Figure 10A.

      (below is response to (4) and (5) together)

      We agree that the substantial presence of co-localized H2A.Z and DNA methylation specifically in the sperm pronuclei samples and the changes in pattern between nuclear types are highly interesting and require further investigation. However, we faced technical challenges in our sequencing experiments that made us refrain from conducting a more detailed analysis for fear of over-interpreting potential artifacts. These challenges mainly stemmed from the difficulties in collecting enough material from Xenopus egg extracts and Tn5’s innate bias towards accessible regions of the genome. Because of this, open regions of the genome tend to be overrepresented in our data (as noted in our Discussion), making it challenging to rigorously compare methylation profiles and H2A.Z/H3 associated genomic elements.

      While the degree of separation seems to be dependent on nuclei type, we still believe the antagonism exists in both the sperm pronuclei and XTC-2 samples when comparing H2A.Z methylation profiles to the corresponding H3 condition. Our study also demonstrates that H2A.Z is preferentially deposited to hypomethylated DNA in a manner dependent of SRCAP-C (the loss of SRCAP only reduces H2A.Z on unmethylated substrates) but an additional methylation-insensitive H2A.Z deposition mechanism also exists. We realized that this interesting point was not clearly highlighted in Abstract, so we will revise it accordingly.

      (6) Although H2A.Z accumulates less efficiently on exogenous methylated substrates in egg extract, substantial deposition still occurs (~50%). This observation directly challenges the strong antagonistic model described in the manuscript, yet the authors do not acknowledge or discuss it. Moreover, differences between unmethylated and methylated 601 DNA raise further questions about the biological relevance of the cryo-EM 601 structures.

      As depicted in Figure 6 and described in the Discussion, we clearly indicated that both methylation-sensitive and methylation-insensitive pathways exist to deposit H2A.Z within the genome. We also directly stated in our Discussion that a substantial proportion of H2A.Z colocalizes with DNA methylation both in our study as well as in previous reports, which is of major interest for future study. Additionally, we further discussed how the absence of transcription in Xenopus eggs is a likely reason for the more limited effect of DNA methylation restricting H2A.Z deposition in our egg extract system.

      As noted in our response to (2), the lack of a clear impact on our 601L structures implies that this is due to the extraordinarily strong artificial nucleosome positioning capacity of the 601 sequence and its variants. Since 601 is heavily used in chromatin biology, including within DNA methylation research, such negative data are still useful to include and publish.

      (7) The SRCAP depletion is insufficiently validated i.e., the antibody-mediated depletion of SRCAP lacks quantitative verification. A minimum of three biological replicates with quantification is required to substantiate the claims.

      We are willing to address this concern. However, please note that our data showed that methylation-dependent H2A.Z deposition is almost completely erased upon SRCAP depletion, indicating functionally effective depletion. The specificity of the custom antibody against Xenopus SRCAP was verified by mass spectrometry. Additionally, we have obtained the same effect using another commercially available SRCAP antibody, though we did not include this preliminary result in our original manuscript. Due to its relatively low abundance and high molecular weight, SRCAP western blot signals are weak, making it challenging to quantify the degree of depletion. We also believe that the value of quantification in this context, with the points noted above, is rather limited. In the past, our lab has published papers on depleting the H3T3 kinase Haspin from Xenopus egg extracts (Ghenoiu et al., 2013; Kelly et al., 2010) but were never able to detect Haspin via western blot. This protein was only detected by mass spectrometry specifically on nucleosome array beads with H3K9me3 (Jenness et al., 2018). However, depletion of Haspin was readily monitored by erasure of H3T3ph, the enzymatic product of Haspin. In these experiments, it was impossible, and not critical, to quantitatively monitor the depletion of Haspin protein in order to investigate its molecular functions. Similarly, in this current study, the important fact is that depletion of SRCAP suppressed methylation-sensitive H2A.Z deposition and quantifying the degree of SRCAP depletion would not have a major impact on this conclusion.

      (8) It appears that the role of p400-Tip60 has been completely overlooked. This complex is the second major H2A.Z deposition complex. Because p400 exhibits DNA methylation-insensitive binding (Supplementary Figure 14), it may account for the deposition of H2A.Z onto methylated DNA. This possibility is highly significant and must be addressed by repeating the key experiments in Figure 5 following p400-Tip60 depletion.

      We are aware that the Tip60 complex is a very likely candidate for mediating DNA methylation-insensitive H2A.Z deposition, which is why we tested whether DNA binding of p400 is methylation sensitive. Therefore, the reviewer's statement that we "completely overlooked" Tip60-C’s role does not fairly report on our efforts. We wished to test the potential contribution of Tip60-C, but, unfortunately, the antibodies we currently have available to us were not successful in depleting the complex from egg extract. Since we had no direct experimental evidence indicating the role Tip60-C plays, we decided to take a conservative approach to our model and leave the methylation-insensitive pathway as mediated by something still unidentified. While further investigating Tip60-C’s contribution to this pathway is of definite value, we do not believe that it impacts our major conclusion that SRCAP-C is the main mediator responsible for H2A.Z deposition on unmethylated DNA and thus remains a subject for future study.

      (9) The manuscript repeatedly states that H2A.Z nucleosomes are intrinsically unstable; however, this is an oversimplification. Although some DNA unwrapping is observed, multiple studies show that H3/H4 tetramer-H2A.Z/H2B interactions are more stable (important recent studies include the following: DOI: 10.1038/s41594-021-00589-3; 10.1038/s41467-021-22688-x; and reviewed in 10.1038/s41576-024-00759-1).

      We understand that the H2A.Z stability field is highly controversial. We have introduced the many conflicting reports that have been published in the field but can further expand on the controversies if desired. We also understand that the term “nucleosome stability” is broad and encompasses many physical aspects. As noted in a prior response, we will better specify our use of the term within the manuscript. In our assays, we are most focused on the DNA wrapping stability of the nucleosome and have consistently seen in our hands that H2A.Z nucleosomes are much more open and accessible compared to canonical H2A on satellite II-derived sequences, regardless of methylation status. However, we do understand that many groups have observed the opposite findings while others have obtained results similar to us. We reported on our findings of the general H2A.Z stability with the hopes to help clarify some of the field’s controversies.

      In summary, the current manuscript does not present a convincing mechanistic explanation for the antagonism between DNA methylation and H2A.Z. The observation that H2A.Z can substantially coexist with DNA methylation in sperm pronuclei, perhaps, should be the conceptual focus.

      We appreciate this reviewer’s advice. However, please note that the first author who led this project has already successfully defended their PhD thesis primarily based on this project, making it impractical and unrealistic to completely change the focus of this manuscript to include an entirely new avenue of research. We believe that our data provide important insights into the mechanisms by which H2A.Z is excluded from methylated DNA, particularly via the DNA methylation-sensitive binding of SRCAP-C, which has never been described before. We agree that many questions are still left unanswered, including the exact molecular mechanism behind how DNA methylation prevents SRCAP-C binding. We have preliminary data that suggest none of the known DNA-binding modules of SRCAP-C, including ZNHIT1, by themselves can explain this sensitivity. This implies that domain dissection in the context of the holo-SRCAP complex is required to fully address this question. We believe this represents a very exciting future avenue of study; however, it does not negate our finding that SRCAP-C itself is important for maintaining the DNA methylation/H2A.Z antagonism. Therefore, we respectfully disagree with this reviewer's summary statement, which misleadingly undermines the impact of our work.

      Reviewer #3 (Public review):

      Summary:

      Histone variant H2A.Z is evolutionarily conserved among various species. The selective incorporation and removal of histone variants on the genome play crucial roles in regulating nuclear events, including transcription. Shih et al. aimed to address antagonistic mechanisms between histone variant H2A.Z deposition and DNA methylation. To this end, the authors reconstituted H2A.Z nucleosomes in vitro using methylated or unmethylated human satellite II DNA sequence and examined how DNA methylation affects H2A.Z nucleosome structure and dynamics. The cryo-EM analysis revealed that DNA methylation induces a more open conformation in H2A.Z nucleosomes. Consistent with this, their biochemical assays showed that DNA methylation subtly increases restriction enzyme accessibility in H2A.Z nucleosomes compared with canonical H2A nucleosomes. The authors identified genome-wide profiles of H2A.Z and DNA methylation using genomic assays and found their unique distribution between Xenopus sperm pronuclei and fibroblast cells. Using Xenopus egg extract systems, the authors showed SRCAP complex, the chromatin remodelers for H2A.Z deposition, preferentially deposit H2A.Z on unmethylated DNA.

      Strengths:

      The study is solid, and most conclusions are well-supported. The experiments are rigorously performed, and interpretations are clear. The study presents a high-resolution cryo-EM structure of human H2A.Z nucleosome with methylated DNA. The discovery that the SRCAP complex senses DNA methylation is novel and provides important mechanistic insight into the antagonism between H2A.Z and DNA methylation.

      We are grateful that this reviewer recognizes the importance of our study.

      Weaknesses:

      The study is already strong, and most conclusions are well supported. However, it can be further strengthened in several ways.

      (1) It is difficult to interpret how DNA methylation alters the orientation of the H4 tail and leads to the additional density on the acidic patch. The data do not convincingly support whether DNA methylation enhances interactions with H2A.Z mono-nucleosomes, nor whether this effect is specific to methylated H2A.Z nucleosomes.

      The altered H4 tail orientation and extra density seen on the acidic patch were incidental findings that we thought could be interesting for the field to be aware of but decided not to follow up on as there were other structural differences that were more directly related to our central question. We do believe that the above two differences are linked to each other because we used a highly purified and homogenous sample for cryo-EM analysis and the H4 tail/acidic patch interaction is a well characterized contact that mediates inter-nucleosome interactions. Additionally, other groups have reported that the presence of DNA methylation causes condensation of both chromatin and bare DNA (cited within our manuscript), though the mechanics behind this phenomenon remain to be elucidated. We believed that our structure data may also align with those findings. However, the reviewer is fair in pointing out that we do not provide further experimental evidence in verifying the existence of these increased interactions. We can revise our writing to clarify that these points are currently hypotheses rather than validated results.

      (2) It remains unclear whether DNA methylation alters global H2A.Z nucleosome stability or primarily affects local DNA end flexibility. Moreover, while the authors showed locus-specific accessibility by HinfI digestion, an unbiased assay such as MNase digestion would strengthen the conclusions.

      We would like to thank the reviewer for bringing up these issues. Although our current data cannot explicitly clarify these possibilities, we favor an idea that DNA methylation specifically alters histone to DNA contacts and that this effect is felt globally across the entire nucleosome rather than only at specific locations. The intrinsic flexibility of linker DNA ends means that that region tends to exhibit the greatest differences under different physical influences, hence the focus on characterizing that area; flexibility of a thread on a spool is most pronounced at the ends. However, we also found that the DNA backbone of H2A.Z on methylated DNA had a lower local resolution compared to its unmethylated counterpart, despite that structure having a higher global resolution, which suggested to us that DNA positioning along the nucleosome is overall weaker under the presence of DNA methylation. This is corroborated by the increased population of open/shifted structures in our classification analysis. The reviewer raises a fair point about the use of a specific restriction enzyme versus MNase. We agree that our accessibility assay is highly influenced by the position of the restriction site and have previously seen that moving the cut site too close to the linker DNA end will abolish any DNA methylation-dependent differences. We did initially attempt an MNase digestion-based assay, but the data were not as reproducible as with the use of a specific restriction enzyme. We do not know the reason behind this irreproducibility though we believe that the processivity of MNase could make it difficult to capture subtle effects like those induced by DNA methylation on already highly accessible H2A.Z nucleosomes. Overall, while we believe that DNA methylation does exert a physical effect, its subtlety may explain the many contradictory studies present within the DNA methylation and nucleosome stability field.

      References

      Berta, D.G., H. Kuisma, N. Valimaki, M. Raisanen, M. Jantti, A. Pasanen, A. Karhu, J. Kaukomaa, A. Taira, T. Cajuso, S. Nieminen, R.M. Penttinen, S. Ahonen, R. Lehtonen, M. Mehine, P. Vahteristo, J. Jalkanen, B. Sahu, J. Ravantti, N. Makinen, K. Rajamaki, K. Palin, J. Taipale, O. Heikinheimo, R. Butzow, E. Kaasinen, and L.A. Aaltonen. 2021. Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma. Nature. 596:398–403.

      Capurso, D., H. Xiong, and M.R. Segal. 2012. A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome. BMC Genomics. 13:630.

      Chodavarapu, R.K., S. Feng, Y.V. Bernatavichute, P.Y. Chen, H. Stroud, Y. Yu, J.A. Hetzel, F. Kuo, J. Kim, S.J. Cokus, D. Casero, M. Bernal, P. Huijser, A.T. Clark, U. Kramer, S.S. Merchant, X. Zhang, S.E. Jacobsen, and M. Pellegrini. 2010. Relationship between nucleosome positioning and DNA methylation. Nature. 466:388–392.

      Choy, J.S., S. Wei, J.Y. Lee, S. Tan, S. Chu, and T.H. Lee. 2010. DNA methylation increases nucleosome compaction and rigidity. J Am Chem Soc. 132:1782–1783.

      Chua, E.Y., D. Vasudevan, G.E. Davey, B. Wu, and C.A. Davey. 2012. The mechanics behind DNA sequence-dependent properties of the nucleosome. Nucleic Acids Res. 40:6338–6352.

      Collings, C.K., P.J. Waddell, and J.N. Anderson. 2013. Effects of DNA methylation on nucleosome stability. Nucleic Acids Res. 41:2918–2931.

      Davey, C., S. Pennings, and J. Allan. 1997. CpG methylation remodels chromatin structure in vitro. J Mol Biol. 267:276–288.

      Davey, C.S., S. Pennings, C. Reilly, R.R. Meehan, and J. Allan. 2004. A determining influence for CpG dinucleotides on nucleosome positioning in vitro. Nucleic Acids Res. 32:4322–4331.

      Funabiki, H., I.E. Wassing, Q. Jia, J.D. Luo, and T. Carroll. 2023. Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases. Elife. 12.

      Ghenoiu, C., M.S. Wheelock, and H. Funabiki. 2013. Autoinhibition and polo-dependent multisite phosphorylation restrict activity of the histone h3 kinase haspin to mitosis. Mol Cell. 52:734–745.

      Jenness, C., S. Giunta, M.M. Muller, H. Kimura, T.W. Muir, and H. Funabiki. 2018. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc Natl Acad Sci U S A. 115:E876–E885.

      Jimenez-Useche, I., J. Ke, Y. Tian, D. Shim, S.C. Howell, X. Qiu, and C. Yuan. 2013. DNA methylation regulated nucleosome dynamics. Sci Rep. 3:2121.

      Jimenez-Useche, I., D. Shim, J. Yu, and C. Yuan. 2014. Unmethylated and methylated CpG dinucleotides distinctively regulate the physical properties of DNA. Biopolymers. 101:517–524.

      Kelly, A.E., C. Ghenoiu, J.Z. Xue, C. Zierhut, H. Kimura, and H. Funabiki. 2010. Survivin reads phosphorylated histone H3 threonine 3 to activate the mitotic kinase Aurora B. Science. 330:235–239.

      Li, S., Y. Peng, D. Landsman, and A.R. Panchenko. 2022. DNA methylation cues in nucleosome geometry, stability and unwrapping. Nucleic Acids Res. 50:1864–1874.

      Minary, P., and M. Levitt. 2014. Training-free atomistic prediction of nucleosome occupancy. Proc Natl Acad Sci U S A. 111:6293–6298.

      Ngo, T.T., J. Yoo, Q. Dai, Q. Zhang, C. He, A. Aksimentiev, and T. Ha. 2016. Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. Nat Commun. 7:10813.

      Nishiyama, A., L. Yamaguchi, J. Sharif, Y. Johmura, T. Kawamura, K. Nakanishi, S. Shimamura, K. Arita, T. Kodama, F. Ishikawa, H. Koseki, and M. Nakanishi. 2013. Uhrf1-dependent H3K23 ubiquitylation couples maintenance DNA methylation and replication. Nature. 502:249–253.

      Osakabe, A., F. Adachi, Y. Arimura, K. Maehara, Y. Ohkawa, and H. Kurumizaka. 2015. Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biol. 5.

      Perez, A., C.L. Castellazzi, F. Battistini, K. Collinet, O. Flores, O. Deniz, M.L. Ruiz, D. Torrents, R. Eritja, M. Soler-Lopez, and M. Orozco. 2012. Impact of methylation on the physical properties of DNA. Biophys J. 102:2140–2148.

      Segal, E., Y. Fondufe-Mittendorf, L. Chen, A. Thastrom, Y. Field, I.K. Moore, J.P. Wang, and J. Widom. 2006. A genomic code for nucleosome positioning. Nature. 442:772–778.

      Wassing, I.E., A. Nishiyama, R. Shikimachi, Q. Jia, A. Kikuchi, M. Hiruta, K. Sugimura, X. Hong, Y. Chiba, J. Peng, C. Jenness, M. Nakanishi, L. Zhao, K. Arita, and H. Funabiki. 2024. CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes. Sci Adv. 10:eadp5753.

      Zilberman, D., D. Coleman-Derr, T. Ballinger, and S. Henikoff. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456:125–129.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      The Reviewer structured their review such that their first two recommendations specifically concerned the two major weaknesses they viewed in the initial submission. For clarity and concision, we have copied their recommendations to be placed immediately following their corresponding points on weaknesses.

      Strengths:

      Studying prediction error from the lens of network connectivity provides new insights into predictive coding frameworks. The combination of various independent datasets to tackle the question adds strength, including two well-powered fMRI task datasets, resting-state fMRI interpreted in relation to behavioral measures, as well as EEG-fMRI.

      Weaknesses:

      Major:

      (R1.1) Lack of multiple comparisons correction for edge-wise contrast:

      The analysis of connectivity differences across three levels of prediction error was conducted separately for approximately 22,000 edges (derived from 210 regions), yet no correction for multiple comparisons appears to have been applied. Then, modularity was applied to the top 5% of these edges. I do not believe that this approach is viable without correction. It does not help that a completely separate approach using SVMs was FDR-corrected for 210 regions.

      [Later recommendation] Regarding the first major point: To address the issue of multiple comparisons in the edge-wise connectivity analysis, I recommend using the Network-Based Statistic (NBS; Zalesky et al., 2010). NBS is well-suited for identifying clusters (analogous to modules) of edges that show statistically significant differences across the three prediction error levels, while appropriately correcting for multiple comparisons.

      Thank you for bringing this up. We acknowledge that our modularity analysis does not evaluate statistical significance. Originally, the modularity analysis was meant to provide a connectome-wide summary of the connectivity effects, whereas the classification-based analysis was meant to address the need for statistical significance testing. However, as the reviewer points out, it would be better if significance were tested in a manner more analogous to the reported modules. As they suggest, we updated the Supplemental Materials (SM) to include the results of Network-Based Statistic analysis (SM p. 1-2):

      “(2.1) Network-Based Statistic

      Here, we evaluate whether PE significantly impacts connectivity at the network level using the Network-Based Statistic (NBS) approach.[1] NBS relied on the same regression data generated for the main-text analysis, whereby a regression is performed examining the effect of PE (Low = –1, Medium = 0, High = +1) on connectivity for each edge. This was done across the connectome, and for each edge, a z-score was computed. For NBS, we thresholded edges to |Z| > 3.0, which yielded one large network cluster, shown in Figure S3. The size of the cluster – i.e., number of edges – was significant (p < .05) per a permutation-test using 1,000 random shuffles of the condition data for each participant, as is standard.[1] These results demonstrate that the networklevel effects of PE on connectivity are significant. The main-text modularity analysis converts this large cluster into four modules, which are more interpretable and open the door to further analyses”.

      We updated the Results to mention these findings before describing the modularity analysis (p. 8-9):

      “After demonstrating that PE significantly influences brain-wide connectivity using Network-Based Statistic analysis (Supplemental Materials 2.1), we conducted a modularity analysis to study how specific groups of edges are all sensitive to high/low-PE information.”

      (R1.2) Lack of spatial information in EEG:

      The EEG data were not source-localized, and no connectivity analysis was performed. Instead, power fluctuations were averaged across a predefined set of electrodes based on a single prior study (reference 27), as well as across a broader set of electrodes. While the study correlates these EEG power fluctuations with fMRI network connectivity over time, such temporal correlations do not establish that the EEG oscillations originate from the corresponding network regions. For instance, the observed fronto-central theta power increases could plausibly originate from the dorsal anterior cingulate cortex (dACC), as consistently reported in the literature, rather than from a distributed network. The spatially agnostic nature of the EEG-fMRI correlation approach used here does not support interpretations tied to specific dorsal-ventral or anterior-posterior networks. Nonetheless, such interpretations are made throughout the manuscript, which overextends the conclusions that can be drawn from the data.

      [Later recommendation] Regarding the second major point: I suggest either adopting a source-localized EEG approach to assess electrophysiological connectivity or revising all related sections to avoid implying spatial specificity or direct correspondence with fMRI-derived networks. The current approach, which relies on electrode-level power fluctuations, does not support claims about the spatial origin of EEG signals or their alignment with specific connectivity networks.

      We thank the reviewer for this important point, which allows us to clarify the specific and distinct contributions of each imaging modality in our study. Our primary goal for Study 3 was to leverage the high temporal resolution of EEG to identify the characteristic frequency at which the fMRI-defined global connectivity states fluctuate. The study was not designed to infer the spatial origin of these EEG signals, a task for which fMRI is better suited and which we addressed in Studies 1 and 2.

      As the reviewer points out, fronto-central theta is generally associated with the dACC. We agree with this point entirely. We suspect that there is some process linking dACC activation to the identified network fluctuations – some type of relationship that does not manifest in our dynamic functional connectivity analyses – although this is only a hypothesis and one that is beyond the present scope.

      We updated the Discussion to mention these points and acknowledge the ambiguity regarding the correlation between network fluctuation amplitude (fMRI) and Delta/Theta power (EEG) (p. 24):

      “We specifically interpret the fMRI-EEG correlation as reflecting fluctuation speed because we correlated EEG oscillatory power with the fluctuation amplitude computed from fMRI data. Simply correlating EEG power with the average connectivity or the signed difference between posterior-anterior and ventral-dorsal connectivity yields null results (Supplemental Materials 6), suggesting that this is a very particular association, and viewing it as capturing fluctuation amplitude provides a parsimonious explanation. Yet, this correlation may be interpreted in other ways. For example, resting-state Theta is also a signature of drowsiness,[2] which may correlate with PE processing, but perhaps should be understood as some other mechanism. Additionally, Theta is widely seen as a sign of dorsal anterior cingulate cortex activity,3 and it is unclear how to reconcile this with our claims about network fluctuations. Nonetheless, as we show with simulations (Supplemental Materials 5), a correlation between slow fMRI network fluctuations and fast EEG Delta/Theta oscillations is also consistent with a common global neural process oscillating rapidly and eliciting both measures.”

      Regarding source-localization, several papers have described known limitations of this strategy for drawing precise anatomical inferences,[4–6] and this seems unnecessary given that our fMRI analyses already provide more robust anatomical precision. We intentionally used EEG in our study for what it measures most robustly: millisecond-level temporal dynamics.

      (R1.2a)Examples of problematic language include:

      Line 134: "detection of network oscillations at fast speeds" - the current EEG approach does not measure networks.

      This is an important issue. We acknowledge that our EEG approach does not directly measure fMRI-defined networks. Our claim is inferential, designed to estimate the temporal dynamics of the large-scale fMRI patterns we identified. The correlation between our fMRI-derived fluctuation amplitude (|PA – VD|) and 3-6 Hz EEG power provides suggestive evidence that the transitions between these network states occur at this frequency, rather than being a direct measurement of network oscillations.

      To support the validity of this inference, we performed two key analyses (now in Supplemental Materials). First, a simulation study provides a proof-of-concept, confirming our method can recover the frequency of a fast underlying oscillator from slow fMRI and fast EEG data. Second, a specificity analysis shows the EEG correlation is unique to our measure of fluctuation amplitude and not to simpler measures like overall connectivity strength. These analyses demonstrate that our interpretation is more plausible than alternative explanations.

      Overall, we have revised the manuscript to be more conservative in the language employed, such as presenting alternative explanations to the interpretations put forth based on correlative/observational evidence (e.g., our modifications above described in our response to comment R1.2). In addition, we have made changes throughout the report to state the issues related to reverse inference more explicitly and to better communicate that the evidence is suggestive – please see our numerous changes described in our response to comment R3.1. For the statement that the reviewer specifically mentioned here, we revised it to be more cautious (p. 7):

      “Although such speed outpaces the temporal resolution of fMRI, correlating fluctuations in dynamic connectivity measured from fMRI data with EEG oscillations can provide an estimate of the fluctuations’ speed. This interpretation of a correlation again runs up against issues related to reverse inference but would nonetheless serve as initial suggestive evidence that spontaneous transitions between network states occur rapidly.”

      (R1.2b) Line 148: "whether fluctuations between high- and low-PE networks occur sufficiently fast" - this implies spatial localization to networks that is not supported by the EEG analysis.

      Building on our changes described in our immediately prior response, we adjusted our text here to say our analyses searched for evidence consistent with the idea that the network fluctuations occur quickly rather than searching for decisive evidence favoring this idea (p. 7-8):

      “Finally, we examined rs-fMRI-EEG data to assess whether we find parallels consistent with the high/low-PE network fluctuations occurring at fast timescales suitable for the type of cognitive operations typically targeted by PE theories.”

      (R1.2c) Line 480: "how underlying neural oscillators can produce BOLD and EEG measurements" - no evidence is provided that the same neural sources underlie both modalities.

      As described above, these claims are based on the simulation study demonstrating that this is a possibility, and we have revised the manuscript overall to be clearer that this is our interpretation while providing alternative explanations.

      Reviewer #2 (Public review):

      Strengths:

      Clearly, a lot of work and data went into this paper, including 2 task-based fMRI experiments and the resting state data for the same participants, as well as a third EEG-fMRI dataset. Overall, well written with a couple of exceptions on clarity, as per below, and the methodology appears overall sound, with a couple of exceptions listed below that require further justification. It does a good job of acknowledging its own weakness.

      Weaknesses:

      (R2.1) The paper does a good job of acknowledging its greatest weakness, the fact that it relies heavily on reverse inference, but cannot quite resolve it. As the authors put it, "finding the same networks during a prediction error task and during rest does not mean that the networks' engagement during rest reflects prediction error processing". Again, the authors acknowledge the speculative nature of their claims in the discussion, but given that this is the key claim and essence of the paper, it is hard to see how the evidence is compelling to support that claim.

      We thank the reviewer for this comment. We agree that reverse inference is a fundamental challenge and that our central claim requires a particularly high bar of evidence. While no single analysis resolves this issue, our goal was to build a cumulative case that is compelling by converging on the same conclusion from multiple, independent lines of evidence.

      For our investigation, we initially established a task-general signature of prediction error (PE). By showing the same neural pattern represents PE in different contexts, we constrain the reverse inference, making it less likely that our findings are a task-specific artifact and more likely that they reflect the core, underlying process of PE. Building on this, our most compelling evidence comes from linking task and rest at the individual level. We didn't just find the same general network at rest; we showed that an individual’s unique anatomical pattern of PE-related connectivity during the task specifically predicts their own brain's fluctuation patterns at rest. This highly specific, person-by-person correspondence provides a direct bridge between an individual's task-evoked PE processing and their intrinsic, resting-state dynamics. Furthermore, these resting-state fluctuations correlate specifically with the 3-6 Hz theta rhythm—a well-established neural marker for PE.

      While reverse inference remains a fundamental limitation for many studies on resting-state cognition, the aspects mentioned above, we believe, provide suggestive evidence, favoring our PE interpretation. Nonetheless, we have made changes throughout the manuscript to be more conservative in the language we use to describe our results, to make it clear what claims are based on correlative/observational evidence, and to put forth alternative explanations for the identified effects. Please find our numerous changes detailed in our response to comment R3.1.

      (R2.2) Given how uncontrolled cognition is during "resting-state" experiments, the parallel made with prediction errors elicited during a task designed for that effect is a little difficult to make. How often are people really surprised when their brains are "at rest", likely replaying a previously experienced event or planning future actions under their control? It seems to be more likely a very low prediction error scenario, if at all surprising.

      We (and some others) take a broad interpretation of PE and believe it is often more intuitive to think about PE minimization in terms of uncertainty rather than “surprise”; the word “surprise” usually implies a sudden emotive reaction from the violation of expectations, which is not useful here.

      When planning future actions, each step of the plan is spurred by the uncertainty of what is the appropriate action given the scenario set up by prior steps. Each planned step erases some of that uncertainty. For example, you may be mentally simulating a conversation, what you will say, and what another person will say. Each step of this creates uncertainty of “what is the appropriate response?” Each reasoning step addresses contingencies. While planning, you may also uncover more obvious forms of uncertainty, sparking memory retrieval to finish it. A resting-state participant may think to cook a frozen pizza when they arrive home, but be uncertain about whether they have any frozen pizzas left, prompting episodic memory retrieval to address this uncertainty. We argue that every planning step or memory retrieval can be productively understood as being sparked by uncertainty/surprise (PE), and the subsequent cognitive response minimizes this uncertainty.

      We updated the Introduction to include a paragraph near the start providing this explanation (p. 3-4):

      “PE minimization may broadly coordinate brain functions of all sorts, including abstract cognitive functions. This includes the types of cognitive processes at play even in the absence of stimuli (e.g., while daydreaming). While it may seem counterintuitive to associate this type of cognition with PE – a concept often tied to external surprises – it has been proposed that the brain's internal generative model is continuously active.[12–14] Spontaneous thought, such as planning a future event or replaying a memory, is not a passive, low-PE process. Rather, it can be seen as a dynamic cycle of generating and resolving internal uncertainty. While daydreaming, you may be reminded of a past conversation, where you wish you had said something different. This situation contains uncertainty about what would have been the best thing to say. Wondering about what you wish you said can be viewed as resolving this uncertainty, in principle, forming a plan if the same situation ever arises again in the future. Each iteration of the simulated conversation repeatedly sparks and then resolves this type of uncertainty.”

      (R2.3)The quantitative comparison between networks under task and rest was done on a small subset of the ROIs rather than on the full network - why? Noting how small the correlation between task and rest is (r=0.021) and that's only for part of the networks, the evidence is a little tenuous. Running the analysis for the full networks could strengthen the argument.

      We thank the reviewer for this opportunity to clarify our method. A single correlation between the full, aggregated networks would be conceptually misaligned with what we aimed to assess. To test for a personspecific anatomical correspondence, it is necessary to examine the link between task and rest at a granular level. We therefore asked whether the specific parts of an individual's network most responsive to PE during the task are the same parts that show the strongest fluctuations at rest. Our analysis, performed iteratively across all 3,432 possible ROI subsets, was designed specifically to answer this question, which would be obscured by an aggregated network measure.

      We appreciate the reviewer's concern about the modest effect size (r = .021). However, this must be contextualized, as the short task scan has very low reliability (.08), which imposes a severe statistical ceiling on any possible task-rest correlation. Finding a highly significant effect (p < .001) in the face of such noisy data, therefore, provides robust evidence for a genuine task-rest correspondence.

      We updated the Discussion to discuss this point (p. 22-23):

      “A key finding supporting our interpretation is the significant link between individual differences in task-evoked PE responses and resting-state fluctuations. One might initially view the effect size of this correspondence (r = .021) as modest. However, this interpretation must be contextualized by the considerable measurement noise inherent in short task-fMRI scans; the split-half reliability of the task contrast was only .08. This low reliability imposes a severe statistical ceiling on any possible task-rest correlation. Therefore, detecting a highly significant (p < .001) relationship despite this constraint provides robust evidence for a genuine link. Furthermore, our analytical approach, which iteratively examined thousands of ROI subsets rather than one aggregated network, was intentionally granular. The goal was not simply to correlate two global measures, but to test for a personspecific anatomical correspondence – that is, whether the specific parts of an individual's network most sensitive to PE during the task are the same parts that fluctuate most strongly at rest. An aggregate analysis would obscure this critical spatial specificity. Taken together, this granular analysis provides compelling evidence for an anatomically consistent fingerprint of PE processing that bridges task-evoked activity and spontaneous restingstate dynamics, strengthening our central claim.”

      (R2.4) Looking at the results in Figure 2C, the four-quadrant description of the networks labelled for low and high PE appears a little simplistic. The authors state that this four-quadrant description omits some ROIs as motivated by prior knowledge. This would benefit from a more comprehensive justification.Which ROIs are excluded, and what is the evidence for exclusion?

      Our four-quadrant model is a principled simplification designed to distill the dominant, large-scale connectivity patterns from the complex modularity results. This approach focuses on coherent, well-documented anatomical streams while setting aside a few anatomically distant and disjoint ROIs that were less central to the main modules. This heuristic additionally unlocks more robust and novel analyses.

      The two low-PE posterior-anterior (PA) pathways are grounded in canonical processing streams. (i) The OCATL connection mirrors the ventral visual stream (the “what” pathway), which is fundamental for object recognition and is upregulated during the smooth processing of expected stimuli. (ii) The IPL-LPFC connection represents a core axis of the dorsal attention stream and the Fronto-Parietal Control Network (FPCN), reflecting the maintenance of top-down cognitive control when information is predictable; the IPL-LPFC module excludes ROIs in the middle temporal gyrus, which are often associated with the FPCN but are not covered here.

      In contrast, the two high-PE ventral-dorsal (VD) pathways reflect processes for resolving surprise and conflict. (i) The OC-IPL connection is a classic signature of attentional reorienting, where unexpected sensory input (high PE) triggers a necessary shift in attention; the OC-IPL module excludes some ROIs that are anterior to the occipital lobe and enter the fusiform gyrus and inferior temporal lobe. (ii) The ATL-LPFC connection aligns with mechanisms for semantic re-evaluation, engaging prefrontal control regions to update a mental model in the face of incongruent information.

      Beyond its functional/anatomical grounding, this simplification provides powerful methodological and statistical advantages. It establishes a symmetrical framework that makes our dynamic connectivity analyses tractable, such as our “cube” analysis of state transitions, which required overlapping modules. Critically, this model also offers a statistical safeguard. By ensuring each quadrant contributes to both low- and high-PE connectivity patterns, we eliminate confounds like region-specific signal variance or global connectivity. This design choice isolates the phenomenon to the pattern of connectivity itself (posterior-anterior vs. ventral-dorsal), making our interpretation more robust.

      We updated the end of the Study 1A results (p. 10-11):

      “Some ROIs appear in Figure 2C but are excluded from the four targeted quadrants (Figures 2C & 2D) – e.g., posterior inferior temporal lobe and fusiform ROIs are excluded from the OC-IPL module, and middle temporal gyrus ROIs are excluded from the IPL-LPFC modules. These exclusions, in favor of a four-quadrant interpretation, are motivated by existing knowledge of prominent structural pathways among these quadrants. This interpretation is also supported by classifier-based analyses showing connectivity within each quadrant is significantly influenced by PE (Supplemental Materials 2.2), along with analyses of single-region activity showing that these areas also respond to PE independently (Supplemental Materials 3). Hence, we proceeded with further analyses of these quadrants’ connections, which summarize PE’s global brain effects.

      “This four-quadrant setup also imparts analytical benefits. First, this simplified structure may better generalize across PE tasks, and Study 1B would aim to replicate these results with a different design. Second, the four quadrants mean that each ROI contributes to both the posterior-anterior and ventral-dorsal modules, which would benefit later analyses and rules out confounds such as PE eliciting increased/decreased connectivity between an ROI and the rest of the brain. An additional, less key benefit is that this setup allows more easily evaluating whether the same phenomena arise using a different atlas (Supplemental Materials Y).”

      (R2.5) The EEG-fMRI analysis claiming 3-6Hz fluctuations for PE is hard to reconcile with the fact that fMRI captures activity that is a lot slower, while some PEs are as fast as 150 ms. The discussion acknowledges this but doesn't seem to resolve it - would benefit from a more comprehensive argument.

      We thank the reviewer for raising this important point, which allows us to clarify the logic of our multimodal analysis. Our analysis does not claim that the fMRI BOLD signal itself oscillates at 3-6 Hz. Instead, it is based on the principle that the intensity of a fast neural process can be reflected in the magnitude of the slow BOLD response. It’s akin to using a long-exposure photograph to capture a fast-moving object; while the individual movements are blurred, the intensity of the blur in the photo serves as a proxy for the intensity of the underlying motion. In our case, the magnitude of the fMRI network difference (|PA – VD|) acts as the "blur," reflecting the intensity of the rapid fluctuations between states within that time window.

      Following this logic, we correlated this slow-moving fMRI metric with the power of the fast EEG rhythms, which reflects their amplitude. To bridge the different timescales, we averaged the EEG power over each fMRI time window and convolved it with the standard hemodynamic response function (HRF) – a crucial step to align the timing of the neural and metabolic signals. The resulting significant correlation specifically in the 3-6 Hz band demonstrates that when this rhythm is stronger, the fMRI data shows a greater divergence between network states. This allows us to infer the characteristic frequency of the underlying neural fluctuations without directly measuring them at that speed with fMRI, thus reconciling the two timescales.

      Reviewer #3 (Public review):

      Bogdan et al. present an intriguing and timely investigation into the intrinsic dynamics of prediction error (PE)-related brain states. The manuscript is grounded in an intuitive and compelling theoretical idea: that the brain alternates between high and low PE states even at rest, potentially reflecting an intrinsic drive toward predictive minimization. The authors employ a creative analytic framework combining different prediction tasks and imaging modalities. They shared open code, which will be valuable for future work.

      (R3.1) Consistency in Theoretical Framing

      The title, abstract, and introduction suggest inconsistent theoretical goals of the study.

      The title suggests that the goal is to test whether there are intrinsic fluctuations in high and low PE states at rest. The abstract and introduction suggest that the goal is to test whether the brain intrinsically minimizes PE and whether this minimization recruits global brain networks. My comments here are that a) these are fundamentally different claims, and b) both are challenging to falsify. For one, task-like recurrence of PE states during resting might reflect the wiring and geometry of the functional organization of the brain emerging from neurobiological constraints or developmental processes (e.g., experience), but showing that mirroring exists because of the need to minimize PE requires establishing a robust relationship with behavior or showing a causal effect (e.g., that interrupting intrinsic PE state fluctuations affects prediction).

      The global PE hypothesis-"PE minimization is a principle that broadly coordinates brain functions of all sorts, including abstract cognitive functions"-is more suitable for discussion rather than the main claim in the abstract, introduction, and all throughout the paper.

      Given the above, I recommend that the authors clarify and align their core theoretical goals across the title, abstract, introduction, and results. If the focus is on identifying fluctuations that resemble taskdefined PE states at rest, the language should reflect that more narrowly, and save broader claims about global PE minimization for the discussion. This hypothesis also needs to be contextualized within prior work. I'd like to see if there is similar evidence in the literature using animal models.

      Thank you for bringing up this issue. We have made changes throughout the paper to address these points. First, we have omitted reference to a “global PE hypothesis” from the Abstract and Introduction, in favor of structuring the Introduction in terms of a falsifiable question (p. 4):

      “We pursued this goal using three studies (Figure 1) that collectively targeted a specific question: Do the taskdefined connectivity signatures of high vs. low PE also recur during rest, and if so, how does the brain transition between exhibiting high/low signatures?”

      We made changes later in the Introduction to clarify that the investigation is based on correlative evidence and requires interpretations that may be debated (p. 5-7):

      “Although this does not entirely address the reverse inference dilemma and can only produce correlative evidence, the present research nonetheless investigates these widely speculated upon PE ideas more directly than any prior work.

      Although such speed outpaces the temporal resolution of fMRI, correlating fluctuations in dynamic connectivity measured from fMRI data with EEG oscillations can provide an estimate of the fluctuations’ speed. This interpretation of a correlation again runs up against issues related to reverse inference but would nonetheless serve as initial suggestive evidence that spontaneous transitions between network states occur rapidly.

      Second, we examined the recruitment of these networks during rs-fMRI, and although the problems related to reverse inference are impossible to overcome fully, we engage with this issue by linking rs-fMRI data directly to task-fMRI data of the same participants, which can provide suggestive evidence that the same neural mechanisms are at play in both.”

      We made changes throughout the Results now better describing the results as consistent with a hypothesis rather than demonstrating it (p. 12-19):

      “In other words, we essentially asked whether resting-state participants are sometimes in low PE states and sometimes in high PE states, which would be consistent with spontaneous PE processing in the absence of stimuli.

      These emerging states overlap strikingly with the previous task effects of PE, suggesting that rs-fMRI scans exhibit fluctuations that resemble the signatures of low- and high-PE states. 

      To be clear, this does not entirely dissuade concerns about reverse inference, which would require a type of causal manipulation that is difficult (if not impossible) to perform in a resting state scan. Nonetheless, these results provide further evidence consistent with our interpretation that the resting brain spontaneously fluctuates between high/low PE network states.

      These patterns are most consistent with a characteristic timescale near 3–6 Hz for the amplitude of the putative high/low-PE fluctuations. This is notably consistent with established links between PE and Delta/Theta and is further consistent with an interpretation in which these fluctuations relate to PE-related processing during rest.”

      We have also made targeted edits to the Discussion to present the findings in a more cautious way, more clearly state what is our interpretation, and provide alternative explanations (p. 19-26):

      “The present research conducted task-fMRI, rs-fMRI, and rs-fMRI-EEG studies to clarify whether PE elicits global connectivity effects and whether the signatures of PE processing arise spontaneously during rest. This investigation carries implications for how PE minimization may characterize abstract task-general cognitive processes. […] Although there are different ways to interpret this correlation, it is consistent with high/low PE states generally fluctuating at 3-6 Hz during rest. Below, we discuss these three studies’ findings.

      Our rs-fMRI investigation examined whether resting dynamics resemble the task-defined connectivity signatures of high vs. low PE, independent of the type of stimulus encountered. The resting-state analyses indeed found that, even at rest, participants’ brains fluctuated between strong ventral-dorsal connectivity and strong posterior-anterior connectivity, consistent with shifts between states of high and low PE. This conclusion is based on correlative/observational evidence and so may be controversial as it relies on reverse inference.

      These patterns resemble global connectivity signatures seen in resting-state participants, and correlations between fMRI and EEG data yield associations, consistent with participants fluctuating between high-PE (ventral-dorsal) and low-PE (posterior-anterior) states at 3-6 Hz. Although definitively testing these ideas is challenging, given that rs-fMRI is defined by the absence of any causal manipulations, our results provide evidence consistent with PE minimization playing a role beyond stimulus process.”

      (R3.2) Interpretation of PE-Related Fluctuations at Rest and Its Functional Relevance. It would strengthen the paper to clarify what is meant by "intrinsic" state fluctuations. Intrinsic might mean taskindependent, trait-like, or spontaneously generated. Which do the authors mean here? Is the key prediction that these fluctuations will persist in the absence of a prediction task?

      Of the three terms the reviewer mentioned, “spontaneous” and “task-independent” are the most accurate descriptors. We conceptualize these fluctuations as a continuous background process that persists across all facets of cognition, without requiring a task explicitly designed to elicit prediction error – although we, along with other predictive coding papers, would argue that all cognitive tasks are fundamentally rooted in PE mechanisms and thus anything can be seen as a “prediction task” (see our response to comment R2.2 for our changes to the Introduction that provide more intuition for this point). The proposed interactions can be seen as analogous to cortico-basal-thalamic loops, which are engaged across a vast and diverse array of cognitive processes.

      The prior submission only used the word “intrinsic” in the title. We have since revised it to “spontaneous,” which is more specific than “intrinsic,” and we believe clearer for a title than “task-independent” (p. 1): “Spontaneous fluctuations in global connectivity reflect transitions between states of high and low prediction error”

      We have also made tweaks throughout the manuscript to now use “spontaneously” throughout (it now appears 8 times in the paper).

      Regardless of the intrinsic argument, I find it challenging to interpret the results as evidence of PE fluctuations at rest. What the authors show directly is that the degree to which a subset of regions within a PE network discriminates high vs. low PE during task correlates with the magnitude of separation between high and low PE states during rest. While this is an interesting relationship, it does not establish that the resting-state brain spontaneously alternates between high and low PE states, nor that it does so in a functionally meaningful way that is related to behavior. How can we rule out brain dynamics of other processes, such as arousal, that also rise and fall with PE? I understand the authors' intention to address the reverse inference concern by testing whether "a participant's unique connectivity response to PE in the reward-processing task should match their specific patterns of resting-state fluctuation". However, I'm not fully convinced that this analysis establishes the functional role of the identified modules to PE because of the following:

      Theoretically, relating the activities of the identified modules directly to behavior would demonstrate a stronger functional role.

      (R3.2a) Across participants: Do individuals who exhibit stronger or more distinct PE-related fluctuations at rest also perform better on tasks that require prediction or inference? This could be assessed using the HCP prediction task, though if individual variability is limited (e.g., due to ceiling effects), I would suggest exploring a dataset with a prediction task that has greater behavioral variance.

      This is a good idea, but unfortunately difficult to test with our present data. The HCP gambling task used in our study was not designed to measure individual differences in prediction or inference and likely suffers from ceiling effects. Because the task outcomes are predetermined and not linked to participants' choices, there is very little meaningful behavioral variance in performance to correlate with our resting-state fluctuation measure.

      While we agree that exploring a different dataset with a more suitable task would be ideal, given the scope of the existing manuscript, this seems like it would be too much. Although these results would be informative, they would ultimately still not be a panacea for the reverse inference issues.

      Or even more broadly, does this variability in resting state PE state fluctuations predict general cognitive abilities like WM and attention (which the HCP dataset also provides)? I appreciate the inclusion of the win-loss control, and I can see the intention to address specificity. This would test whether PE state fluctuations reflect something about general cognition, but also above and beyond these attentional or WM processes that we know are fluctuating.

      This is a helpful suggestion, motivating new analyses: We measured the degree of resting-state fluctuation amplitude across participants and correlated it with the different individual differences measures provided with the HCP data (e.g., measures of WM performance). We computed each participant’s fluctuation amplitude measure as the average absolute difference between posterior-anterior and ventral-dorsal connectivity; this is the average of the TR-by-TR fMRI amplitude measure from Study 3. We correlated this individual difference score with all of the ~200 individual difference measures provided with the HCP dataset (e.g., measures of intelligence or personality). We measured the Spearman correlation between mean fluctuation amplitude with each of those ~200 measures, while correcting for multiple hypotheses using the False Discovery Rate approach.[18]

      We found a robust negative association with age, where older participants tend to display weaker fluctuations (r = -.16, p < .001). We additionally find a positive association with the age-adjusted score on the picture sequence task (r = .12, p<sub>corrected</sub> = .03) and a negative association with performance in the card sort task (r = -.12, p<sub>corrected</sub> = 046). It is unclear how to interpret these associations, without being speculative, given that fluctuation amplitude shows one positive association with performance and one negative association, albeit across entirely different tasks.  We have added these correlation results as Supplemental Materials 8 (SM p. 11):

      “(8) Behavioral differences related to fluctuation amplitude 

      To investigate whether individual differences in the magnitude of resting-state PE-state fluctuations predict general cognitive abilities, we correlated our resting-state fluctuation measure with the cognitive and demographic variables provided in the HCP dataset.

      (8.1) Methods

      For each of the 1,000 participants, we calculated a single fluctuation amplitude score. This score was defined as the average absolute difference between the time-varying posterior-anterior (PA) and ventral-dorsal (VD) connectivity during the resting-state fMRI scan (the average of the TR-by-TR measure used for Study 3). We then computed the Spearman correlation between this score and each of the approximately 200 individual difference measures provided in the HCP dataset. We corrected for multiple comparisons using the False Discovery Rate (FDR) approach.

      (8.2) Results

      The correlations revealed a robust negative association between fluctuation amplitude and age, indicating that older participants tended to display weaker fluctuations (r = -.16, p<sub>corrected</sub> < .001). After correction, two significant correlations with cognitive performance emerged: (i) a positive association with the age-adjusted score on the Picture Sequence Memory Test (r = .12, p<sub>corrected</sub> = .03), (ii) a negative association with performance on the Card Sort Task (r = -.12, p<sub>corrected</sub> = .046). As greater fluctuation amplitude is linked to better performance on one task but worse performance on another, it is unclear how to interpret these findings.”

      We updated the main text Methods to direct readers to this content (p. 39-40):

      “(4.4.3) Links between network fluctuations and behavior

      We considered whether the extent of PE-related network expression states during resting-state is behaviorally relevant. We specifically investigated whether individual differences in the overall magnitude of resting-state fluctuations could predict individual difference measures, provided with the HCP dataset. This yielded a significant association with age, whereby older participants tended to display weaker fluctuations. However, associations with cognitive measures were limited. A full description of these analyses is provided in Supplemental Materials 8.”

      (R3.2b) Within participants: Do momentary increases in PE-network expression during tasks relate to better or faster prediction? In other words, is there evidence that stronger expression of PE-related states is associated with better behavioral outcomes?

      This is a good question that probes the direct behavioral relevance of these network states on a trial-by-trial basis. We agree with the reviewer's intuition; in principle, one would expect a stronger expression of the low-PE network state on trials where a participant correctly and quickly gives a high likelihood rating to a predictable stimulus.

      Following this suggestion, we performed a new analysis in Study 1A to test this. We found that while network expression was indeed linked to participants’ likelihood ratings: higher likelihood ratings correspond to stronger posterior-anterior connectivity, whereas lower ratings correspond to stronger ventral-dorsal connectivity (Connectivity-Direction × likelihood, β [standardized] = .28, p = .02). Yet, this is not a strong test of the reviewer’s hypothesis, and different exploratory analyses of response time yield null results (p > .05). We suspect that this is due to the effect being too subtle, so we have insufficient statistical power. A comparable analysis was not feasible for Study 1B, as its design does not provide an analogous behavioral measure of trialby-trial prediction success.

      (R3.3) A priori Hypothesis for EEG Frequency Analysis.

      It's unclear how to interpret the finding that fMRI fluctuations in the defined modules correlate with frontal Delta/Theta power, specifically in the 3-6 Hz range. However, in the EEG literature, this frequency band is most commonly associated with low arousal, drowsiness, and mind wandering in resting, awake adults, not uniquely with prediction error processing. An a priori hypothesis is lacking here: what specific frequency band would we expect to track spontaneous PE signals at rest, and why? Without this, it is difficult to separate a PE-based interpretation from more general arousal or vigilance fluctuations.

      This point gets to the heart of the challenge with reverse inference in resting-state fMRI. We agree that an interpretation based on general arousal or drowsiness is a potential alternative that must be considered. However, what makes a simple arousal interpretation challenging is the highly specific nature of our fMRI-EEG association. As shown in our confirmatory analyses (Supplemental Materials 6), the correlation with 3-6 Hz power was found exclusively with the absolute difference between our two PE-related network states (|PA – VD|)—a measure of fluctuation amplitude. We found no significant relationship with the signed difference (a bias toward one state) or the sum (the overall level of connectivity). This specificity presents a puzzle for a simple drowsiness account; it seems less plausible that drowsiness would manifest specifically as the intensity of fluctuation between two complex cognitive networks, rather than as a more straightforward change in overall connectivity. While we cannot definitively rule out contributions from arousal, the specificity of our finding provides stronger evidence for a structured cognitive process, like PE, than for a general, undifferentiated state. 

      We updated the Discussion to make the argument above and also to remind readers that alternative explanations, such as ones based on drowsiness, are possible (p. 24):

      “We specifically interpret the fMRI-EEG correlation as reflecting fluctuation speed because we correlated EEG oscillatory power with the fluctuation amplitude computed from fMRI data. Simply correlating EEG power with the average connectivity or the signed difference between posterior-anterior and ventral-dorsal connectivity yields null results (Supplemental Materials 6), suggesting that this is a very particular association, and viewing it as capturing fluctuation amplitude provides a parsimonious explanation. Yet, this correlation may be interpreted in other ways. For example, resting-state Theta is also a signature of drowsiness,[2] which may correlate with PE processing, but perhaps should be understood as some other mechanism.”

      (R3.4) Significance Assessment

      The significance of the correlation above and all other correlation analyses should be assessed through a permutation test rather than a single parametric t-test against zero. There are a few reasons: a) EEG and fMRI time series are autocorrelated, violating the independence assumption of parametric tests;

      Standard t-tests can underestimate the true null distribution's variance, because EEG-fMRI correlations often involve shared slow drifts or noise sources, which can yield spurious correlations and inflating false positives unless tested against an appropriate null.

      Building a null distribution that preserves the slow drifts, for example, would help us understand how likely it is for the two time series to be correlated when the slow drifts are still present, and how much better the current correlation is, compared to this more conservative null. You can perform this by phase randomizing one of the two time courses N times (e.g., N=1000), which maintains the autocorrelation structure while breaking any true co-occurrence in patterns between the two time series, and compute a non-parametric p-value. I suggest using this approach in all correlation analyses between two time series.

      This is an important statistical point to clarify, and the suggested analysis is valuable. The reviewer is correct that the raw fMRI and EEG time series are autocorrelated. However, because our statistical approach is a twolevel analysis, we reasoned that non-independence at the correlation-level would not invalidate the higher-level t-test. The t-test’s assumption of independence applies to the individual participants' coefficients, which are independent across participants. Thus, we believe that our initial approach is broadly appropriate, and its simplicity allows it to be easily communicated.

      Nonetheless, the permutation-testing procedure that the Reviewer describes seems like an important analysis to test, given that permutation-testing is the gold standard for evaluating statistical significance, and it could guarantee that our above logic is correct. We thus computed the analysis as the reviewer described. For each participant, we phase-randomized the fMRI fluctuation amplitude time series. Specifically, we randomized the Fourier phases of the |PA–VD| series (within run), while retaining the original amplitude spectrum; inverse transforms yielded real surrogates with the same power spectrum. This was done for each participant once per permutation. Each participant’s phase-randomized data was submitted to the analysis of each oscillatory power band as originally, generating one mean correlation for each band. This was done 1,000 times.

      Across the five bands, we find that the grand mean correlation is near zero (M<sub>r</sub> = .0006) and the 97.5<sup>th</sup> percentile critical value of the null distribution is r = ~.025; this 97.5<sup>th</sup> percentile corresponds to the upper end of a 95% confidence interval for a band’s correlation; the threshold minimally differs across bands (.024 < rs < .026). Our original correlation coefficients for Delta (M<sub>r</sub> = .042) and Theta (M<sub>r</sub> = .041), which our conclusions focused on, remained significant (p ≤ .002); we can perform family-wise error-rate correction by taking the highest correlation across any band for a given permutation, and the Delta and Theta effects remain significant (p<sub>FWE</sub>corrected ≤ .003); previously Reviewer comment R1.4c requested that we employ family-wise error correction.

      These correlations were previously reported in Table 1, and we updated the caption to note what effects remain significant when evaluated using permutation-testing and with family-wise error correction (p. 19):

      “The effects for Delta, Theta, Beta, and Gamma remain significant if significance testing is instead performed using permutation-testing and with family-wise error rate correction (p<sub>corrected</sub> < .05).”

      We updated the Methods to describe the permutation-testing analysis (p. 43):

      “To confirm the significance of our fMRI-EEG correlations with a non-parametric approach, we performed a group-level permutation-test. For each of 1,000 permutations, we phase-randomized the fMRI fluctuation amplitude time series. Specifically, we randomized the Fourier phases of the |PA–VD| series (within run), while retaining the original amplitude spectrum; inverse transforms yielded real surrogates with the same power spectrum. This procedure breaks the true temporal relationship between the fMRI and EEG data while preserving its structure. We then re-computed the mean Spearman correlation for each frequency band using this phase-randomized data. We evaluated significance using a family-wise error correction approach that accounts for us analyzing five oscillatory power bands. We thus create a null distribution composed of the maximum correlation value observed across all frequency bands from each permutation. Our observed correlations were then tested for significance against this distribution of maximums.”

      (R3.5) Analysis choices

      If I'm understanding correctly, the algorithm used to identify modules does so by assigning nodes to communities, but it does not itself restrict what edges can be formed from these modules. This makes me wonder whether the decision to focus only on connections between adjacent modules, rather than considering the full connectivity, was an analytic choice by the authors. If so, could you clarify the rationale? In particular, what justifies assuming that the gradient of PE states should be captured by edges formed only between nearby modules (as shown in Figure 2E and Figure 4), rather than by the full connectivity matrix? If this restriction is instead a by-product of the algorithm, please explain why this outcome is appropriate for detecting a global signature of PE states in both task and rest.

      We discuss this matter in our response to comment R2.(4).

      When assessing the correspondence across task-fMRI and rs-fMRI in section 2.2.2, why was the pattern during task calculated from selecting a pair of bilateral ROIs (resulting in a group of eight ROIs), and the resting state pattern calculated from posterior-anterior/ventral-dorsal fluctuation modules? Doesn't it make more sense to align the two measures? For example, calculating task effects on these same modules during task and rest?

      We thank the reviewer for this question, as it highlights a point in our methods that we could have explained more clearly. The reviewer is correct that the two measures must be aligned, and we can confirm that they were indeed perfectly matched.

      For the analysis in Section 2.2.2, both the task and resting-state measures were calculated on the exact same anatomical substrate for each comparison. The analysis iteratively selected a symmetrical subset of eight ROIs from our larger four quadrants. For each of these 3,432 iterations, we computed the task-fMRI PE effect (the Connectivity Direction × PE interaction) and the resting-state fluctuation amplitude (E[|PA – VD|]) using the identical set of eight ROIs. The goal of this analysis was precisely to test if the fine-grained anatomical pattern of these effects correlated within an individual across the task and rest states. We will revise the text in Section 2.2.2 to make this direct alignment of the two measures more explicit.

      Recommendations for authors:

      Reviewer #1 (Recommendations for authors):

      (R1.3) Several prior studies have described co-activation or connectivity "templates" that spontaneously alternate during rest and task states, and are linked to behavioral variability. While they are interpreted differently in terms of cognitive function (e.g., in terms of sustained attention: Monica Rosenberg; alertness: Catie Chang), the relationship between these previously reported templates and those identified in the current study warrants discussion. Are the current templates spatially compatible with prior findings while offering new functional interpretations beyond those already proposed in the literature? Or do they represent spatially novel patterns?

      Thank you for this suggestion. Broadly, we do not mean to propose spatially novel patterns but rather focus on how these are repurposed for PE processing. In the Discussion, we link our identified connectivity states to established networks (e.g., the FPCN). We updated this paragraph to mention that these patterns are largely not spatially novel (p. 20):

      “The connectivity patterns put forth are, for the most part, not spatially novel and instead overlap heavily with prior functional and anatomical findings.”

      Regarding the specific networks covered in the prior work by Rosenberg and Chang that the reviewer seems to be referring to, [7,8] this research has emphasized networks anchored heavily in sensorimotor, subcortical– cerebellar, and medial frontal circuits, and so mostly do not overlap with the connectivity effects we put forth.

      (R1.4) Additional points:

      (R1.4a) I do not think that the logic for taking the absolute difference of fMRI connectivity is convincing. What happens if the sign of the difference is maintained ?

      Thank you for pointing out this area that requires clarification. Our analysis targets the amplitude of the fluctuation between brain states, not the direction. We define high fluctuation amplitude as moments when the brain is strongly in either the PA state (PA > VD) or the VD state (VD > PA). The absolute difference |PA – VD| correctly quantifies this intensity, whereas a signed difference would conflate these two distinct high-amplitude moments. Our simulation study (Supplemental Materials, Section 5) provides the theoretical validation for this logic, showing how this absolute difference measure in slow fMRI data can track the amplitude of a fast underlying neural oscillator.

      When the analysis is tested in terms of the signed difference, as suggested by the Reviewer, the association between the fMRI data and EEG power is insignificant for each power band (ps<sub>uncorrected</sub> ≥ .47). We updated Supplemental Materials 6 to include these results. Previously, this section included the fluctuation amplitude (fMRI) × EEG power results while controlling for: (i) the signed difference between posterior-anterior and ventral-dorsal connectivity, (ii) the sum of posterior-anterior and ventral-dorsal connectivity, and (iii) the absolute value of the sum of posterior-anterior and ventral-dorsal connectivity. For completeness, we also now report the correlation between each EEG power band and each of those other three measures (SM, p. 9)

      “We additionally tested the relationship between each of those three measures and the five EEG oscillation bands. Across the 15 tests, there were no associations (ps<sub>uncorrected</sub>  ≥ .04); one uncorrected p-value was at p = .044, although this was expected given that there were 15 tests. Thus, the association between EEG oscillations and the fMRI measure is specific to the absolute difference (i.e., amplitude) measure.”

      (R1.4b) Reasoning of focus on frontal and theta band is weak, and described as "typical" (line 359) based on a single study.

      Sorry about this. There is a rich literature on the link between frontal theta and prediction error,[3,9–11] and we updated the Introduction to include more references to this work (p. 18): “The analysis was first done using power averaged across frontal electrodes, as these are the typical focus of PE research on oscillations.[3,9–11]”

      We have also updated the Methods to cite more studies that motivate our electrode choice (p. 41): “The analyses first targeted five midline frontal electrodes (F3, F1, Fz, F2, F4; BioSemi64 layout), given that this frontal row is typically the focus of executive-function PE research on oscillations.[9–11]”

      (R1.4c) No correction appears to have been applied for the association between EEG power and fMRI connectivity. Given that 100 frequency bins were collapsed into 5 canonical bands, a correction for 5 comparisons seems appropriate. Notably, the strongest effects in the delta and theta bands (particularly at fronto-central electrodes) may still survive correction, but this should be explicitly tested and reported.

      Thanks for this suggestion. We updated the Table 1 caption to mention what results survive family-wise error rate correction – as the reviewer suggests, the Delta/Theta effects would survive Bonferroni correction for five tests, although per a later comment suggesting that we evaluate statistical significance with a permutationtesting approach (comment R3.4), we instead report family-wise error correction based on that. The revised caption is as follows (p. 19):

      “The effects for Delta, Theta, Beta, and Gamma remain significant if significance testing is instead performed using permutation-testing and with family-wise error rate correction (p<sub>corrected</sub> < .05).”

      (R1.4d) Line 135. Not sure I understand what you mean by "moods". What is the overall point here?

      The overall argument is that the fluctuations occur rapidly rather than slowly. By slow “moods” we refer to how a participant could enter a high anxiety state of >10 seconds, linked to high PE fluctuations, and then shift into a low anxiety state, linked to low PE fluctuations. We argue that this is not occurring. Regardless, we recognize that referring to lengths of time as short as 10 seconds or so is not a typical use of the word “mood” and is potentially ambiguous, so we have omitted this statement, which was originally on page 6: “Identifying subsecond fluctuations would broaden the relevance of the present results, as they rule out that the PE states derive from various moods.”

      (R1.4e) Line 100. "Few prior PE studies have targeted PE, contrasting the hundreds that have targeted BOLD". I don't understand this sentence. It's presumably about connectivity vs activity?

      Yes, sorry about this typo. The reviewer is correct, and that sentence was meant to mention connectivity. We corrected (p. 5): “Few prior PE studies have targeted connectivity, contrasting the hundreds that have targeted BOLD.”

      (R1.4f) Line 373: "0-0.5Hz" in the caption is probably "0-50Hz".

      Yes, this was another typo, thank you. We have corrected it (p. 19): “… every 0.5 Hz interval from 0-50 Hz.”

      Reviewer #2 (Recommendations for authors):

      (R2.6) (Page 3) When referring to the "limited" hypothesis of local PE, please clarify in what sense is it limited. That statement is unclear.

      Thank you for pointing out this text, which we now see is ambiguous. We originally use "limited" to refer to the hypothesis's constrained scope – namely, that PE is relevant to various low-level operations (e.g., sensory processing or rewards) but the minimization of PE does not guide more abstract cognitive processes. We edited this part of the Introduction to be clearer (p. 3)

      “It is generally agreed that the brain uses PE mechanisms at neuronal or regional levels,[15,16] and this idea has been useful in various low-level functional domains, including early vision [15] and dopaminergic reward processing.[17] Some theorists have further argued that PE propagates through perceptual pathways and can elicit downstream cognitive processes to minimize PE.”

      (R2.7) (Page 5) "Few prior PE have targeted PE"... this statement appears contradictory. Please clarify.

      Sorry about this typo, which we have corrected (p. 5):

      “Few prior PE studies have targeted connectivity, contrasting the hundreds that have targeted BOLD.”

      (R2.8) What happened to the data of the medium PE condition in Study 1A?

      The medium PE condition data were not excluded. We modeled the effect of prediction error on connectivity using a linear regression across the three conditions, coding them as a continuous variable (Low = -1, Medium = 0, High = +1). This approach allowed us to identify brain connections that showed a linear increase or decrease in strength as a function of increasing PE. This linear contrast is a more specific and powerful way to isolate PErelated effects than a High vs. Low contrast. We updated the Results slightly to make this clearer (p. 8-9):

      “In the fMRI data, we compared the three PE conditions’ beta-series functional connectivity, aiming to identify network-level signatures of PE processing, from low to high. […] For the modularity analysis, we first defined a connectome matrix of beta values, wherein each edge’s value was the slope of a regression predicting that edge’s strength from PE (coded as Low = -1, Medium = 0, High = +1; Figure 2A).”

      (R2.9) (Page 15) The point about how the dots in 6H follow those in 6J better than those in 6I is a little subjective - can the authors provide an objective measure?

      Thank you for pointing out this issue. The visual comparison using Figure 6 was not meant as a formal analysis but rather to provide intuition. However, as the reviewer describes, this is difficult to convey. Our formal analysis is provided in Supplemental Materials 5, where we report correlation coefficients between a very large number of simulated fMRI data points and EEG data points corresponding to different frequencies. We updated this part of the Results to convey this (p. 16-17):

      “Notice how the dots in Figure 6H follow the dots in Figure 6J (3 Hz) better than the dots in Figure 6I (0.5 Hz) or Figure 6K (10 Hz); this visual comparison is intended for illustrative purposes only, and quantitative analyses are provided in Supplemental Materials 5.”

      References

      (1) Zalesky, A., Fornito, A. & Bullmore, E. T. Network-based statistic: identifying differences in brain networks. Neuroimage 53, 1197–1207 (2010)

      (2) Strijkstra, A. M., Beersma, D. G., Drayer, B., Halbesma, N. & Daan, S. Subjective sleepiness correlates negatively with global alpha (8–12 Hz) and positively with central frontal theta (4–8 Hz) frequencies in the human resting awake electroencephalogram. Neuroscience letters 340, 17–20 (2003).

      (3) Cavanagh, J. F. & Frank, M. J. Frontal theta as a mechanism for cognitive control. Trends in cognitive sciences 18, 414–421 (2014).

      (4) Grech, R. et al. Review on solving the inverse problem in EEG source analysis. Journal of neuroengineering and rehabilitation 5, 25 (2008)

      (5) Palva, J. M. et al. Ghost interactions in MEG/EEG source space: A note of caution on inter-areal coupling measures. Neuroimage 173, 632–643 (2018).

      (6) Koles, Z. J. Trends in EEG source localization. Electroencephalography and clinical Neurophysiology 106, 127–137 (1998).

      (7) Rosenberg, M. D. et al. A neuromarker of sustained attention from whole-brain functional connectivity. Nature neuroscience 19, 165–171 (2016).

      (8) Goodale, S. E. et al. fMRI-based detection of alertness predicts behavioral response variability. elife 10, e62376 (2021).

      (9) Cavanagh, J. F. Cortical delta activity reflects reward prediction error and related behavioral adjustments, but at different times. NeuroImage 110, 205–216 (2015)

      (10) Hoy, C. W., Steiner, S. C. & Knight, R. T. Single-trial modeling separates multiple overlapping prediction errors during reward processing in human EEG. Communications Biology 4, 910 (2021).

      (11) Neo, P. S.-H., Shadli, S. M., McNaughton, N. & Sellbom, M. Midfrontal theta reactivity to conflict and error are linked to externalizing and internalizing respectively. Personality neuroscience 7, e8 (2024).

      (12) Friston, K. J. The free-energy principle: a unified brain theory? Nature reviews neuroscience 11, 127–138 (2010)

      (13) Feldman, H. & Friston, K. J. Attention, uncertainty, and free-energy. Frontiers in human neuroscience 4, 215 (2010).

      (14) Friston, K. J. et al. Active inference and epistemic value. Cognitive neuroscience 6, 187–214 (2015).

      (15) Rao, R. P. & Ballard, D. H. Predictive coding in the visual cortex: a functional interpretation of some extraclassical receptive-field effects. Nature neuroscience 2, 79–87 (1999)

      (16) Walsh, K. S., McGovern, D. P., Clark, A. & O’Connell, R. G. Evaluating the neurophysiological evidence for predictive processing as a model of perception. Annals of the new York Academy of Sciences 1464, 242– 268 (2020)

      (17) Niv, Y. & Schoenbaum, G. Dialogues on prediction errors. Trends in cognitive sciences 12, 265–272 (2008).

      (18) Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal statistical society: series B (Methodological) 57, 289–300 (1995).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review)

      Summary

      We thank the reviewer for the constructive and thoughtful evaluation of our work. We appreciate the recognition of the novelty and potential implications of our findings regarding UPR activation and proteasome activity in germ cells.

      (1) The microscopy images look saturated, for example, Figure 1a, b, etc. Is this a normal way to present fluorescent microscopy?

      The apparent saturation was not present in the original images, but likely arose from image compression during PDF generation. While the EMA granule was still apparent, in the revised submission, we will provide high-resolution TIFF files to ensure accurate representation of fluorescence intensity and will carefully optimize image display settings to avoid any saturation artifacts.

      (2) The authors should ensure that all claims regarding enrichment/lower vs. lower values have indicated statistical tests.

      We fully agree. In the revised version, we will correct any quantitative comparisons where statistical tests were not already indicated, with a clear statement of the statistical tests used, including p-values in figure legends and text.

      (a) In Figure 2f, the authors should indicate which comparison is made for this test. Is it comparing 2 vs. 6 cyst numbers?

      We acknowledge that the description was not sufficiently detailed. Indeed, the test was not between 2 vs 6 cyst numbers, but between all possible ways 8-cell cysts or the larger cysts studied could fragment randomly into two pieces, and produce by chance 6-cell cysts in 13 of 15 observed examples. We will expand the legend and main text to clarify that a binomial test was used to determine that the proportion of cysts producing 6-cell fragments differed very significantly from chance.

      Revised text:

      “A binomial test was used to assess whether the observed frequency of 6-cell cyst products differed from random cyst breakage. Production of 6-cell cysts was strongly preferred (13/15 cysts; ****p < 0.0001).”

      (b) Figures 4d and 4e do not have a statistical test indicated.

      We will include the specific statistical test used and report the corresponding p-values directly in the figure legends.

      (3) Because the system is developmentally dynamic, the major conclusions of the work are somewhat unclear. Could the authors be more explicit about these and enumerate them more clearly in the abstract?

      We will revise the abstract to better clarify the findings of this study. We will also replace the term Visham with mouse fusome to reflect its functional and structural analogy to the Drosophila and Xenopus fusomes, making the narrative more coherent and conclusive.

      (4) The references for specific prior literature are mostly missing (lines 184-195, for example).

      We appreciate this observation of a problem that occurred inadvertently when shortening an earlier version.  We will add 3–4 relevant references to appropriately support this section.

      (5) The authors should define all acronyms when they are first used in the text (UPR, EGAD, etc).

      We will ensure that all acronyms are spelled out at first mention (e.g., Unfolded Protein Response (UPR), Endosome and Golgi-Associated Degradation (EGAD)).

      (6) The jumping between topics (EMA, into microtubule fragmentation, polarization proteins, UPR/ERAD/EGAD, GCNA, ER, balbiani body, etc) makes the narrative of the paper very difficult to follow.

      We are not jumping between topics, but following a narrative relevant to the central question of whether female mouse germ cells develop using a fusome.  EMA, microtubule fragmentation, polarization proteins, ER, and balbiani body are all topics with a known connection to fusomes. This is explained in the general introduction and in relevant subsections. We appreciate this feedback that further explanations of these connections would be helpful. In the revised manuscript, use of the unified term mouse fusome will also help connect the narrative across sections.  UPR/ERAD/EGAD are processes that have been studied in repair and maintenance of somatic cells and in yeast meiosis.  We show that the major regulator XbpI is found in the fusome, and that the fusome and these rejuvenation pathway genes are expressed and maintained throughout oogenesis, rather than only during limited late stages as suggested in previous literature.

      (7) The heading title "Visham participates in organelle rejuvenation during meiosis" in line 241 is speculative and/or not supported. Drawing upon the extensive, highly rigorous Drosophila literature, it is safe to extrapolate, but the claim about regeneration is not adequately supported.

      We believe this statement is accurate given the broad scope of the term "participates." It is supported by localization of the UPR regulator XbpI to the fusome. XbpI is the ortholog of HacI a key gene mediating UPR-mediated rejuvenation during yeast meiosis.  We also showed that rejuvenation pathway genes are expressed throughout most of meiosis (not previously known) and expanded cytological evidence of stage-specific organelle rejuvenation later in meiosis, such as mitochondrial-ER docking, in regions enriched in fusome antigens. However, we recognize the current limitations of this evidence in the mouse, and want to appropriately convey this, without going to what we believe would be an unjustified extreme of saying there is no evidence.

      Reviewer #2 (Public review):

      We thank the reviewer for the comprehensive summary and for highlighting both the technical achievement and biological relevance of our study. We greatly appreciate the thoughtful suggestions that have helped us refine our presentation and terminology.

      (1) Some titles contain strong terms that do not fully match the conclusions of the corresponding sections.

      (1a) Article title “Mouse germline cysts contain a fusome-like structure that mediates oocyte development”

      We will change the statement to: “Mouse germline cysts contain a fusome that supports germline cyst polarity and rejuvenation.”

      (1b) Result title “Visham overlaps centrosomes and moves on microtubules”

      We acknowledge that “moves” implies dynamics. We will include additional supplementary images showing small vesicular components of the mouse fusome on spindle-derived microtubule tracks.

      (1c) Result title “Visham associates with Golgi genes involved in UPR beginning at the onset of cyst formation”

      We will revise this title to: “The mouse fusome associates with the UPR regulatory protein Xbp1 beginning at the onset of cyst formation” to reflect the specific UPR protein that was immunolocalized.

      (1d) Result title “Visham participates in organelle rejuvenation during meiosis”

      We will revise this to: “The mouse fusome persists during organelle rejuvenation in meiosis.”

      (2) The authors aim to demonstrate that Visham is a fusome-like structure. I would suggest simply referring to it as a "fusome-like structure" rather than introducing a new term, which may confuse readers and does not necessarily help the authors' goal of showing the conservation of this structure in Drosophila and Xenopus germ cells. Interestingly, in a preprint from the same laboratory describing a similar structure in Xenopus germ cells, the authors refer to it as a "fusome-like structure (FLS)" (Davidian and Spradling, BioRxiv, 2025).

      We appreciate the reviewer’s insightful comment. To maintain conceptual clarity and align with existing literature, we will refer to the structure as the mouse fusome throughout the manuscript, avoiding introduction of a new term.

      Reviewer #3 (Public review):

      We thank the reviewer for emphasizing the importance of our study and for providing constructive feedback that will help us clarify and strengthen our conclusions.

      (1) Line 86 - the heading for this section is "PGCs contain a Golgi-rich structure known as the EMA granule"

      We agree that the enrichment of Golgi within the EMA PGCs was not shown until the next section. We will revise this heading to:

      “PGCs contain an asymmetric EMA granule.” 

      (2) Line 105-106, how do we know if what's seen by EM corresponds to the EMA1 granule?

      We will clarify that this identification is based on co-localization with Golgi markers (GM130 and GS28) and response to Brefeldin A treatment, which will be included as supplementary data. These findings support that the mouse fusome is Golgi-derived and can therefore be visualized by EM. The Golgi regions in E13.5 cyst cells move close together and associate with ring canals as visualized by EM (Figure 1E), the same as the mouse fusomes identified by EMA.

      (3) Line 106-107-states "Visham co-stained with the Golgi protein Gm130 and the recycling endosomal protein Rab11a1". This is not convincing as there is only one example of each image, and both appear to be distorted.

      Space is at a premium in these figures, but we have no limitation on data documenting this absolutely clear co-localization. We will replace the existing images with high-resolution, noncompressed versions for the final figures to clearly illustrate the co-staining patterns for GM130 and Rab11a1.

      (4) Line 132-133---while visham formation is disrupted when microtubules are disrupted, I am not convinced that visham moves on microtubules as stated in the heading of this section.

      We will include additional supplementary data showing small mouse fusome vesicles aligned along microtubules.

      (5) Line 156 - the heading for this section states that Visham associates with polarity and microtubule genes, including pard3, but only evidence for pard3 is presented.

      We agree and will revise the heading to: “Mouse fusome associates with the polarity protein Pard3.” We are adding data showing association of small fusome vesicles on microtubules.

      (6) Lines 196-210 - it's strange to say that UPR genes depend on DAZ, as they are upregulated in the mutants. I think there are important observations here, but it's unclear what is being concluded.

      UPR genes are not upregulated in DAZ in the sense we have never documented them increasing. We show that UPR genes during this time behave like pleuripotency genes and normally decline, but in DAZ mutants their decline is slowed.  We will rephrase the paragraph to clarify that Dazl mutation partially decouples developmental processes that are normally linked, which alters UPR gene expression relative to cyst development.

      (7) Line 257-259-wave 1 and 2 follicles need to be explained in the introduction, and how these fits with the observations here clarified.

      Follicle waves are too small a focus of the current study to explain in the introduction, but we will request readers to refer to the cited relevant literature (Yin and Spradling, 2025) for further details.

      We sincerely thank all reviewers for their insightful and constructive feedback. We believe that the planned revisions—particularly the refined terminology, improved image quality, clarified statistics, and restructured abstract—will substantially strengthen the manuscript and enhance clarity for readers.

      Reviewer #1 (Recommendations for the authors):

      (1) Figure 1E: need to use some immuno-gold staining to identify the Visham. Just circling an area of cytoplasm that contains ER between germ cell pairs is not enough.

      We appreciate the reviewer’s insistence that the association between the mouse fusome and Golgi be clearly demonstrated. However, the EMA granule is a large structure discovered and defined by light microscopy, and presents no inherent challenge to documenting its Golgi association by immunofluorescence experiments, which we presented and now further strengthened as described in the next paragraph.  We believe that the suggested EM experiment would add little to the EM we already presented (Figure 1E, E')  Moreover, due to facility limitations, we are currently unable to perform immunogold staining. 

      To strengthen previous immunolocalization experiments, we have now included additional immunostaining data showing the clear colocalization of the fusome region with the Golgi markers GM130 and GS28 (Figure S1H). We have also incorporated a new experiment using the Golgi-specific inhibitor Brefeldin A (BFA) see Figure S1I.  Treatment of in vitro–cultured gonads with BFA, disrupted EMA granule formation, demonstrating that EMA granules not only associate with Golgi, but require Golgi function to to be maintained.

      Additionally, in Figure 2, we showed that the fusome overlaps with the peri-centriolar region—a characteristic locus for Golgi due to its movement on microtubules.  We showed that the dynamic behavior of the fusome during the cell cycle, parallels Golgi dispersal and reassembly, and all these facts provide further strong support for the Golgi-association of the EMA granule and fusome.

      (2) Figure 1F: is this image compressed?

      We have now substituted the image in Figure 1F with a better image and have avoided the compression of the image. 

      (3) In the figure legends, are the sample sizes individual animals or individual sections? Please ensure that all figure legends for each figure panel consistently contain the sample size.

      We have now included the number of measurements (N) in every figure legend. Each experiment was performed using samples from at least three different animals, and in most cases from more than three. This information has also been added to the Methods section under Statistics. In addition, N values are now consistently provided for each graph throughout the figures.

      (4) Figure 2b/c: seemly likely based on the snapshot of different stages of cytokinesis that the "newly formed" visham is accurate, but without live imaging, this claim of "newly formed" is putative/speculative. It is OK if it is labeled as "putative" in the figure panel.  

      The behavior of the Drosophila fusome during mitosis was deduced without live imaging (deCuevas et al. 1998). We clarified that the conversion of a single mouse germ cell with one round fusome to an interconnected pair of cells with two round fusomes of greater total volume following mitosis is the basis for deducing that new fusome formation occurs each cell cycle. However, we agree with the reviewer that the phrase "newly formed" in the original label on Figure 2c suggested a specific mechanism of fusome increase that was not intended and this phrase has been removed entirely.  

      (5) Figure 2e/e is extremely difficult to follow. In order to improve the readability of these figure panels, can individual panels with a single stain be shown? The 'gap' between YFP+ sister cells is not immediately obvious in panel e or e" with the current layout. Since this is a key aspect of the author's claim about cleavage of the cyst, it would be best to make this claim more robust by showing more convincing images. In Figure 2E, the staining pattern of EMA needs to be clarified and described more fully in the text.

      We mapped discontinuities in the microtubule connections, not the fusome or YFP.  YFP is the lineage marker indicating that the cells of a single cyst are being studied. Consequently, no gap between YFP cytoplasmic expression is expected because only in the last example (figure E”), has fragmentation already occurred (and here there is a YFP gap).  The acetylated tubulin gap proceeds fragmentation.  The mitotic spindle remnants labeled by AcTub link the cells into two groups separated by a gap, which is clearly shown in the data images and in the third column where only the relevant AcTub from the cyst itself is shown. In response to the reviewers question about the fusome, which is not directly relevant to fragmentation, we have now provided images of the separate fusome channel and corresponding measurements for all three Figure 2E-E'' cysts in the supplementary Figure S4H. We have improved the text regarding this important figure to try and make it easier to follow, and also added a new example of a 10-cell cyst also in S2H (lower panels).  We also added, movies allowing full 3D study of one of the 8 cell cysts and the new 10-cell cyst.  I also suggest that the reviewer examine how the deduced mechanism of fragmentation explains previously published but not fully understood data on cyst fragmentation going back to 1998 as described in the expanded Discussion on this topic.  

      (6) It would be best to support the proposed model in Figure 2G (4+4+4) with microscopy images of a 12-cell or 16-cell cyst? Would these 12-cell or 16-cell cysts be too large to technically recover in a section?

      Unfortunately the reviewer 's suggestion that 12- or 16-cell cysts are too large to recover and present convincingly is correct. Because our analysis depends on capturing lineage-labeled cysts specifically at telophase with acetylated-tubulin connections, the likelihood of obtaining the correct stage is very low.  In addition, the dense packing of germ cells in the mouse gonad further limits our ability to fully reconstruct all the cells in large cysts, with difficulty increasing as cyst size grows.

      However, as noted, we added a well-resolved 10-cell cyst—the largest size we could confidently analyze—in a 3D video in Supplementary Figure S2H (lower panel), which shows a 6 + 4 breakage pattern.

      (7) We did not find a reference in the text for Figure 2G.

      We have now provided reference for 2G in the text and in the discussion section. 

      (8) Line 189: ERAD is used as an acronym, but is not defined until the discussion.

      We have now provided full form of acronym at its first usage in the text.

      (9) Fig 3i/i': the increase of UPR pathway components, increasing expression during zygotene, is interesting to note, but is not commented enough in the text of the paper.

      We have discussed this issue in the discussion section with specific reference to figure 3I. Please find the detailed discussion under the heading “Germ cell rejuvenation is highly active during cyst formation.”

      (10) Please quantify DNMT3A expression levels in WT control vs Dazl KO germ cells in Figure 4a.

      We have now quantified DNMT3A expression levels in WT control vs Dazl KO germ cells and have added the data in the Figure 4A.

      (11) Please introduce the rationale behind selecting DazL KO for studying cyst formation (text in line 197). This comes out of nowhere.

      True.  We significantly expanded our discussion of Dazl and citations of previous work, including evidence that it can affect cyst structures like ring canals, in the Introduction.  

      (12) It would be best to stain WT control vs DazL KO oogonia in Figure 4a with 5mC antibodies to support their claim that DNA methylation might be affected in the mutants.

      We respectfully disagree that this additional experiment is necessary within the scope of the current study. At the developmental stage examined (E12.5), germ cells in the Dazl mutant are clearly in an arrested and hypomethylated state, as supported by previous evidence (Haston et al. 2009).This initial experiments was designed to show that in our hands Dazl mutants show this known pkuripotency delay. However, the effects of Dazl mutation on female germline cyst development as it relates to polarity or the fusome was not studied before, and that is what the paper addresses, building on previous work.

      Because our study does not focus on germ-cell epigenetic modifications but rather on the consequences of Dazl loss on germ cell cyst development, adding 5mC immunostaining would not substantially advance the main conclusions. The existing data and previous published work already provide sufficient background.

      (13) Figure 4c: a very interesting figure, it would be best to quantify developmental pseudotime (perhaps using monocle3 analysis) and compare more rigorously the developmental stage of WT control vs DazL KO.

      Developmental pseudotime, such as through Monocle3 analysis, might sometimes be valuable but involves assumptions that when possible are better addressed by direct experimental examination. Our conclusions regarding cyst developmental stage are supported by straightforward evidence rather to which computational trajectory inference would add little. Specifically, we have performed analysis of germ-cell methylation state, ring canal formation, pluripotency markers, UPR pathway activity assay (Xbp1 and Proteomic assay), Golgi-stress analysis and Pard3 which collectively document the developmental status of the WT and Dazl KO germ cells. These empirical data demonstrate the same developmental pattern reflected in Figure 4c, making the less reliable pseudotime-based computational method superfluous.

      (14) Figure 4d has two panels labeled as "d".

      We have now corrected the labelling of the figure

      (15) Color coding in 4d, d', d" is confusing; please harmonize some visual presentation here.

      We have now harmonized the visual representation of all the graph in figure 4

      (16) Fig 4e' is labeled as DazL +/- but is this really a typo?

      Thank you for pointing it out. We have now corrected the typo

      (17) Figure F': typo labeled as E3.5, which is E13.5?

      Thank you for pointing it out. We have now corrected the typo

      (18) Figure F': was DazL KO mutant but no WT control.

      The WT control was not provided to avoid the redundancy. Please refer to earlier figure 3A-B, Fig S3C and D and videos S3A and S3b to refer to WT control at every stage.

      (19) Figure G: unusual choice in punctuation marks for cartoon schematic. No key to guide the reader for color-coded structures would be helpful to have something similar to 4h.

      We have now provided the key to guide the readers in the mentioned figure 4G.

      (20) The authors use WGA and EMA as interchangeable markers (Figure 5a) without fully explaining why they have switched markers.

      Because it is germ cell specific, we used EMA as a fusome marker during the time when it is found up through E13.5.  After that point we used WGA which is still usable, but also labels somatic cells.  This rationale is explicitly described at the end of the section “Fusome is highly enriched in Golgi and vesicles”, where we state:

      “EMA staining disappears from germ cells at E14.5 (Figure 1I). However, very similar (but non–germ-cell-specific) staining continued with wheat germ agglutinin (WGA) at later stages (Figure 1G, G’; Figure S1G).”

      To ensure this is fully clear to readers, we have now added an additional statement in the start of the text section discussing the figure 5:

      “For the reasons explained previously (see text for Figure 1G), WGA was used as a fusome marker beyond stage E14.5.”

      (21) Figure 5b' is compressed.

      We have now decompressed the image

      (22) Line 267, Balbiani body is misspelled.  

      We have now corrected the spelling.

      (23) The explanation of why the authors switch focus from DazL KO to DazL +/- is not adequately described. The authors should also explain the phenotype of the DazL +/- animals or reference a paper citing the hets are sterile or subfertile.

      We have now added the explanation of why Dazl KO is used in our introduction section where we have mentioned the phenotype of Dazl homozygous and heterozygous mouse.

      (24) Is Figure 5i actually DazL +/-? It is not labeled clearly in the text, the figure legend, or the figure panel. 

      We have now labelled the figure correctly in figure and in the legend.

      (25) The paper ends abruptly at line 275 with no context or summary.

      The manuscript does not end at line 275; the apparent interruption is due to a page break occurring immediately before the beginning of the Discussion section. We hope that continuation is fully visible in the reviewer 1 (your) version of the PDF.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 93: Fig. 1B: DDX4 marks germ cells; do all the red and yellow cells in the NE inset originate from the same PGC? There are only 2 cells marked in yellow among the group of red cells. Is it a z-projection issue? Or do they come from different PGCs?

      This experiment used vasa staining to identify all germ cells, which are produced by multiple PGCs. Green labeling is a lineage marker derived from a single PGC (due to the low frequency of tamoxifen-activated labeling). Consequently, the two yellow cells observed in the NE inset of Fig. 1B represent YFP-labeled germ cells (YFP + DDX4 double-positive) that have arisen from a single, lineage-traced PGC. This approach, introduced in 2013, is described in the Methods, and represents the field's single largest technical advance that has made it possible to analyze mouse germ cell development at single cell resolution.

      To ensure clarity, we have added a brief explanatory note to the figure legend indicating that yellow cells represent the lineage-traced progeny of a single PGC, while the red staining marks all germ cells.

      (2) Line 96: Figure 1C vs 1C'. The difference between female and male Visham is not obvious, although quantification shows a clear difference. How was the quantification made? Manual or automatic thresholding? Would it be possible to show only the Visham channel?

      We thank the reviewer for pointing out this problem. We have now more clearly described in the text that the female fusome increases in some cells with close attachments to other cells (future oocytes) and decreases in distant nurse cells.  It branches due to rosette formation..  In males, the fusome remains much like the initial EMA granules present in early germ cells, with only fine and difficult to see connections.  The quantification shown in Figures 1C and 1C′ was performed manually, based on the presence of either (i) fused, branched EMA-positive fusome structures or (ii) dispersed, punctate EMA granules. This assessment was carried out across multiple E13.5 male and female gonad samples to ensure robustness.  To facilitate independent evaluation, we have already provided supplementary videos S3B1 and S3B2, which display the EMA-stained E13.5 male and female gonads in three dimensions. These videos allow the structural differences to be examined more clearly than in static images.

      In response to the reviewer’s request, we now additionally include the single-channel fusome image in Supplementary Figure S1E′. This presentation highlights the fusome signal alone and further clarifies the morphological differences underlying the quantification.

      (3) L118: Figure 2A, third row = 2-cell cyst? Please specify PCNT in the legend.

      We appreciate the reviewer’s observation. In Figure 2A (third row), the cells were not specifically labeled as a 2-cell cyst; rather, the intention was to illustrate the presence of two distinct centrosomes positioned on a fused fusome structure, a configuration we frequently observe.

      We have now updated the figure legend to explicitly define PCNT.

      (4) L169: Missing reference to S3B and video S3B1?

      We have now included the reference to S3B1 and S3B2 in the text and in the legend

      (5) L170: Please describe the graph in the Figure 3D legend.

      We have now described the Graph in the legend

      (6) L171: Would it be possible to have a close-up showing both Pard3 and Visham in a ringlike pattern related to RACGAP (RC) staining? The images are too small.

      It is difficult to capture this relationship perfectly in a two dimensional picture. The images represent the maximum close-up possible that still includes enough relevant area for the necessary conclusions. We have now provided additional three close-up images exclusively for ring-canal and Pard3 association in the supplementary Figure S3C for further clarity. However, we also note that the quality of the image permits the reader of a pdf to zoom and to visualize the images in great detail.

      (7) L181: Wrong reference, should be 3 then 3I.

      Thank you for pointing it out, we have now corrected the reference.

      (8) L199: In Figure S4B, was DNMT3 staining quantified? Red intensity differs globally between images; use the somatic red level as a reference? Note: EMA seems higher in Dazl- vs. WT?

      We have now performed quantification of DNMT3 staining, which is presented in Figure 4A. While the red intensity (DNMT3 or EMA) can appear to differ between images, this variation can result from biological differences between tissues or minor technical variability despite using consistent microscope settings. To account for this, we normalized the staining intensity using the somatic cell signal as an internal reference, ensuring that the quantification reflects genuine differences between WT and Dazl-/- samples rather than global intensity variation.

      (9) L229: Should be "proteasome."

      We have now corrected the spelling error.

      (10) L233: Quantify fragmentation of Gs28? EMA doesn't seem affected. Could you quantify both Gs28 and EMA? Images are too small.

      We thank the reviewer for this suggestion. While the current images are small, they can be examined in detail using zoom to visualize the structures clearly. As noted, EMA staining is not affected, (we agree) as cells are in arrested state. This arrested state creates stress on Golgi. The fragmentation of Gs28-labeled Golgi membranes is a classical indicator of Golgi stress, even though the fragmented membranes may remain functionally active. Our results show that Dazl deletion specifically affects Golgi in germ cells, while Golgi in neighboring somatic cells appears healthy. To quantify this effect, we have now included manual quantification of Golgi fragmentation in Figure 4F, assessing tissues for the presence of fragmented versus intact Golgi structures. This confirms that Golgi fragmentation is a germ cell–specific phenotype in Dazl– samples, while pre-formed EMA-positive fusomes remain unaffected but probably in arrested state.

      (11) L237: Figure 4F graph shows E3.5, not E13.5.

      We have now corrected the typo in the figure 

      (12) L257: Figure 5D: quantify as in 5A? overlap?

      Yes, it's an overlap and shown as two separate image with ring canal for better clarity. We have now quantified the image and have produced combined graph for fusome and pard3 in Figure 5A graph.

      (13) L261: Figure 5E-E': black arrowhead not mentioned in legend.

      We have now mentioned the black arrowhead in the legend

      (14) L262: Figure 5C: arrowhead not mentioned in legend. Figure 5F: oocyte appears separated from nurse cells compared to 5C.

      Yes, that may happen as cysts undergo fragmentation; what matters is all cells are lineage labelled and hence are members of a single cyst derived from one PGC.

      (15) L263: Figure 5G has no legend reference; nurse cells are not outlined as in 5C.

      We have now outlined the nurse cells and have added the reference to the graph in the legend.

      (16) L279: "The fusome and Visham and both..." should be replaced with "Both fusome and Visham...".

      We have now replaced the term Visham with fusome as suggested by reviewers and editor.  We updated the statement to correct the grammatical error.

      (17) L1127: Video S3B1: It is unclear what to focus on.

      We have now added the Rectangle area and arrow to highlight what to focus on

      (18) L1128: Video "S3B1" should be "S3B2."

      We have now corrected the legend

      (19) Finally: curiosity question: have the authors tried to use known markers of the Drosophila fusome in mice, such as Spectrin or other markers described in Lighthouse, Buszczak and Spradling, Dev Bio, 2008? And conversely, do EMA and WGA label the fusome in Drosophila?

      Yes, we and others used the most specific markers of the Drosophila fusome such alpha-spectrin, adducin-like Hts, tropomodulin, etc. to search for fusomes in vertebrate species. It was unsuccessful in clarifying the situation, because Hts and alpha-spectrin in Drosophila and other insects generate a protein skeleton that stabilizes the fusome and is easily stained. But this structure is simply not conserved in vertebrates. The polarity behavior of the fusome, it core developmental property, is conserved, however. The mammalian fusome still acquires and maintains cyst polarity, and goes even farther and reflects both initial cyst formation and cyst cleavage, before marking oocyte vs nurse cell development in the smaller cysts.  Expression of the inner microtubule-rich portion of the fusome, its Par proteins, and many ER-related and lysosomal fusome proteins are mostly conserved but their ability to mark the fusome alone varies with time and context (only some of the examples are shown in Figure 3I'). Nearly all of the proteins identified in Lighthouse et al. 2008 are expressed.  These proteins may be involved in rejuvenation as studied here.  We modified the first section of the Discussion to explicitly compare mouse, Xenopus and Drosophila fusomes, which was not possible before this work.  

      Reviewer #3 (Recommendations for the authors):

      The authors should either revise the conclusions or add additional evidence to support their claims. In addition, minor corrections are listed below.

      We have added additional evidence as noted in responses above, and revised some claims that were stated inaccurately.  In addition, we have attempted to clarify the evidence we do present, so that its full significance is more easily grasped by readers.    

      (1) Lines 20-21 are unclear - the cyst doesn't get sent into meiosis, each oocyte does.

      Research is showing that it's more complicated than that.  All cyst cells enter "pre-meiotic S phase", and most cell cycles are conventionally considered to start after the previous M phase-

      i.e. in G1 or S, not in the next prophase, an ancient view limited just to meiosis. Absent this old tradition from meiosis cytology, pre-meiotic S would just be called meiotic S as some workers on meiosis do.  In addition, in different species, nurse cells diverge from meiosis on different schedules, including many much later in the meiotic cycle.  Two cyst cells in Drosophila fully enter meiosis by all criteria, the oocyte and one nurse cell that only exits in late zygotene.  In Xenopus and mouse, scRNAseq shows that many cyst cells enter meiosis up to leptotene and zygotene, including nurse cells that specifically downregulate meiotic genes during this time, possibly to assist their nurse cell functions, while others remain in meiosis even longer (Davidian and Spradling, 2025; Niu and Spradling, 2022). Eventually, only the oocytes within each fragmented mouse cyst complete meiosis. 

      (2) Many places in the manuscript abbreviations are never defined or not defined the first time they are used (but the second or third time): Line 23-ER, Line 29-UPR, Line 33-PGC (not defined until line 45), Line 79-EGAD.

      We have defined full acronyms now upon their first occurrence.

      (3) Line 5 should be the pachytene substage of meiosis I.

      We have now updated the statement to “In pachytene stage of meiosis I…”

      (4) Line 59-61 - this statement needs a reference(s).

      These statements are a continuation from the references cited in the previous statements. However, for further clarity we have again cited the relevant reference here (Niu and Spradling, 2022).

      (5) Line 80 - should it be oocyte proteome quality control?

      We have now updated the statement to “Oocyte proteome quality control begins early”.

      (6) Line 87 - in this case, EMA does not stand for epithelial membrane antigen (AI will call it that, but it is not correct). I believe it originally was the abbrev for (Em)bryonic (a)ntigen, though some papers call it (e)mbryonic (m)ouse (a)ntigen. And the reference here is Hahnel and Eddy, 1986, but in the reference list is a different paper, 1987 (both refer to EMA-1).

      We have now updated the acronym EMA-1 in corrected form and have corrected the citation.

      (7) Line 176 - RNA seq.

      We have now updated the statement to “We performed single cell RNA sequencing (scRNA seq) of mouse gonad”.

      (8) Line 181 - Figure 4E and 4I should be 3E and 3I.

      We have now updated the figure reference in the text to correct one.

      (9) Line 183 - missing period.

      Added.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      (1) The network they propose is extremely simple. This simplicity has pros and cons: on the one hand, it is nice to see the basic phenomenon exposed in the simplest possible setting. On the other hand, it would also be reassuring to check that the mechanism is robust when implemented in a more realistic setting, using, for instance, a network of spiking neurons similar to the one they used in the 2008 paper. The more noisy and heterogeneous the setting, the better.

      The choice of a minimal model to illustrate our hypothesis is deliberate. Our main goal was to suggest a physiologically-grounded mechanism to rapidly encode temporally-structured information (i.e., sequences of stimuli) in Working Memory, where none was available before. Indeed, as discussed in the manuscript, previous proposals were unsatisfactory in several respects. In view of our main goal, we believe that a spiking implementation is beyond the scope of the present work.

      We would like to note that the mechanism originally proposed in Mongillo et al. (2008), has been repeatedly implemented, by many different groups, in various spiking network models with different levels of biological realism (see, e.g., Lundquivst et al. (2016), for an especially ‘detailed’ implementation) and, in all cases, the relevant dynamics has been observed. We take this as an indication of ‘robustness’; the relevant network dynamics doesn’t critically depend on many implementation details and, importantly, this dynamics is qualitatively captured by a simple rate model (see, e.g., Mi et al. (2017)).

      In the present work, we make a relatively ‘minor’ (from a dynamical point of view) extension of the original model, i.e., we just add augmentation. Accordingly, we are fairly confident that a set of parameters for the augmentation dynamics can be found such that the spiking network behaves, qualitatively, as the rate model. A meaningful study, in our opinion, then would require extensively testing the (large) parameters’ space (different models of augmentation?) to see how the network behavior compares with the relevant experimental observations (which ones? Behavioral? Physiological?). As said above, we believe that this is beyond the scope of the present work.

      This being said, we definitely agree with the reviewer that not presenting a spiking implementation is a limitation of the present work. We have clearly acknowledged this limitation here, by adding the following paragraph to the Discussion.

      “To illustrate our theory in a simple setting, we used a minimal model network that neglects many physiological details. This, however, constitutes a limitation of the present study. It would be reassuring to see that the mechanism we propose here is robust enough to reliably operate also in spiking networks, in the presence of heterogeneity in both single-cell and synaptic properties. While we are fairly confident that this is the case, a spiking implementation of our model is beyond the scope of the present study and will be addressed in the future. Also, because of the simplicity of the model network, a comparison between the model behavior and the electrophysiological observations cannot be completely direct. Nevertheless the model qualitatively accounts for a diverse set of experimental data”.

      (2) One major issue with the population spike scenario is that (to my knowledge) there is no evidence that these highly synchronized events occur in delay periods of working memory experiments. It seems that highly synchronized population spikes would imply (a) a strong regularity of spike trains of neurons, at odds with what is typically observed in vivo (b) high synchronization of neurons encoding for the same item (and also of different items in situations where multiple items have to be held in working memory), also at odds with in vivo recordings that typically indicate weak synchronization at best. It would be nice if the authors at least mention this issue, and speculate on what could possibly bridge the gap between their highly regular and synchronized network, and brain networks that seem to lie at the opposite extreme (highly irregular and weakly synchronized). Of course, if they can demonstrate using a spiking network simulation that they can bridge the gap, even better.

      Direct experimental evidence (in monkeys) in support of the existence of highly synchronized events -- to be identified with the ‘population spikes’ of our model -- during the delay period of a memory task is available in the literature, i.e., Panichello et al. (2024). we provide a short discussion of the results of Panichello et al. (2024) and how these results directly relate to our model. We also provide a short discussion of the results of Liebe et al. (2025), which, again, are fully consistent with our model.

      We note that there is no fundamental contradiction between highly synchronized events in ‘small’ neural populations (e.g., a cell assembly) on one hand, and temporally irregular (i.e., Poisson-like) spiking at the single-neuron level and weakly synchronized activity at the network level, on the other hand. This was already illustrated in our original publication, i.e., Mongillo et al. (2008) (see, in particular, Fig. S2). We further note that the mechanism we propose to encode temporal order -- a temporal gradient in the synaptic efficacies brought about by synaptic augmentation -- would also work if the memory of the items is maintained by ‘tonic’ persistent activity (i.e., without highly synchronized events), provided this activity occurs at suitably low rates such as to prevent the saturation of the synaptic augmentation.

      We have added the following two paragraphs to the Discussion.

      “More direct support to this interpretation comes from recent electrophysiological studies [Panichello et al., 2024, Liebe et al., 2025]. By recording large neuronal populations (∼ 300) simultaneously in the prefrontal cortex of monkeys performing a WM task, [Panichello et al., 2024] found that, during the maintenance period, the decoding of the actively held item from neural activity was ’intermittent’; that is, decoding was only possible during short epochs (∼ 100ms) interleaved with epochs (also ∼ 100ms) where decoding was at chance level. The inability to decode resulted from a loss of selectivity at the population level, with a return of the single-neuron firing rates to their spontaneous (pre-stimulus) activity levels. The transitions between these two activity states (decodable/not-decodable) were coordinated across large populations of neurons in PFC. By recording single-neuron activity in the medial temporal lobe of humans performing a sequential multi-item WM task, [Liebe et al., 2025] found that during maintenance, neurons coding for a given item tended to fire at a specific phase of the underlying theta rhythm, again suggesting that the corresponding neuronal populations reactivate briefly and sequentially. In summary, these experimental results suggest that active memory maintenance relies on brief reactivations of the neural representations of the items, which we identify with the population spikes in our model, and that these reactivatations occur sequentially in time, as predicted by our theory”.

      “We note that the proposed mechanism would still work if the items were maintained by tonically-enhanced firing rates, instead of population spikes, provided that those firing rates were suitably low. However, obtaining low firing rates in model networks of persistent activity is quite difficult”.

      Reviewer #2 (Public review):

      The study relates to the well-known computational theory for working memory, which suggests short-term synaptic facilitation is required to maintain working memory, but doesn't rely on persistent spiking. This previous theory appears similar to the proposed theory, except for the change from facilitation to augmentation. A more detailed explanation of why the authors use augmentation instead of facilitation in this paper is warranted: is the facilitation too short to explain the whole process of WM? Can the theory with synaptic facilitation also explain the immediate storage of novel sequences in WM?

      In the model, synaptic dynamics displays both short-term facilitation and augmentation (and shortterm depression). Indeed, synaptic facilitation, alone, would be too short-lived to encode novel sequences. This is illustrated in Fig. 1B.

      We provide a discussion of this important point, by adding the following paragraph to the Results section.

      “If augmentation was the only form of synaptic plasticity present in the network, the encoding of an item in WM would require long presentation times, or alternatively high firing rates upon presentation, precisely because K_A is small. Instead, rapid encoding is made possible by the presence of the short-term facilitation, which builds up significantly faster than augmentation, as U >> K_A . For the same reason, however, the level of facilitation rapidly reaches the steady state; therefore, short-term facilitation alone is unable to encode temporal order (see Fig. 1B). Thus, our model requires the existence of transitory synaptic enhancement on at least two time scales, such that longer decays are accompanied by slower build-ups. Intriguingly, this pattern is experimentally observed [Fisher et al., 1997]”.

      In Figure 1, the authors mention that synaptic augmentation leads to an increased firing rate even after stimulus presentation. It would be good to determine, perhaps, what the lowest threshold is to see the encoding of a WM task, and whether that is biologically plausible.

      We believe that this comment is related to the above point. The reviewer is correct; augmentation alone would require fairly long stimulus presentations to encode an item in WM. ‘Fast’ encoding, indeed, is guaranteed by the presence of short-term facilitation. This important point is emphasized; see above.

      In the middle panel of Figure 4, after 15-16 sec, when the neuronal population prioritizes with the second retro-cue, although the second retro-cue item's synaptic spike dominates, why is the augmentation for the first retro-cue item higher than the second-cue augmentation until the 20 sec?

      This is because of the slow build-up and decay of the augmentation. When the second item is prioritized, and the corresponding neuronal population re-activates, its augmentation level starts to increase. At the same time, as the first item is now de-prioritized and the corresponding neuronal population is now silent, its augmentation level starts to decrease. Because of the ‘slowness’ of both processes (i.e., augmentation build-up and decay), it takes about 5 seconds for the augmentation level of the second item to overcome the augmentation level of the first item.

      We note that the slow time scales of the augmentation dynamics, consistently with experimental observations, are necessary for our mechanism to work; see above.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Line 46 identify -> identity.

      (2) Line 207 scale -> scales.

      Fixed. Thank you.

      (3) Lines 222-224 what about behavioral time-scale plasticity? This type of plasticity can apparently be induced very quickly.

      We have removed the corresponding paragraph.

      (4) Line 231 identification of `gamma bursts' with population spikes: These two phenomena seem to be very different - one can be weakly synchronized and can be consistent with highly irregular activity, while it is not clear whether the other can (see major issue 2). Also, it seems that population spikes occur at frequencies that are an order of magnitude lower than gamma.

      We have rewritten the corresponding paragraph and we rely now on more direct electrophysiological evidence (i.e., on the simultaneous recording of large neuronal populations) to identify putative population spikes; see above.

      Reviewer #2 (Recommendations for the authors):

      (1) On page 7, the behavioral study of Rose et al. (2016) is quite important for readers to understand the 'low-activity regime', and to fully appreciate Figure 4, it would be beneficial to explain that study in greater detail.

      We have added a panel to Fig. 4, and accompanying text in the caption, to better illustrate the main task events in the experiment of Rose et al. (2016).

      (2) Line 17: "wrong order", but wrong timing matters too

      Definitely, depending on the task. Specifically, in our example, timing is immaterial.

      (3) Line 33-34: "special training", what is considered special? One could argue that the number of trials needed to learn, depending on the TI timing, is special, depending on the task.

      We have removed the sentence as apparently it was confusing. We simply meant that ‘naive’ human subjects can perform the task (e.g., serial recall); that is, they didn’t undergo any kind of practice that can be construed as ‘training’.

      (4) Line 40-41: but timing is also part of working memory processing. Perhaps it can be merged with the next sentence.

      We have merged the two sentences.

      (5) Line 53: Is the implication here that what happens in the synapses is what drives WM, and not just that the neurons stay persistently on?

      Yes. The idea is that information can be maintained in the synaptic facilitation level, without enhanced spiking activity. Reading-out and refreshing the memory contents, however, requires neuronal activity. We explain this in some detail in the next paragraph (i.e., lines 60-65 in the revised submission).

      (6) Line 102: could a lack of excitatory activity be explained by inhibitory signaling? It appears the inhibitory component is quite understated here.

      Here we are just defining A-bar; according to Eq. (6), if r_a is 0 (i.e., no synaptic activity, for whatever reason), then A_a will converge to A-bar after a time much longer than \tau_A (i.e., a long period). We have rephrased the sentence to improve clarity.

      (7) Line 158-172: please consider revising this paragraph for a more general audience.

      We have rewritten this paragraph to improve clarity. For the same purpose, we have also slightly modified Fig. 3.

      (8) Line 227: it would seem this is due to a singular inhibitory group making the model highly dependent on the excitatory groups.

      We are not sure that we understand this comment. Here, we are just saying that if the item-coding populations don’t reactivate during the maintenance period (i.e., activity-silent regime) then the augmentation gradient cannot build up. If, on the other hand, the item-coding populations are constantly active at high rates during the maintenance period (i.e., persistent-activity regime) then then augmentation levels will rapidly saturate and, again, there will be no augmentation gradient. This is independent of how ‘silence’ or ‘activity’ of the item-coding populations is determined by the interplay of excitation and inhibition.

      (9) Line 284: this would certainly be an interesting take, but it isn't clear that the model proved this type of decoupling of the temporal aspect of the recall.

      This is an ‘educated’ speculation, based on the model and on a specific interpretation of some experimental results, as discussed in the paper and, in particular, in the last paragraph of the Discussion. We believe that the phrasing of the paragraph makes clear that this is, indeed, a speculation.

    1. Author response:

      The following is the authors’ response to the previous reviews

      eLife Assessment

      This valuable study combines a computational language model, i.e., HM-LSTM, and temporal response function (TRF) modeling to quantify the neural encoding of hierarchical linguistic information in speech, and addresses how hearing impairment affects neural encoding of speech. The analysis has been significantly improved during the revision but remain somewhat incomplete - The TRF analysis should be more clearly described and controlled. The study is of potential interest to audiologists and researchers who are interested in the neural encoding of speech.

      We thank the editors for the updated assessment. In the revised manuscript, we have added a more detailed description of the TRF analysis on p. of the revised manuscript. We have also updated Figure 1 to better visualize the analyses pipeline. Additionally, we have included a supplementary video to illustrate the architecture of the HM-LSTM model, the ridge regression methods using the model-derived features, and mTRF analysis using the acoustic envelop and the binary rate models.

      Public Reviews:

      Reviewer #1 (Public review):

      About R squared in the plots:

      The authors have used a z-scored R squared in the main ridge regression plots. While this may be interpretable, it seems non-standard and overly complicated. The authors could use a simple Pearson r to be most direct and informative (and in line with similar work, including Goldstein et al. 2022 which they mentioned). This way the sign of the relationships is preserved.

      We did not use Pearson’s r as in Goldstein et al. (2022) because our analysis did not involve a train-test split, which was a key aspect of their approach. Specifically, Goldstein et al. (2022) divided their data into training and testing sets, trained a ridge regression model on the training set, and then used the trained model to predict neural responses on the test set. They calculated Pearson’s r to assess the correlation between the predicted and observed neural responses, making the correlation coefficient (r) their primary measure of model performance. In contrast, our analysis focused on computing the model fitting performance (R²) of the ridge regression model for each sensor and time point for each subject. At the group level, we conducted one-sample t-tests with spatiotemporal cluster-based correction on the R² values to identify sensors and time windows where R² values were significantly greater than baseline. We established the baseline by normalizing the R² values using Fisher z-transformation across sensors within each subject. We have added this explanation on p.13 of the revised manuscript.

      About the new TRF analysis:

      The new TRF analysis is a necessary addition and much appreciated. However, it is missing the results for the acoustic regressors, which should be there analogous to the HM-LSTM ridge analysis. The authors should also specify which software they have utilized to conduct the new TRF analysis. It also seems that the linguistic predictors/regressors have been newly constructed in a way more consistent with previous literature (instead of using the HM-LSTM features); these specifics should also be included in the manuscript (did it come from Montreal Forced Aligner, etc.?). Now that the original HM-LSTM can be compared to a more standard TRF analysis, it is apparent that the results are similar.

      We used the Python package Eelbrain (https://eelbrain.readthedocs.io/en/r0.39/auto_examples/temporal-response-functions/trf_intro.html) to conduct the multivariate temporal response function (mTRF) analyses. As we previously explained in our response to R3, we did not apply mTRF to the acoustic features due to the high dimensionality of the input. Specifically, our acoustic representation consists of a 130-dimensional vector sampled every 10 ms throughout the speech stimuli (comprising a 129-dimensional spectrogram and a 1dimensional amplitude envelope). This led to interpreting the 130-dimensional TRF estimation difficult to interpret. A similar constraint applied to the hidden-layer activations from our HMLSTM model for the five linguistic features. After dimensionality reduction via PCA, each still resulted in 150-dimensional vectors. To address this, we instead used binary predictors marking the offset of each linguistic unit (phoneme, syllable, word, phrase, sentence). Since our speech stimuli were computer-synthesized, the phoneme and syllable boundaries were automatically generated. The word boundaries were manually annotated by a native Mandarin as in Li et al. (2022). The phrase boundaries were automatically annotated by the Stanford parser and manually checked by a native Mandarin speaker. These rate models are represented as five distinct binary time series, each aligned with the timing of the corresponding linguistic unit, making them well-suited for mTRF analysis. Although the TRF results from the 1-dimensional rate predictors and the ridge regression results from the high-dimensional HM-LSTM-derived features are similar, they encode different things: The rate regressors only encode the timing of linguistic unit boundaries, while the model-derived features encode the representational content of the linguistic input. Therefore, we do not consider the mTRF analyses to be analogous to the ridge regression analyses. Rather, these results complement each other and both provide informative results into the neural tracking of linguistic structures at different levels for the attended and unattended speech.

      Since the TRF result for the continuous acoustic features also concerns R2, we have added an mTRF analysis where we fitted the one-dimensional speech envelope to the EEG. We extracted the envelope at 10 ms intervals for both attended and unattended speech and computed mTRFs independently for each subject and sensor using a basis of 50 ms Hamming windows spanning –100 ms to 300 ms relative to envelope onset. The results showed that in hearing-impaired participants, attended speech elicited a significant cluster in the bilateral temporal regions from 270 to 300 ms post-onset (t = 2.40, p = 0.01, Cohen’s d = 0.63). Unattended speech elicited an early cluster in right temporal and occipital regions from –100 ms to –80 ms (t = 3.07, p = 0.001, d = 0.83). Normal-hearing participants showed significant envelope tracking in the left temporal region at 280–300 ms after envelope onset (t = 2.37, p = 0.037, d = 0.48), with no significant cluster for unattended speech. These results further suggest that hearing-impaired listeners may have difficulty suppressing unattended streams. We have added the new TRF results for envelope to Figure S3 and the “mTRF results for attended and unattended speech” on p.7 and the “mTRF analysis” in Material and Methods of the revised manuscript.

      The authors' wording about this suggests that these new regressors have a nonzero sample at each linguistic event's offset, not onset. This should also be clarified. As the authors know, the onset would be more standard, and using the offset has implications for understanding the timing of the TRFs, as a phoneme has a different duration than a word, which has a different duration from a sentence, etc.

      In our rate‐model mTRF analyses, we initially labelled linguistic boundaries as “offsets” because our ridge‐regression with HM-LSTM features was aligned to sentence offsets rather than onsets. However, since each offset coincides with the next unit’s onset—and our regressors simply mark these transition points as 1—the “offset” and “onset” models yield identical mTRFs. To avoid confusion, we have relabeled “offset” as “boundary” in Figure S2.

      As discussed in our prior responses, this design was based on the structure of our input to the HM-LSTM model, where each input consists of a pair of sentences encoded in phonemes, such as “t a_1 n əŋ_2 f ei_1 <sep> zh ə_4 sh iii_4 f ei_1 j ii_1” (“It can fly <sep> This is an airplane”). The two sentences are separated by a special <sep> token, and the model’s objective is to determine whether the second sentence follows the first, similar to a next-sentence prediction task. Since the model processes both sentences in full before making a prediction, the neural activations of interest should correspond to the point at which the entire sentence has been processed by humans. To enable a fair comparison between the model’s internal representations and brain responses, we aligned our neural analyses with the sentence offsets, capturing the time window after the sentence has been fully perceived by the participant. Thus, we extracted epochs from -100 to +300 ms relative to each sentence offset, consistent with our model-informed design.

      We understand that phonemes, syllables, words, phrases, and sentences differ in their durations. However, the five hidden activity vectors extracted from the model are designed to capture the representations of these five linguistic levels across the entire sentence. Specifically, for a sentence pair such as “It can fly <sep> This is an airplane,” the first 2048-dimensional vector represents all the phonemes in the two sentences (“t a_1 n əŋ_2 f ei_1 <sep> zh ə_4 sh iii_4 f ei_1 j ii_1”), the second vector captures all the syllables (“ta_1 nəŋ_2 fei_1 <sep> zhə_4 shiii_4 fei_1jii_1”), the third vector represents all the words, the fourth vector captures the phrases, and the fifth vector represents the sentence-level meaning. In our dataset, input pairs consist of adjacent sentences from the stimuli (e.g., Sentence 1 and Sentence 2, Sentence 2 and Sentence 3, and so on), and for each pair, the model generates five 2048-dimensional vectors, each corresponding to a specific linguistic level. To identify the neural correlates of these model-derived features—each intended to represent the full linguistic level across a complete sentence—we focused on the EEG signal surrounding the completion of the second sentence rather than on incremental processing. Accordingly, we extracted epochs from -100 ms to +300 ms relative to the offset of the second sentence and performed ridge regression analyses using the five model features (reduced to 150 dimensions via PCA) at every 50 ms across the epoch. We have added this clarification on p.12 of the revised manuscript.

      About offsets:

      TRFs can still be interpretable using the offset timings though; however, the main original analysis seems to be utilizing the offset times in a different, more confusing way. The authors still seem to be saying that only the peri-offset time of the EEG was analyzed at all, meaning the vast majority of the EEG trial durations do not factor into the main HM-LSTM response results whatsoever. The way the authors describe this does not seem to be present in any other literature, including the papers that they cite. Therefore, much more clarification on this issue is needed. If the authors mean that the regressors are simply time-locked to the EEG by aligning their offsets (rather than their onsets, because they have varying onsets or some such experimental design complexity), then this would be fine. But it does not seem to be what the authors want to say. This may be a miscommunication about the methods, or the authors may have actually only analyzed a small portion of the data. Either way, this should be clarified to be able to be interpretable.

      We hope that our response in RE4, along with the supplementary video, has helped clarify this issue. We acknowledge that prior studies have not used EEG data surrounding sentence offsets to examine neural responses at the phoneme or syllable levels. However, this is largely due to a lack of model that represent all linguistic levels across an entire sentence. There is abundant work comparing model predictors with neural data time-locked to offsets because they mark the point at which participants has already processed the relevant information (Brennan, 2016; Brennan et al., 2016; Gwilliams et al., 2024, 2025). Similarly, in our model– brain alignment study, our goal is to identify neural correlates for each model-derived feature. If we correlate model activity with EEG data aligned to sentence onsets, we would be examining linguistic representations at all levels (from phoneme to sentence) of the whole sentence at the time when participants have not heard the sentence yet. Although this limits our analysis to a subset of the data (143 sentences × 400 ms windows × 4 conditions), it targets the exact moment when full-sentence representations emerge against background speech, allowing us to examine each model-derived feature onto its neural signature. We have added this clarification on p.12 of the revised manuscript.

      Reviewer #2 (Public review):

      This study presents a valuable finding on the neural encoding of speech in listeners with normal hearing and hearing impairment, uncovering marked differences in how attention to different levels of speech information is allocated, especially when having to selectively attend to one speaker while ignoring an irrelevant speaker. The results overall support the claims of the authors, although a more explicit behavioural task to demonstrate successful attention allocation would have strengthened the study. Importantly, the use of more "temporally continuous" analysis frameworks could have provided a better methodology to assess the entire time course of neural activity during speech listening. Despite these limitations, this interesting work will be useful to the hearing impairment and speech processing research community. The study compares speech-in-quiet vs. multi-talker scenarios, allowing to assess within-participant the impact that the addition of a competing talker has on the neural tracking of speech. Moreover, the inclusion of a population with hearing loss is useful to disentangle the effects of attention orienting and hearing ability. The diagnosis of high-frequency hearing loss was done as part of the experimental procedure by professional audiologists, leading to a high control of the main contrast of interest for the experiment. Sample size was big, allowing to draw meaningful comparisons between the two populations.

      We thank you very much for your appreciation of our research and we have now added a more description of the mTRF analyses on p.13-14 of the revised manuscript.

      An HM-LSTM model was employed to jointly extract speech features spanning from the stimulus acoustics to word-level and phrase-level information, represented by embeddings extracted at successive layers of the model. The model was specifically expanded to include lower level acoustic and phonetic information, reaching a good representation of all intermediate levels of speech. Despite conveniently extracting all features jointly, the HMLSTM model processes linguistic input sentence-by-sentence, and therefore only allows to assess the corresponding EEG data at sentence offset. If I understood correctly, while the sentence information extracted with the HM-LSTM reflects the entire sentence - in terms of its acoustic, phonetic and more abstract linguistic features - it only gives a condensed final representation of the sentence. As such, feature extraction with the HM-LSTM is not compatible with a continuous temporal mapping on the EEG signal, and this is the main reason behind the authors' decision to fit a regression at nine separate time points surrounding sentence offsets.

      Yes, you are correct. As explained in RE4, the model generates five hidden-layer activity vectors, each intended to represent all the phonemes, syllables, words, phrases within the entire sentence (“a condensed final representation”). This is the primary reason we extract EEG data surrounding the sentence offsets—this time point reflects when the full sentence has been processed by the human brain. We assume that even at this stage, residual neural responses corresponding to each linguistic level are still present and can be meaningfully analyzed.

      While valid and previously used in the literature, this methodology, in the particular context of this experiment, might be obscuring important attentional effects impacted by hearing-loss. By fitting a regression only around sentence-final speech representations, the method might be overlooking the more "online" speech processing dynamics, and only assessing the permanence of information at different speech levels at sentence offset. In other words, the acoustic attentional bias between Attended and Unattended speech might exist even in hearing-impaired participants but, due to a lower encoding or permanence of acoustic information in this population, it might only emerge when using methodologies with a higher temporal resolution, such as Temporal Response Functions (TRFs). If a univariate TRF fit simply on the continuous speech envelope did not show any attentional bias (different trial lengths should not be a problem for fitting TRFs), I would be entirely convinced of the result. For now, I am unsure on how to interpret this finding.

      We agree and we have added the mTRF results using the rate models for the 5 linguistic levels in the prior revision. The rate model aligns with the boundaries of each linguistic unit at each level. As explained in RE3, the rate regressors encode the timing of linguistic unit boundaries, while the model-derived features encode the representational content of the linguistic input. The mTRF results showed similar patterns to those observed using features from our HM-LSTM model with ridge regression (see Figure S2). These results complement each other and both provide informative results into the neural tracking of linguistic structures at different levels for the attended and unattended speech.

      We have also added TRF results fitting the envelope of attended and unattended speech at every 10 ms to the whole 10-minute EEG data at every 10 ms. Our results showed that in hearing-impaired participants, attended speech elicited a significant cluster in the bilateral temporal regions from 270 to 300 ms post-onset (t = 2.40, p = 0.01, Cohen’s d = 0.63). Unattended speech elicited an early cluster in right temporal and occipital regions from –100 ms to –80 ms (t = 3.07, p = 0.001, d = 0.83). Normal-hearing participants showed significant envelope tracking in the left temporal region at 280–300 ms after envelope onset (t = 2.37, p = 0.037, d = 0.48), with no significant cluster for unattended speech. These results further suggest that hearing-impaired listeners may have difficulty suppressing unattended streams. We have added the new TRF results for envelope to Figure S3 and the “mTRF results for attended and unattended speech” on p.7 and the “mTRF analysis” in Material and Methods of the revised manuscript.

      Despite my doubts on the appropriateness of condensed speech representations and singlepoint regression for acoustic features in particular, the current methodology allows the authors to explore their research questions, and the results support their conclusions. This work presents an interesting finding on the limits of attentional bias in a cocktail-party scenario, suggesting that fundamentally different neural attentional filters are employed by listeners with highfrequency hearing loss, even in terms of the tracking of speech acoustics. Moreover, the rich dataset collected by the authors is a great contribution to open science and will offer opportunities for re-analysis.

      We sincerely thank you again for your encouraging comments regarding the impact of our study.

      Reviewer #3 (Public review):

      Summary:

      The authors aimed to investigate how the brain processes different linguistic units (from phonemes to sentences) in challenging listening conditions, such as multi-talker environments, and how this processing differs between individuals with normal hearing and those with hearing impairments. Using a hierarchical language model and EEG data, they sought to understand the neural underpinnings of speech comprehension at various temporal scales and identify specific challenges that hearing-impaired listeners face in noisy settings.

      Strengths:

      Overall, the combination of computational modeling, detailed EEG analysis, and comprehensive experimental design thoroughly investigates the neural mechanisms underlying speech comprehension in complex auditory environments. The use of a hierarchical language model (HM-LSTM) offers a data-driven approach to dissect and analyze linguistic information at multiple temporal scales (phoneme, syllable, word, phrase, and sentence). This model allows for a comprehensive neural encoding examination of how different levels of linguistic processing are represented in the brain. The study includes both single-talker and multi-talker conditions, as well as participants with normal hearing and those with hearing impairments. This design provides a robust framework for comparing neural processing across different listening scenarios and groups.

      Weaknesses:

      The analyses heavily rely on one specific computational model, which limits the robustness of the findings. The use of a single DNN-based hierarchical model to represent linguistic information, while innovative, may not capture the full range of neural coding present in different populations. A low-accuracy regression model-fit does not necessarily indicate the absence of neural coding for a specific type of information. The DNN model represents information in a manner constrained by its architecture and training objectives, which might fit one population better than another without proving the non-existence of such information in the other group. It is also not entirely clear if the DNN model used in this study effectively serves the authors' goal of capturing different linguistic information at various layers. More quantitative metrics on acoustic/linguistic-related downstream tasks, such as speaker identification and phoneme/syllable/word recognition based on these intermediate layers, can better characterize the capacity of the DNN model.

      We agree that, before aligning model representations with neural data, it is essential to confirm that the model encodes linguistic information at multiple hierarchical levels. This is the purpose of our validation analysis: We evaluated the model’s representations across five layers using a test set of 20 four-syllable sentences in which every syllable shares the same vowel—e.g., “mā ma mà mǎ” (mother scolds horse), “shū shu shǔ shù” (uncle counts numbers; see Table S1). We hypothesized that the activity in the phoneme and syllable layer would be more similar than other layers for same-vowel sentences. The results confirmed our hypothesis: Hidden-layer activity for same-vowel sentences exhibited much more similar distributions at the phoneme and syllable levels compared to those at the word, phrase and sentence levels Figure 3C displays the scatter plot of the model activity at the five linguistic levels for each of the 20 4-syllable sentences, post dimension reduction using multidimensional scaling (MDS). We used color-coding to represent the activity of five hidden layers after dimensionality reduction. Each dot on the plot corresponds to one test sentence. Only phonemes are labeled because each syllable in our test sentences contains the same vowels (see Table S1).The plot reveals that model representations at the phoneme and syllable levels are more dispersed for each sentence, while representations at the higher linguistic levels—word, phrase, and sentence—are more centralized. Additionally, similar phonemes tend to cluster together across the phoneme and syllable layers, indicating that the model captures a greater amount of information at these levels when the phonemes within the sentences are similar.

      Apart from the DNN model, we also included the rate models which simply mark 1 at each unit boundaries across the 5 levels. We performed mTRF analyses with these rate models and found similar patterns to our ridge‐regression results with the DNN: (see Figure S2). This provides further evidence that the model reliably captures information across all five hierarchical levels.

      Since EEG measures underlying neural activity in near real-time, it is expected that lower-level acoustic information, which is relatively transient, such as phonemes and syllables, would be distributed throughout the time course of the entire sentence. It is not evident if this limited time window effectively captures the neural responses to the entire sentence, especially for lower-level linguistic features. A more comprehensive analysis covering the entire time course of the sentence, or at least a longer temporal window, would provide a clearer understanding of how different linguistic units are processed over time.

      We agree that lower-level linguistic features may be distributed throughout the whole sentence, however, using the entire sentence duration was not feasible, as the sentences in the stimuli vary in length, making statistical analysis challenging. Additionally, since the stimuli consist of continuous speech, extending the time window would risk including linguistic units from subsequent sentences. This would introduce ambiguity as to whether the EEG responses correspond to the current or the following sentence. Additionally, our model activity represents a “condensed final representation” at the five linguistic levels for the whole sentence, rather than incrementally during the sentence. We think the -100 to 300 ms time window relative to each sentence offset targets the exact moment when full-sentence representations are comprehended and a “condensed final representation” for the whole sentence across five linguistic level have been formed in the brain. We have added this clarification on p.13 of the revised manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Here are some specifics and clarifications of my public review:

      Initially I was interpreting the R squared as a continuous measure of predicted EEG relative to actual EEG, based on an encoding model, but this does not appear to be correct. Thank you for pointing out that the y axis is z-scored R squared in your main ridge regression plots. However, I am not sure why/how you chose to represent this that way. It seems to me that a simple Pearson r would be most informative here (and in line with similar work, including Goldstein et al. 2022 that you mentioned). That way you preserve the sign of the relationships between the regressors and the EEG. With R squared, we have a different interpretation, which is maybe also ok, but I also don't see the point of z-scoring R squared. Another possibility is that when you say "z-transformed" you are referring to the Fisher transformation; is that the case? In the plots you say "normalized", so that sounds like a z-score, but this needs to be clarified; as I say, a simple Pearson r would probably be best.

      We did not use Pearson’s r, as in Goldstein et al. (2022), because our analysis did not involve a train-test split, which was central to their approach. In their study, the data were divided into training and testing sets, and a ridge regression model was trained on the training set. They then used the trained model to predict neural responses on the held-out test set, and calculated Pearson’s r to assess the correlation between the predicted and observed neural responses. As a result, their final metric of model performance was the correlation coefficient (r). In contrast, our analysis is more aligned with standard temporal response function (TRF) approaches. We did not perform a train-test split; instead, we computed the model fitting performance (R²) of the ridge regression model at each sensor and time point for each subject. At the group level, we conducted one-sample t-tests with spatiotemporal cluster-based correction on the R² values to determine which sensors and time windows showed significantly greater R² values than baseline. To establish a baseline, we z-scored the R² values across sensors and time points, effectively centering the distribution around zero. This normalization allowed us to interpret deviations from the mean R² as meaningful increases in model performance and provided a suitable baseline for the statistical tests. We have added this clarification on p.13 of the revised manuscript.

      Thank you for doing the TRF analysis, but where are the acoustic TRFs, analogous to the acoustic results for your HM-LSTM ridge analyses? And what tools did you use to do the TRF analysis? If it is something like the mTRF MATLAB toolbox, then it is also using ridge regression, as you have already done in your original analysis, correct? If so, then it is pretty much the same as your original analysis, just with more dense timepoints, correct? This is what I meant by referring to TRFs originally, because what you have basically done originally was to make a 9-point TRF (and then the plots and analyses are contrasts of pairs of those), with lags between -100 and 300 ms relative to the temporal alignment between the regressors and the EEG, I think (more on this below).

      Also with the new TRF analysis, you say that the regressors/predictors had "a value of 1 at each unit boundary offset". So this means you re-made these predictors to be discrete as I and reviewer 3 were mentioning before (rather than using the HM-LSTM model layer(s)), and also, that you put each phoneme/word/etc. marker at its offset, rather than its onset? I'm also confused as to why you would do this rather than the onset, but I suppose it doesn't change the interpretation very much, just that the TRFs are slid over by a small amount.

      We used the Python package Eelbrain (https://eelbrain.readthedocs.io/en/r0.39/auto_examples/temporal-response-functions/trf_intro.html) to conduct the multivariate temporal response function (mTRF) analyses. As we previously explained in our response to Reviewer 3, we did not apply mTRF to the acoustic features due to the high dimensionality of the input. Specifically, our acoustic representation consists of a 130-dimensional vector sampled every 10 ms throughout the speech stimuli (comprising a 129-dimensional spectrogram and a 1-dimensional amplitude envelope). This renders the 130 TRF weights to the acoustic features uninterpretable. However, we have now added TRF results from the 1- dimension envelope to the attended and unattended speech at every 10 ms.

      A similar constraint applied to the hidden-layer activations from our HM-LSTM model for the five linguistic features. After dimensionality reduction via PCA, each still resulted in 150-dimensional vectors, further preventing their use in mTRF analyses. To address this, we instead used binary predictors marking the offset of each linguistic unit (phoneme, syllable, word, phrase, sentence). These rate models are represented as five distinct binary time series, each aligned with the timing of the corresponding linguistic unit, making them well-suited for mTRF analysis. It is important to note that these rate predictors differ from the HM-LSTMderived features: They encode only the timing of linguistic unit boundaries, not the content or representational structure of the linguistic input. Therefore, we do not consider the mTRF analyses to be equivalent to the ridge regression analyses based on HM-LSTM features

      For onset vs. offset, as explained RE4, we labelled them “offsets” because our ridge‐regression with HM-LSTM features was aligned to sentence offsets rather than onsets (see RE4 and RE15 below for the rationale of using sentence offset). However, since each unit offset coincides with the next unit’s onset—and the rate model simply mark these transition points as 1—the “offset” and “onset” models yield identical mTRFs. To avoid confusion, we have relabeled “offset” as “boundary” in Figure S2.

      I'm still confused about offsets generally. Does this maybe mean that the EEG, and each predictor, are all aligned by aligning their endpoints, which are usually/always the ends of sentences? So e.g. all the phoneme activity in the phoneme regressor actually corresponds to those phonemes of the stimuli in the EEG time, but those regressors and EEG do not have a common starting time (one trial to the next maybe?), so they have to be aligned with their ends instead?

      We chose to use sentence offsets rather than onsets based on the structure of our input to the HM-LSTM model, where each input consists of a pair of sentences encoded in phonemes, such as “t a_1 n əŋ_2 f ei_1 <sep> zh ə_4 sh iii_4 f ei_1 j ii_1” (“It can fly <sep> This is an airplane”). The two sentences are separated by a special <sep> token, and the model’s objective is to determine whether the second sentence follows the first, similar to a next-sentence prediction task. Since the model processes both sentences in full before making a prediction, the neural activations of interest should correspond to the point at which the entire sentence has been processed. To enable a fair comparison between the model’s internal representations and brain responses, we aligned our neural analyses with the sentence offsets, capturing the time window after the sentence has been fully perceived by the participant. Thus, we extracted epochs from -100 to +300 ms relative to each sentence offset, consistent with our modelinformed design. If we align model activity with EEG data aligned to sentence onsets, we would be examining linguistic representations at all levels (from phoneme to sentence) of the whole sentence at the time when participants have not heard the sentence yet. By contrast, aligning to sentence offsets ensures that participants have constructed a full-sentence representation.

      We understand that it is a bit confusing why the regressor of each level is not aligned to their own offsets in the data. The hidden-layer activations of the HM-LSTM model corresponding to the five linguistic levels (phoneme, syllable, word, phrase, sentence) are consistently 150-dimensional vectors after PCA reduction. As a result, for each input sentence pair, the model produces five distinct hidden-layer activations, each capturing the representational content associated with one linguistic level for the whole sentence. We believe our -100 to 300 ms time window relative to sentence offset reflects a meaningful period during which the brain integrates and comprehends information across multiple linguistic levels.

      Being "time-locked to the offset of each sentence at nine latencies" is not something I can really find in any of the references that you mentioned, regarding the offset aspect of this method. Can you point me more specifically to what you are trying to reference with that, or further explain? You said that "predicting EEG signals around the offset of each sentence" is "a method commonly employed in the literature", but the example you gave of Goldstein 2022 is using onsets of words, which is indeed much more in line with what I would expect (not offsets of sentences).

      You are correct that Goldstein (2022) aligned model predictions to onsets rather than offsets; however, many studies in the literature also align model predictions with unit offsets. typically because they mark the point at which participants has already processed the relevant information (Brennan, 2016; Brennan et al., 2016; Gwilliams et al., 2024, 2025). Similarly, in our study, we aim to identify neural correlates for each model-derived feature. If we correlate model activity with EEG data aligned to sentence onsets, we would be examining linguistic representations at all levels (from phoneme to sentence) of the whole sentence at the time when participants have not heard the sentence yet. By contrast, aligning to sentence offsets ensures that participants have constructed a full-sentence representation. Although this limits our analysis to a subset of the data (143 sentences × 400 ms windows × 4 conditions), it targets the exact moment when full-sentence representations emerge against background speech, allowing us to examine each model-derived feature onto its neural signature. We have added this clarification on p.12 of the revised manuscript.

      This new sentence does not make sense to me: "The regressors are aligned to sentence offsets because all our regressors are taken from the hidden layer of our HM-LSTM model, which generates vector representations corresponding to the five linguistic levels of the entire sentence".

      Thank you for the suggestion. We hope our responses in RE4, 15 and 16, along with our supplementary video have now clarified the issue. We have deleted the sentence and provided a more detailed explanation on p.12 of the revised manuscript: The regressors are aligned to sentence offsets because our goal is to identify neural correlates for each model-derived feature of a whole sentence. If we align model activity with EEG data time-locked to sentence onsets, we would be finding neural responses to linguistic levels (from phoneme to sentence) of the whole sentence at the time when participants have not processed the sentence yet. By contrast, aligning to sentence offsets ensures that participants have constructed a full-sentence representation. Although this limits our analysis to a subset of the data (143 sentences × 2 sections × 400 ms windows), it targets the exact moment when full-sentence representations emerge against background speech, allowing us to examine each model-derived feature onto its neural signature. We understand that phonemes, syllables, words, phrases, and sentences differ in their durations. However, the five hidden activity vectors extracted from the model are designed to capture the representations of these five linguistic levels across the entire sentence Specifically, for a sentence pair such as “It can fly <sep> This is an airplane,” the first 2048dimensional vector represents all the phonemes in the two sentences (“t a_1 n əŋ_2 f ei_1 <sep> zh ə_4 sh iii_4 f ei_1 j ii_1”), the second vector captures all the syllables (“ta_1 nəŋ_2 fei_1 <sep> zhə_4 shiii_4 fei_1jii_1”), the third vector represents all the words, the fourth vector captures the phrases, and the fifth vector represents the sentence-level meaning. In our dataset, input pairs consist of adjacent sentences from the stimuli (e.g., Sentence 1 and Sentence 2, Sentence 2 and Sentence 3, and so on), and for each pair, the model generates five 2048dimensional vectors, each corresponding to a specific linguistic level. To identify the neural correlates of these model-derived features—each intended to represent the full linguistic level across a complete sentence—we focused on the EEG signal surrounding the completion of the second sentence rather than on incremental processing. Accordingly, we extracted epochs from -100 ms to +300 ms relative to the offset of the second sentence and performed ridge regression analyses using the five model features (reduced to 150 dimensions via PCA) at every 50 ms across the epoch.

      More on the issue of sentence offsets: In response to reviewer 3's question about -100 - 300 ms around sentence offset, you said "Using the entire sentence duration was not feasible, as the sentences in the stimuli vary in length, making statistical analysis challenging. Additionally, since the stimuli consist of continuous speech, extending the time window would risk including linguistic units from subsequent sentence." This does not make sense to me, so can you elaborate? It sounds like you are actually saying that you only analyzed 400 ms of each trial, but that cannot be what you mean.

      Yes, we analyzed only the 400 ms window surrounding each sentence offset. Although this represents just a subset of our data (143 sentences × 400 ms × 4 conditions), it precisely captures when full-sentence representations emerge against background speech. Because our model produces a single, condensed representation for each linguistic level over the entire sentence—rather than incrementally—we think it is more appropriate to align to the period surrounding sentence offsets. Additionally, extending the window (e.g. to 2 seconds) would risk overlapping adjacent sentences, since sentence lengths vary. Our focus is on the exact period when integrated, level-specific information for each sentence has formed in the brain, and our results already demonstrate different response patterns to different linguistic levels for the two listener groups within this interval. We have added this clarification on p.13 of the revised manuscript.

      In your mTRF analysis, you are now saying that the discrete predictors have "a value of 1" at each of the "boundary offsets", and those TRFs look very similar to your original plots. It sounds to me like you should not be referring to time zero in your original ridge analysis as "sentence offset". If what you mean is that sentence offset time is merely how you aligned the regressors and EEG in time, then your time zero still has a standard, typical TRF interpretation. It is just the point in time, or lag, at which the regressor(s) and EEG are aligned. So activity before zero is "predictive" and activity after zero is "reactive", to think of it crudely. So also in the text, when you say things like "50-150 ms after the sentence offsets", I think this is not really what you mean. I think you are referring to the lags of 50 - 150 ms, relative to the alignment of the regressor and the EEG.

      Thank you very much for the explanation. We agree that, in our ridge‐regression time course, pre zero lags index “predictive” processing and post-zero lags index “reactive” processing. Unlike TRF analysis, we applied ridge regression to our high-dimensional model features at nine discrete lags around the sentence offset. At each lag, we tested whether the regression score exceeded a baseline defined as the mean regression score across all lags. For example, finding a significantly higher regression score between 50 and 150 ms suggests that our regressor reliably predicted EEG activity in that time window. So here time zero refers to the precise moment of the sentence offset—not the the alignment of the regressor and the EEG.

      I look forward to discussing how much of my interpretation here makes sense or doesn't, both with the authors and reviewers.

      Thank you very much for these very constructive feedback and we hope that we have addressed all your questions.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      The researchers conducted their study using advanced techniques. They found almost no difference in calcium binding between the two proteins and observed no impact on calcium signaling, specifically store-operated calcium entry (SOCE). The study also noted an increase in ER luminal calcium-binding chaperone proteins. Surprisingly, the authors selected flow cytometry as a technique for measurements of ER luminal calcium. Considering the limitations of this approach, it would be better to use alternative approaches.

      The flow cytometric assay shows good responsiveness to conditions expected to alter ER calcium levels (Figure 4C), is high throughput compared to microscopy, and allows for averaging of signals across a large number of cells. This was thus our original method of choice.

      This is particularly important as previous reports, using cells from MPN patients, indicate reduced ER luminal calcium and effects on SOCE (Blood, 2020). This issue matters because earlier research with MPN patient cells reported reduced ER luminal calcium levels and altered SOCE (Blood, 2020). How do the authors explain the difference between their results and previous findings about lower ER luminal calcium and changed SOCE in MPN patient cells expressing CRTDel52?

      We thank the reviewer for asking for these clarifications. The referenced study (Di Buduo et al. Blood, 135(2):133-143, 2020) first showed that thrombopoietin induces spontaneous cytosolic calcium spikes in cultured megakaryocytes, which is dependent on store operated calcium entry (SOCE). In parallel, STIM1-ORAI interactions were induced by thrombopoietin. On the other hand, the addition of thrombopoietin caused the dissociation of STIM1-calreticulin interactions, based on proximity ligation assays. The implication is that signaling via the thrombopoietin receptor (TPOR/MPL) activation induces the dissociation of calreticulin-STIM1 complexes, and the formation of STIM1-ORAI complexes, which contribute to the measured spontaneous cytosolic calcium spikes. Different MPN mutations induced spontaneous calcium spikes in a thrombopoietin-independent manner, including the JAK2V617F mutations and the CALR type I and type II mutations. The study found that the number of megakaryocytes exhibiting spontaneous calcium spikes was enhanced in the context of both type I and type II CALR mutations compared to the JAK2V617F mutant. Correspondingly, the calreticulin-STIM1 interactions/cell were more significantly reduced for type I and type II CALR mutations compared to the JAK2V617F mutant. It was suggested that defective interactions between mutant calreticulin, ERp57, and STIM1 activated SOCE and generated spontaneous cytosolic calcium spikes. However, based on the findings with thrombopoietin, the spontaneous calcium spikes could simply result from thrombopoietin-independent MPL activation by the mutant calreticulin and JAK2V617F and downstream signaling. Importantly, the referenced studies did not directly measure ER luminal calcium. A number of undefined factors could account for the measured differences between the megakaryocytes from patients with calreticulin mutations vs. JAK2V617F. These include the relative mutant allele burdens, the extent of MPL activation, as well as genetic differences unrelated to calreticulin. Different from these experiments, through the use of purified proteins, our studies show that the Del52 mutant has calcium binding characteristics resembling that of the wild type protein. Additionally, through genetic manipulations in cell lines, our studies directly address the effects of calreticulin KO and its Del52 mutation upon ER luminal and cytosolic calcium levels, and cellular SOCE signals. We did not measure significant differences in any of these parameters between the KO cells and those reconstituted with wild type calreticulin or the Del52 mutant. As noted by the editors, these results show that Ca2+ binding by calreticulin and store-operated Ca2+ entry in a cell are not fundamentally impacted by the type I deletion mutation. On the other hand, in primary megakaryocytes, when co-expressed with MPL, the Del52 mutant, through its known ability to bind and activate TPOR/MPL, is expected to induce SOCE and calcium fluxes similar to those induced by thrombopoietin. These points will be clarified in the revised discussion.

      Other studies have found that unfolded protein responses are activated in MPN cells with CRTDel52 calreticulin (see Blood, 2021), and increased UPR could account for higher levels of some ER-resident calcium-binding proteins observed here.

      Multiple studies have suggested the induction of the unfolded protein response (UPR) in cells expressing MPN mutants of calreticulin.  We don’t know the specific signals that cause the upregulation of various calcium binding proteins in calreticulin-KO cells and cells expressing the Del52 mutant. Indeed, these could result from increased protein misfolding in cells with wild type calreticulin deficiency. Alternatively, the sensing of cellular calcium perturbations could induce their expression. Regardless of the precise mechanisms underlying the expression changes in calcium binding proteins, the upregulated factors are predicted to compensate for calreticulin deficiency and contribute to the maintenance of the overall cellular calcium homeostasis. These points will be clarified in the revised discussion.

      Overall, it remains unclear how this work improves our understanding of MPN or clarifies calreticulin's role in MPN pathophysiology.

      The points discussed above as well as their implications for the understanding of calreticulin’s role in MPN pathophysiology will be clarified in the revised manuscript.

      Reviewer #2 (Public review):

      Tagoe and colleagues present a thorough analysis of the calcium (Ca2+) binding capacity of calreticulin (CRT), an endoplasmic reticulum (ER) Ca2+-buffer protein, using a mutant version (CRT del52) found in myeloproliferative neoplasms (MPNs). The authors use purified human CRT protein variants, CRT-KO cell lines, and an MPN cell line to elucidate the differing Ca2+ dynamics, both on the level of the protein and on cell-wide Ca2+-governed processes. In sum, the authors provide new insights into CRT that can be applied to both normal and malignant cell biology.

      First, the authors purify CRT protein and perform isothermal titration calorimetry to quantify the Ca2+ binding capacity of CRT. They use full-length human CRT, CRT del52, and two truncations of CRT (1-339 and 1-351, the former of which should lead to the entire loss of low-affinity Ca2+ binding). While CRT del52 has previously been shown to lead to a decrease in Ca2+ binding affinity in other models, the ITC data show that this is retained in CRT del52.

      Next, the authors utilize a CRT-KO cell line with subsequent addition of CRT protein variants to validate these findings with flow cytometric analysis. Cells were transfected with a ratiometric ER Ca2+ probe, and fluorescence indicates that CRT del52 is unable to restore basal ER Ca2+ levels to the same extent as CRT wild-type. To translate these findings to MPNs, the authors perform CRT-KO in a megakaryocytic cell line, where reconstitution with either CRT variant did not cause a difference in cytosolic calcium levels. The authors further test store-operated calcium entry (SOCE), an important process for maintaining ER Ca2+ levels, in these cells, and find that CRT-KO cells have lower SOCE activity, and that this can be slightly recovered with CRT addition.

      Finally, the authors ask whether other effects of CRT-KO/reconstitution can affect the cellular Ca2+ signaling pathway and levels. RNASeq analysis revealed that CRT-KO leads to an increase in various chaperone protein expressions, and that reconstitution with CRT del52 is unable to reduce expression to the same extent as reconstitution with CRT wildtype.

      Strengths:

      The authors provide new insights into CRT that can be applied to both normal and malignant cell biology.

      We thank the reviewer for the recognition that this study is important for our understanding of both normal and malignant cell biology.

      Weaknesses:

      (1) The authors should consider discussing the high-affinity Ca2+ binding site more in the introduction. Can they show a proof-of-concept experiment that validates that incubation of recombinant CRT reduces the function of that high-affinity Ca2+ binding site?

      In a previous study (Wijeyesakere et al. 2011 J. Biol Chem, 286 8771-8785), we showed that at a starting calcium concentration of 0 mM and with 3.3 mM injections of CaCl<sub>2</sub>, the measured K<sub>D</sub> value was 16.6 mM for calcium binding to wild type murine calreticulin, (which has  ~95% % sequence identity with human calreticulin), corresponding to the high affinity site. On the other hand, at a starting calcium concentration of 50 mM and with 33 mM CaCl<sub>2</sub>  injections, the measured K<sub>D</sub> value for calcium binding to wild type murine calreticulin was 590 mM (corresponding to the low affinity sites). Thus, we did not measure the high affinity sites when the starting calcium concentration was 50 mM. This point will be clarified in the revised manuscript.

      (2) For Figure 2B, do you have an explanation for why the purified proteins run higher than predicted (48-52kDa) - are these proteins still tagged with pGB1?

      Yes, the purified proteins shown in Figure 2B retained a GB1 tag. This point will be clarified in the revised manuscript.

      (3) The MEG-01 cell line has the BCR:ABL1 translocation, while CRT mutations are strictly found in BCR:ABL1 negative MPNs. Could these experiments be repeated in these cells treated with imatinib to decrease these effects, or see if basal MEG-01 Ca2+ levels/activity are changed with or without imatinib?

      Thank you for the important point. We will assess cytosolic calcium levels in MEG-01 cells with or without imatinib.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors use methylphenidate (MPH) administration after learning a Pavlovian to instrumental transfer (PIT) task to parse decision making from instrumental influences. While the main effects were null, individual differences in working memory ability moderated the tendency of MPH to boost cognitive control in order to override PIT-biased instrumental learning. Importantly, this working memory moderator had symmetrical effects in appetite and aversive conditions, and these patterns replicated within each valence condition across different values of gain/loss (Fig S1c), suggesting a reliable effect that is generalized across instances of Pavlovian influence.

      Strengths:

      The idea of using pharmacological challenge after learning but prior to transfer is a novel technique that highlights the influence of catecholamines on the expression of learning under Pavlovian bias, and importantly it dissociated this decision feature from the learning of stimulus-outcome or action-outcome pairings.

      We thank the reviewer for highlighting the timing of the pharmacological intervention as a strength for this study and for the suggested improvements for clarification.

      Weaknesses:

      While the report is largely straightforward and clearly written, some aspects may be edited to improve the clarity for other readers.

      (1) Theoretical clarity. The authors seem to hedge their bets when it comes to placing these findings within a broader theoretical framework.

      Our findings ask for a revision of theories on how catecholamines are involved in instantiation of Pavlovian biases in decision making. The reviewer rightly notices that we offer three routes to modify current theory to be able to incorporate our findings. Briefly, these routes discuss catecholaminergic modulation of Pavlovian biases (i) through modulation of the putative striatal ‘origin’ of Pavlovian biases, (ii) through top-down control, primarily relying on prefrontal processes, and (ii) a combination of the two, where catecholamines regulate the balance between these striatal and frontal processes.

      Given the systemic nature of the pharmacological manipulation, we cannot dissociate between these three accounts. We believe that discussing these possible explanations enriches our Discussion and strengthens our recommendation in the ultimate paragraph to use pharmacological neuroimaging studies to arbitrate between these options. In the revision, we have made this line of reasoning more clear, in part by adding guiding titles to the Discussion section and adding a summary paragraph in the Discussion (Discussion, page 9-12).

      (2) Analytic clarity: what's c^2?

      C^2 seems a technical pdf conversion error problem: all chi-squares (Χ2) have been converted to C2. This is now corrected in our revision.

      Reviewer #2 (Public review):

      Summary:

      In this study, Geurts et al. investigated the effects of the catecholamine reuptake inhibitor methylphenidate (MPH) on value-based decision making using a combination of aversive and appetitive Pavlovian to Instrumental Transfer (PIT) in a human cohort. Using an elegant behavioural design they showed a valence- and action-specific effects of Pavlovian cues on instrumental responses. Initial analyses show no effect of MPH on these processes. However the authors performed a more in-depth analysis and demonstrated that MPH actually modulates PIT in actionspecific manner depending of individual working memory capacities. The authors interpret that as an effect on cognitive control of Pavlovian biasing of actions and decision making more than an invigoration of motivational biases.

      Strengths:

      A major strength of this study is its experimental design. The elegant combination of appetitive and aversive Pavlovian learning with approach/avoidance instrumental actions allows to precisely investigate the different modulation of value-based decision making depending on the context and environmental stimuli. Important MPH is only administered after Pavlovian and instrumental learning, restricting the effect on PIT performance only. Finally, the use of a placeboontrolled crossover design allows within-comparisons between PIT effect under placebo and MPH and the investigation of the relationships between working memory abilities, PIT and MPH effects.

      We thank the reviewer for highlighting the experimental design as a strength for this study and the suggested improvements for clarification.

      Weaknesses:

      As authors stated in their discussion, this study is purely correlational and their conclusions could be strengthened by the addition of interesting (but time- and resource-consuming) neuroimaging work.

      We employ a pharmacological intervention within a randomized placebo controlled cross-over design, which allows for causal inferences with respect to the placebo-controlled intervention. Thus, the reported interactions of interest include correlations, but these are causally dependent on our intervention.

      Perhaps the reviewer refers to the implications of our findings for hypotheses regarding neural implementation of Pavlovian bias-generation. Indeed, based on our data we are not able to arbitrate between frontal and striatal accounts, due to the systemic nature of the pharmacological intervention. Thus, we agree with the reviewer that neuroimaging (in combination with for example brain stimulation) would be a valuable next step to identify the neural correlates to these pharmacological intervention effects, to dissociate between frontal and striatal basis of the effects. In the revision, as per our reply to reviewer 1, we have made this line of reasoning more clear, in part by adding guiding titles to the Discussion section and adding a summary paragraph in the Discussion (Discussion, page 9-12).

      The originality of this work compared to their previous published work using the same cohort could also be clarified at different stages of the article, as I initially wondered what was really novel. This point is much clearer in the discussion section.

      As recommended, we brought forward parts of the Discussion that clarify the originality of the current experiment to the introduction (page 4/5) and result section (page 8).

      A point which, in my opinion, really requires clarification is when the working memory performance presented in Figure 2B has been determined. Was it under placebo (as I would guess) or under MPH? If it is the former, it would be also interesting to look at how MPH modulates working memory based on initial abilities.

      We now clarified that working memory span was assessed for all participants on Day 2 prior to the start of instrumental training (as illustrated in figure 1A). Importantly, this was done prior to ingestion of the drug or placebo (which subjects received after Pavlovian training, which followed the instrumental training). This design also precludes an assessment of the effects of MPH on working memory capacity.

      A final point is that it could be interesting to also discuss these results, not only regarding dopamine signalling, but also including potential effect of MPH on noradrenaline in frontal regions, considering the known role of this system in modulating behavioural flexibility.

      We indeed focus our Discussion more on dopamine than on noradrenaline. Our revision now also discusses noradrenaline in light of our frontal control hypothesis and the recommendation, in future studies, to use a multi-drug design, incorporating, for example, a session with the drug atomoxetine, which modulates cortical catecholamines, but not striatal dopamine (Discussion, page 12).

      Reviewer #3 (Public review):

      The manuscript by Geurts and colleagues studies the effects of methylphenidate on Pavlovian to instrumental transfer in humans and demonstrates that the effects of the drug depend on the baseline working memory capacity of the participants. The experiment used a well established cognitive task that allows to measure the effects of Pavlovian cues predicting monetary wins and losses on instrumental responding in two different contexts, namely approach and withdraw. By administering the drug after participants went through the instrumental and Pavlovian learning phases of the experiment, the authors limited the effects of the drug to the transfer phase in extinction. This allowed the authors to make inference about the invigorating effects of the cues independently from any learning bias. Moreover, the authors employed a within subject design to study the effect of the drug on 100 participants, which also allows to detect continuous between-subject relationships with covariates such as working memory capacity.

      The study replicates previous findings using this task, namely that appetitive cues promote active responding, and aversive cues promote passive responding in an approach instrumental context, whereas the effect of the cues reverses in a withdraw instrumental context. The results of the methylphenidate manipulation show that the drug decreases the effects of the Pavlovian cues on instrumental responding in participants with low working memory capacity but increases the Pavlovian effects in participants with high working memory capacity. Importantly, in the latter group, methylphenidate increases the invigorating effect of appetitive Pavlovian cues on active approach and aversive Pavlovian cues on active withdrawal as well as the inhibitory effects of aversive Pavlovian cues on active approach and appetitive Pavlovian cues on active withdrawal. These results cannot be explained if catecholamines are just involved in Pavlovian biases by modulating behavioral invigoration driven by the anticipation of reward and punishment in the striatum, as this account can't account for the reversal of the effects of a valence cue on vigor depending on the instrumental context.

      In general, I find the methods of this study very robust and the results very convincing and important. However, I have some concerns:

      We thank the Reviewer for highlighting the robustness of the methods and the importance of the results. We are glad to shortly address the concerns here and have incorporated these in our revision.

      I am not convinced that the inclusion of impulsivity scores in the logistic mixed model to analyze the effects of methylphenidate on PIT is warranted. The authors do not show whether inclusion of this covariate is justified in terms of BIC. Moreover, they include this covariate but do not report the effects. Finally, it is possible that impulsivity is correlated with working memory capacity. In that case, multicollinearity may impact the estimation of the coefficient estimates and may inflate the p-values for the correlated covariates. Are the reported results robust when this factor is not included?

      With regard to the inclusion of impulsivity we first like to mention that this inclusion in our analyses was planned a priori and therefore consistently implemented in the other reports resulting from the overarching study (Froböse et al., 2018; Cook et al., 2019; Rostami Kandroodi et al., 2021), especially the study with regard to which the current report is an e-life research advance (Swart et al., 2017). Moreover, we preregistered both working memory span and impulsivity as potential factors (under secondary measures) that could mediate the effects of catecholamines (see https://onderzoekmetmensen.nl/nl/trial/26989). The inclusion of working memory span was based on evidence from PET imaging studies demonstrating a link with dopamine synthesis capacity (Cools et al., 2008; Landau et al, 2009), whereas the inclusion of trait impulsivity was based on evidence from other PET imaging studies showing a link with dopamine (auto)receptor availability (Buckholtz et al., 2010; Kim et al., 2014; Lee et al., 2009; Reeves et al., 2012). Although there was no significant improvement for the model with impulsivity compared with the model without impulsivity, we feel that we should follow our a priori established analyses.

      We can confirm that impulsivity and working memory were not correlated in this sample (r98=-0.16, p=0.88), which rules out multicollinearity.

      Most importantly, results are robust to excluding impulsivity scores as evidenced by a significant four-way interaction from the omnibus GLMM without impulsivity (Action Context x Valence x Drug x WM span: X<sup>2</sup> = 9.5, p=0.002). We will report these findings in the revised manuscript. We now added the text to the Supplemental Results: Control analyses, page 28.

      The authors state that working memory capacity is an established proxy for dopamine synthesis capacity and cite some studies supporting this view. However, the authors omit a recent reference by van den Bosch et al that provides evidence for the absence of links between striatal dopamine synthesis capacity and working memory capacity. The lack of a robust link between working memory capacity and dopamine synthesis capacity in the striatum strengthens the alternative explanations of the results suggested in the discussion.

      We agree with the Reviewer that the lack of a robust link between working memory capacity and dopamine synthesis capacity in the striatum, as measured with [<sup>18</sup>F]-FDOPA PET imaging, is lending support for the proposed hypothesis incorporating a broader perspective on Pavlovian bias generation than the dopaminergic direct/indirect pathway account (although it is possible that the association will hold in a larger sample when synthesis capacity is measured with [<sup>18</sup>F]-FMT PET imaging, which is sensitive to a different component of the metabolic pathway). We will indeed incorporate in our planned revision the findings from our group reported in van den Bosch et al (2022).

      See Supplemental methods 2: Working memory and impulsivity assessment, page 26.

      ** Recommendations for the authors:**

      Reviewer #1 (Recommendations for the authors):

      (1) Theoretical clarity. Some aspects of the paper are ideally clear: Figure 1 clearly explains the paradigm. The general take-home message is clearly described in the last line of the abstract, the last line of the introduction, the first line of the discussion, and throughout other places in the discussion. Yet the authors seem to hedge their bets when it comes to placing these findings within a broader theoretical framework.

      The discussion includes many possible theoretical interpretations of the findings, which is laudable, but many readers may get lost in this multitude (particularly anyone who isn't an RL/DA aficionado). The group's prior work (i.e. striatal hypothesis) is first described, followed by a rather complex breakdown of valenceaction tendencies, then the seemingly preferred explanation for the current study (i.e. cognitive control hypothesis) is advanced as "an alternative account ...". This is followed by a third, more complex idea (i.e. cortico-striatal balance hypothesis), then the paper ends. A reader may be forgiven for skimming through this discussion and not having a clear idea of how to frame these effects. I think some subheaders would help, as well as clearer labeling of the theoretical interpretations in line with a more authoritative description of the author's preferred interpretation of the empirical effects.

      Our findings ask for a revision of theories on how catecholamines are involved in instantiation of Pavlovian biases in decision making. The reviewer rightly notices that we offer three routes to modify current theory to be able to incorporate our findings. Briefly, these routes discuss catecholaminergic modulation of Pavlovian biases (i) through modulation of the putative striatal ‘origin’ of Pavlovian biases, (ii) through top-down control, primarily relying on prefrontal processes, and (ii) a combination of the two, where catecholamines regulate the balance between these striatal and frontal processes.

      Given the systemic nature of the pharmacological manipulation, we cannot dissociate between these three accounts. We believe that discussing these possible explanations enriches our Discussion and strengthens our recommendation in the ultimate paragraph to use pharmacological neuroimaging studies to arbitrate between these options. In the revision, we have made this line of reasoning more clear, in part by adding guiding titles to the Discussion section and adding a summary paragraph in the Discussion (Discussion, page 9-12).

      (2) All statistical effects are presented as c^2 with no df. The methods only describe LMER and make no mention of what the c^2 measure represents.

      C^2 seems a technical pdf conversion error problem: all chi-squares (Χ2) have been converted to C2. This is now corrected in our revision.

      Reviewer #2 (Recommendations for the authors):

      Few minor points:

      Figure 2A is not cited in the text I think

      Checked and changed.

      Figure 2C: "C" is not present in the figure. Also I could not see the data corresponding at MPH-Approach context in Neutral Pavlovian condition but I think it is probably masked by another curve.

      Checked and changed. Indeed, the one curve is masked by the other curve.

      As I stated in the public review, a clarification or more detailed analysis of working memory performance depending on if it was measured under MPH or placebo could be a plus.

      Changed this (see public review reply).

      I did not see any statement about the availability of data but I may have missed it.

      Yes, the statement can be found:

      Methods, page 13: Data and code for the study are freely available at https://data.ru.nl/collections/di/dccn/DSC_3017031.02_734.

      Reviewer #3 (Recommendations for the authors):

      The authors should check that inclusion of impulsivity in the logistic mixed model is justified and if it is justified make sure that multicollinearity is not problematic.

      See answer to public review for convenience reiterated below:

      With regard to the inclusion of impulsivity we first like to mention that this inclusion in our analyses was planned a priori and therefore consistently implemented in the other reports resulting from the overarching study (Froböse et al., 2018; Cook et al., 2019; Rostami Kandroodi et al., 2021), especially the study with regard to which the current report is an e-life research advance (Swart et al., 2017). Moreover, we preregistered both working memory span and impulsivity as potential factors (under secondary measures) that could mediate the effects of catecholamines (see https://onderzoekmetmensen.nl/nl/trial/26989). The inclusion of working memory span was based on evidence from PET imaging studies demonstrating a link with dopamine synthesis capacity (Cools et al., 2008; Landau et al, 2009), whereas the inclusion of trait impulsivity was based on evidence from other PET imaging studies showing a link with dopamine (auto)receptor availability (Buckholtz et al., 2010; Kim et al., 2014; Lee et al., 2009; Reeves et al., 2012). Although there was no significant improvement for the model with impulsivity compared with the model without impulsivity, we feel that we should follow our a priori established analyses.

      We can confirm that impulsivity and working memory were not correlated in this sample (r98=-0.16, p=0.88), which rules out multicollinearity.

      Most importantly, results are robust to excluding impulsivity scores as evidenced by a significant four-way interaction from the omnibus GLMM without impulsivity (Action Context x Valence x Drug x WM span: X<sup>2</sup> = 9.5, p=0.002). We will report these findings in the revised manuscript. We now added the text to the Supplemental Results Control analyses, page 28.

      I would recommend that the authors make clear that the effects of methylphenidate are dependent on working memory capacity in the first sentence of the fore last paragraph of the introduction on page 4.

      Changed this accordingly, see Introduction, page 5.

      I would make sure that the text in the figures is readable without needing to enlarge the figures. I would also highlight the significant effects in the figures.

      We changed the font size accordingly and added significance statements to the caption, because depicting the significance of a four-way interaction including one continuous variable is not straightforward.

      The distributions of p(Go) by conditions such as in figure 1D or 2A are very intuitive. Figure 2B is very informative as it shows the continuous effects of working memory capacity on the PIT effect. I would add (in figure 2 or in the supplement) a plot of the p(Go) with a tertile split based on working memory. Considering that the correspondent analysis is being reported, having the plot would strengthen and simplify the understanding of the results.

      The continuous effects of working memory are based on WM values on the listening span ranging from 2.5-7, in steps of 0.5, resulting in 10 different values. A tertile split would result in binning these into two bins of three values, and one bin of four values. Given that all of the datapoints for this tertile split are already presented in the current figures, we strongly prefer not to include this additional figure.

      I would add some sentences in the results section (and maybe in the discussion if needed) addressing the results that the effect of Valence by drug by WM span is only significant in the withdrawal context but not in the approach context.

      We now added an emphasis on the specifically significant drug effects in withdrawal in the Results section, page 8.

    1. Author response:

      The following is the authors’ response to the original reviews

      eLife Assessment

      This is a valuable polymer model that provides insight into the origin of macromolecular mixed and demixed states within transcription clusters. The well-performed and clearly presented simulations will be of interest to those studying gene expression in the context of chromatin. While the study is generally solid, it could benefit from a more direct comparison with existing experimental data sets as well as further discussion of the limits of the underlying model assumptions.

      We thank the editors for their overall positive assessment. In response to the Referees’ comments, we have addressed all technical points, including a more detailed explanation of the methodology used to extract gene transcription from our simulations and its analogy with real gene transcription. Regarding the potential comparison with experimental data and our mixing–demixing transition, we have added new sections discussing the current state of the art in relevant experiments. We also clarify the present limitations that prevent direct comparisons, which we hope can be overcome with future experiments using the emerging techniques.

      Reviewer #1 (Public Review):

      This manuscript discusses from a theory point of view the mechanisms underlying the formation of specialized or mixed factories. To investigate this, a chromatin polymer model was developed to mimic the chromatin binding-unbinding dynamics of various complexes of transcription factors (TFs).

      The model revealed that both specialized (i.e., demixed) and mixed clusters can emerge spontaneously, with the type of cluster formed primarily determined by cluster size. Non-specific interactions between chromatin and proteins were identified as the main factor promoting mixing, with these interactions becoming increasingly significant as clusters grow larger.

      These findings, observed in both simple polymer models and more realistic representations of human chromosomes, reconcile previously conflicting experimental results. Additionally, the introduction of different types of TFs was shown to strongly influence the emergence of transcriptional networks, offering a framework to study transcriptional changes resulting from gene editing or naturally occurring mutations.

      Overall I think this is an interesting paper discussing a valuable model of how chromosome 3D organisation is linked to transcription. I would only advise the authors to polish and shorten their text to better highlight their key findings and make it more accessible to the reader.

      We thank the Referee for carefully reading our manuscript and recognizing its scientific value. As suggested, we tried to better highlight our key findings and make the text more accessible while addressing also the comments from the other Referees.

      Reviewer #2 (Public Review):

      Summary:

      With this report, I suggest what are in my opinion crucial additions to the otherwise very interesting and credible research manuscript ”Cluster size determines morphology of transcription factories in human cells”.

      Strengths:

      The manuscript in itself is technically sound, the chosen simulation methods are completely appropriate the figures are well-prepared, the text is mostly well-written spare a few typos. The conclusions are valid and would represent a valuable conceptual contribution to the field of clustering, 3D genome organization and gene regulation related to transcription factories, which continues to be an area of most active investigation.

      Weaknesses:

      However, I find that the connection to concrete biological data is weak. This holds especially given that the data that are needed to critically assess the applicability of the derived cross-over with factory size is, in fact, available for analysis, and the suggested experiments in the Discussion section are actually done and their results can be exploited. In my judgement, unless these additional analysis are added to a level that crucial predictions on TF demixing and transcriptional bursting upon TU clustering can be tested, the paper is more fitted for a theoretical biophysics venue than for a biology journal such as eLife.

      We thank the Reviewer for their positive assessment of the soundness of our work and its contribution to the field. We have added a paragraph to the Conclusions highlighting the current state of experimental techniques and outlining near-term experiments that could be extended to test our predictions. We also emphasise that our analysis builds on state-of-the-art polymer models of chromatin and on quantitative experimental datasets, which we used both to build the model construction and to validate its outcomes (gene activity). We hope this strengthened link to experiment will catalyse further studies in the field.

      Major points:

      (1) My first point concerns terminology.The Merriam-Webster dictionary describes morphology as the study of structure and form. In my understanding, none of the analyses carried out in this study actually address the form or spatial structuring of transcription factories. I see no aspects of shape, only size. Unless the authors want to assess actual shapes of clusters, I would recommend to instead talk about only their size/extent. The title is, by the same argument, in my opinion misleading as to the content of this study.

      We agree with the Referee that the title could be misleading. In our study we characterized clusters size, that is a morphological descriptor, and cluster composition that isn’t morphology per se but used in the community in a broader sense. Nevertheless to strength the message we have changed the title in: “Cluster size determines internal structure of transcription factories in human cells”

      (2) Another major conceptual point is the choice of how a single TF:pol particle in the model relates to actual macromolecules that undergo clustering in the cell. What about the fact that even single TF factories still contain numerous canonical transcription factors, many of which are also known to undergo phase separation? Mediator, CDK9, Pol II just to name a few. This alone already represents phase separation under the involvement of different species, which must undergo mixing. This is conceptually blurred with the concept of gene-specific transcription factors that are recruited into clusters/condensates due to sequencespecific or chromatin-epigenetic-specific affinities. Also, the fact that even in a canonical gene with a ”small” transcription factory there are numerous clustering factors takes even the smallest factories into a regime of several tens of clustering macromolecules. It is unclear to me how this reality of clustering and factory formation in the biological cell relates to the cross-over that occurs at approximately n=10 particles in the simulations presented in this paper.

      This is a good point. However in our case we can either look at clustering transcription factors or transcription units. In an experimental situation, transcription units could be “coloured”, or assigned different types, by looking at different cell types, so that they can be classified as housekeeping, or cell-type independent, or cell-type specific. This is similar to how DHS can be clustered. In this way the mixing or demixing state can be identified by looking at the type of transcription unit, removing any ambiguity due to the fact that the same protein may participate in different TF complexes..

      (3) The paper falls critically short in referencing and exploiting for analysis existing literature and published data both on 3D genome organization as well as the process of cluster formation in relation to genomic elements. In terms of relevant literature, most of the relevant body of work from the following areas has not been included:

      (i) mechanisms of how the clustering of Pol II, canonical TFs, and specific TFs is aided by sequence elements and specific chromatin states

      (ii) mechanisms of TF selectivity for specific condensates and target genomic elements

      (iii) most crucially, existing highly relevant datasets that connect 3D multi-point contacts with transcription factor identity and transcriptional activity, which would allow the authors to directly test their hypotheses by analysis of existing data

      Here, especially the data under point (iii) are essential. The SPRITE method (cited but not further exploited by the authors), even in its initial form of publication, would have offered a data set to critically test the mixing vs. demixing hypothesis put forward by the authors. Specifically, the SPRITE method offers ordered data on k-mers of associated genomic elements. These can be mapped against the main TFs that associate with these genomic elements, thereby giving an account of the mixed / demixed state of these k-mer associations. Even a simple analysis sorting these associations by the number of associated genomic elements might reveal a demixing transition with increasing association size k. However, a newer version of the SPRITE method already exists, which combines the k-mer association of genomic elements with the whole transcriptome assessment of RNAs associated with a particular DNA k-mer association. This can even directly test the hypotheses the authors put forward regarding cluster size, transcriptional activation, correlation between different transcription units’ activation etc.

      To continue, the Genome Architecture Mapping (GAM) method from Ana Pombo’s group has also yielded data sets that connect the long-range contacts between gene-regulatory elements to the TF motifs involved in these motifs, and even provides ready-made analyses that assess how mixed or demixed the TF composition at different interaction hubs is. I do not see why this work and data set is not even acknowledged? I also strongly suggest to analyze, or if they are already sufficiently analyzed, discuss these data in the light of 3D interaction hub size (number of interacting elements) and TF motif composition of the involved genomic elements.

      Further, a preprint from the Alistair Boettiger and Kevin Wang labs from May 2024 also provides direct, single-cell imaging data of all super-enhancers, combined with transcription detection, assessing even directly the role of number of super-enhancers in spatial proximity as a determinant of transcriptional state. This data set and findings should be discussed, not in vague terms but in detailed terms of what parts of the authors’ predictions match or do not match these data.

      For these data sets, an analysis in terms of the authors’ key predictions must be carried out (unless the underlying papers already provide such final analysis results). In answering this comment, what matters to me is not that the authors follow my suggestions to the letter. Rather, I would want to see that the wealth of available biological data and knowledge that connects to their predictions is used to their full potential in terms of rejecting, confirming, refining, or putting into real biological context the model predictions made in this study.

      References for point (iii):

      - RNA promotes the formation of spatial compartments in the nucleus https://www.cell.com/cell/fulltext/S0092-8674(21)01230-7?dgcid=raven_jbs_etoc_email

      - Complex multi-enhancer contacts captured by genome architecture mapping https://www.nature.com/articles/nature21411

      - Cell-type specialization is encoded by specific chromatin topologies https://www.nature.com/articles/s41586-021-04081-2

      - Super-enhancer interactomes from single cells link clustering and transcription https://www.biorxiv.org/content/10.1101/2024.05.08.593251v1.full

      For point (i) and point (ii), the authors should go through the relevant literature on Pol II and TF clustering, how this connects to genomic features that support the cluster formation, and also the recent literature on TF specificity. On the last point, TF specificity, especially the groups of Ben Sabari and Mustafa Mirx have presented astonishing results, that seem highly relevant to the Discussion of this manuscript.

      We appreciate the Reviewer’s insightful suggestion that a comparison between our simulation results and experimental data would strengthen the robustness of our model. In response, we have thoroughly revised the literature on multi-way chromatin contacts, with particular attention to SPRITE and GAM techniques. However, we found that the currently available experimental datasets lack sufficient statistical power to provide a definitive test of our simulation predictions, as detailed below.

      As noted by the Reviewer, SPRITE experiments offer valuable information on the composition of highorder chromatin clusters (k-mers) that involve multiple genomic loci. A closer examination of the SPRITE data (e.g., Supplementary Material from Ref. [1]) reveals that the majority of reported statistics correspond to 3-mers (three-way contacts), while data on larger clusters (e.g., 8-mers, 9-mers, or greater) are sparse. This limitation hinders our ability to test the demixing-mixing transition predicted in our simulations, which occurs for cluster sizes exceeding 10.

      Moreover, the composition of the k-mers identified by SPRITE predominantly involves genomic regions encoding functional RNAs—such as ITS1 and ITS2 (involved in rRNA synthesis) and U3 (encoding small nucleolar RNA)—which largely correspond to housekeeping genes. Conversely, there is little to no data available for protein-coding genes. This restricts direct comparison to our simulations, where the demixing-mixing transition depends critically on the interplay between housekeeping and tissue-specific genes.

      Similarly, while GAM experiments are capable of detecting multi-way chromatin contacts, the currently available datasets primarily report three-way interactions [2,3].

      In summary, due to the limited statistical data on higher-order chromatin clusters [4], a quantitative comparison between our simulation results and experimental observations is not currently feasible. Nevertheless, we have now briefly discussed the experimental techniques for detecting multi-way interactions in the revised manuscript to reflect the current state of the field, mentioning most of the references that the Reviewer suggested.

      (4) Another conceptual point that is a critical omission is the clarification that there are, in fact, known large vs. small transcription factories, or transcriptional clusters, which are specific to stem cells and ”stressed cells”. This distinction was initially established by Ibrahim Cisse’s lab (Science 2018) in mouse Embryonic Stem Cells, and also is seen in two other cases in differentiated cells in response to serum stimulus and in early embryonic development:

      - Mediator and RNA polymerase II clusters associate in transcription-dependent condensates https://www.science.org/doi/10.1126/science.aar4199

      - Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering https://www.science.org/doi/10.1126/sciadv.aay6515

      - RNA polymerase II clusters form in line with surface condensation on regulatory chromatin https://www.embopress.org/doi/full/10.15252/msb.202110272

      - If ”morphology” should indeed be discussed, the last paper is a good starting point, especially in combination with this additional paper: Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin https://www.science.org/doi/10.1126/science.ade5308

      We thank the Reviewer for pointing out the discussion about small and large clusters observed in stressed cells. Our study aims to provide a broader mechanistic explanation on the formation of TF mixed and demixed clusters depending on their size. However, to avoid to generate confusion between our terminology and the classification that is already used for transcription factories in stem and stressed cells, we have now added some comments and references in the revised text.

      (5) The statement scripts are available upon request is insufficient by current FAIR standards and seems to be non-compliant with eLife requirements. At a minimum, all, and I mean all, scripts that are needed to produce the simulation outcomes and figures in the paper, must be deposited as a publicly accessible Supplement with the article. Better would be if they would be structured and sufficiently documented and then deposited in external repositories that are appropriate for the sharing of such program code and models.

      We fully agree with the Reviewer. We have now included in the main text a link to an external repository containing all the codes required to reproduce and analyze the simulations.

      Recommendations for the authors:

      Minor and technical points

      (6) Red, green, and yellow (mix of green and red) is a particularly bad choice of color code, seeing that red-green blindness is the most common color blindness. I recommend to change the color code.

      We appreciate the Reviewer’s thoughtful comment regarding color accessibility. We fully agree that red–green combinations can pose challenges for color-blind readers. In our figures, however, we chose the red–green–yellow color scheme deliberately because it provides strong contrast and intuitive representation for different TF/TU types. To ensure accessibility, we optimized brightness and saturation within red-green schemes and we carefully verified that the chosen hues are distinguishable under the most common forms of color vision deficiency, i.e. trichromatic color blindness, using color-blindness simulation tools (e.g., Coblis).

      How is the dispersing effect of transcriptional activation and ongoing transcription accounted for or expected to affect the model outcome? This affects both transcriptional clusters (they tend to disintegrate upon transcriptional activation) as well as the large scale organization, where dispersal by transcription is also known.

      We thank the Reviewer for this very insightful question. The current versions of both our toy model and the more complex HiP-HoP model do not incorporate the effects of RNA Polymerase elongation. Our primary goal was to develop a minimalisitc framework that focuses on investigating TF clusters formation and their composition. Nevertheless, we find that this straightforward approach provides a good agreement between simulations and Hi-C and GRO-seq experiments, lending confidence to the reliability of our results concerning TF cluster composition.

      We fully agree, however, that the effects of transcription elongation are an interesting topic for further exploration. For example, modeling RNA Polymerases as active motors that continually drive the system out of equilibrium could influence the chromatin polymer conformation and the structure of TF clusters. Additionally, investigating how interactions between RNA molecules and nuclear proteins, such as SAF-A, might lead to significant changes in 3D chromatin organization and, consequently, transcription [5], is also in intriguing prospect. Although we do not believe that the main findings of our study, particularly regarding cluster composition and mixed-demixed transition, would be impacted by transcription elongation effects, we recognize the importance of this aspect. As such, we have now included some comments in the Conclusions section of the revised manuscript.

      “and make the reasonable assumption that a TU bead is transcribed if it lies within 2.25 diameters (2.25σ) of a complex of the same colour; then, the transcriptional activity of each TU is given by the fraction of time that the TU and a TF:pol lie close together.” How is that justified? I do not see how this is reasonable or not, if you make that statement you must back it up.

      As pointed out by the Referee, we consider a TU to be active if at least one TF is within a distance 2.25σ from that TU. This threshold is a slightly larger than the TU-TF interaction cutoff distance, r<sub>c</sub> \= 1.8σ between TFs and TUs. The rationale for this choice is to ensure that, in the presence of a TU cluster surrounded by TFs, TUs that are not directly in contact with a TF are still considered active. Nonetheless, we find that using slightly different thresholds, such as 1.8σ or 1.1σ, leads to comparable results, as shown in Fig. S11, demonstrating the robustness of our analysis.

      Clearly, close proximity in 1D genomic space favours formation of similarly-coloured clusters. This is not surprising, it is what you built the model to do. Should not be presented as a new insight, but rather as a check that the model does what is expected.

      We believed that this sentence already conveyed that the formation of single-color clusters driven by 1D genomic proximity is not a surprising outcome. However, we have now slightly rephrased it to better emphasize that this is not a novel insight.

      That said, we would like to highlight that while 1D genomic proximity facilitates the formation of clusters of the same color, the unmixed-to-mixed transition in cluster composition is not easily predictable solely from the TU color pattern. Furthermore, in simulations of real chromosomes, where TU patterns are dictated by epigenetic marks, the complexity of these patterns makes it challenging—if not impossible—to predict cluster composition based solely on the input data of our model.

      “…how closely transcriptional activities of different TUs correlate…” Please briefly state over what variable the correlation is carried out, is it cross correlation of transcription activity time courses over time? Would be nice to state here directly in the main text to make it easier for the reader.

      We have now included a brief description in the revised manuscript explaining how the transcriptional correlations were evaluated and how the correlation matrix was constructed.

      “The second concerns how expression quantitative trait loci (eQTLs) work. Current models see them doing so post-transcriptionally in highly-convoluted ways [11, 55], but we have argued that any TU can act as an eQTL directly at the transcriptional level [11].” This text does not actually explain what eQTLs do. I think it should, in concise words.

      We agree with the Referee’s suggestion. We have revised the sentence accordingly and now provide a clear explanation of eQTLs upon their first mention. The revised paragraph now reads as follows:

      “The second concerns how expression quantitative trait loci (eQTLs)—genomic regions that are statistically associated with variation in gene expression levels—function. While current models often attribute their effects to post-transcriptional regulation through complex mechanisms [6,7], we have previously argued that any transcriptional unit (TU) can act as an eQTL by directly influencing gene expression at the transcriptional level [7]. Here, we observe individual TUs up-regulating or down-regulating the activity of others TUs – hallmark behaviors of eQTLs that can give rise to genetic effects such as “transgressive segregation” [8]. This phenomenon refers to cases in which alleles exhibit significantly higher or lower expression of a target gene, and can be, for instance, caused by the creation of a non-parental allele with a specific combination of QTLs with opposing effects on the target gene.”

      “In the string with 4 mutations, a yellow cluster is never seen; instead, different red clusters appear and disappear (Fig. 2Eii)…” How should it be seen? You mutated away most of the yellow beads. I think the kymograph is more informative about the general model dynamics, not the effects of mutations. Might be more appropriate to place a kymograph in Figure 1.

      We agree with the Referee that the kymograph is the most appropriate graphical representation for capturing the effects of mutations. Panel 2E already refers to the standard case shown in Figure 1. We have now clarified this both in the caption and in the main text. In addition, we have rephrased the sentence—which was indeed misleading—as follows:

      “From the activity profiles in Fig. 2C, we can observe that as the number of mutations increases, the yellow cluster is replaced by a red cluster, with the remaining yellow TUs in the region being expelled (Fig. 2B(ii)). This behavior is reflected in the dynamics, as seen by comparing panels E(i) and E(ii): in the string with four mutations, transcription of the yellow TUs is inhibited in the affected region, while prominent red stripes—corresponding to active, transcribing clusters—emerge (Fig. 2E(ii)).” We hope that the comparison is now immediately clear to the reader.

      “…but this block fragments in the string with 4 mutations…” I don’t know or cannot see what is meant by ”fragmentation” in the correlation matrix.

      With the sentence “this block fragments in the string with 4 mutations” we mean that the majority of the solid red pixels within the black box become light-red or white once the mutations are applied. We have now added a clarification of this point in the revised manuscript.

      “Fig. 3D shows the difference in correlation between the case with reduced yellow TFs and the case displayed in Fig. 1E.” Can you just place two halves of the different matrices to be compared into the same panel? Similar to Fig. S5. Will be much easier to compare.

      We thank the Referee for this suggestion. We tried to implement this modification, and report the modified figure below (Author response image 1). As we can see, in the new figure it is difficult to spot the details we refer to in the main text, therefore we prefer to keep the original version of the figure.

      Author response image 1.

      Heatmap comparing activity correlations of TUs in the random string under normal conditions (top half) and with reduced yellow-TF concentration (bottom half).

      What is the omnigenic model? It is not introduced.

      We thank the Reviewer for highlighting this important point. The omnigenic model, first introduced by Boyle et al in Ref. [6], was proposed to explain how complex traits, including disease risk, are influenced by a vast number of genes. Accordingly to this model, the genetic basis of a trait is not limited to a small set of core genes whose expression is directly related to the trait, but also includes peripheral genes. The latter, although not directly involved in controlling the trait, can influence the expression of core genes through gene regulatory networks, thereby contributing to the overall genetic influence on the trait. We have now added a few lines in the revised manuscript to explain this point.

      “Additionally, blue off-diagonal blocks indicate repeating negative correlations that reflect the period of the 6-pattern.” How does that look in a kymograph? Does this mean the 6 clusters of same color steal the TFs from the other clusters when they form?

      The intuition of the Referee is indeed correct. The finite number of TFs leads to competition among TUs of the same colour, resulting in anticorrelation:when a group of six nearby TUs of a given colour is active, other, more distant TUs of the same colour are not transcribing due to the lack of available TFs. As the Referee suggested,this phenomenon is visible in the kymograph showing TU activity. In Author response image 2, it can be observed that typically there is a single TU cluster for each of the three colours (yellow, green, and red). These clusters can be long-lived (e.g., the yellow cluster at the center of the kymograph) or may destroy during the simulation (e.g., the red cluster at the top of the kymograph, which dissolves at t ∼ 600 × 10<sup>5</sup> τ<sub>B</sub>). In the latter case, TFs of the corresponding colour are released into the system and can bind to a different location, forming a new cluster (as seen with the red cluster forming at the bottom of the kymograph for t > 600 × 10<sup>5</sup> τ<sub>B</sub>). This point is further discussed at the point 2.30 of this Reply where additional graphical material is provided.

      Author response image 2.

      Kymograph showing the TU activity during a typical run in the 6-pattern case. Each row reports the transcriptional state of a TU during one simulation. Black pixels correspond to inactive TUs, red (yellow, green) pixels correspond to active red (yellow, green) TUs.

      “Conversely, negative correlations connect distant TUs, as found in the single-color model…” But at the most distal range, the negative correlation is lost again! Why leave this out? Your correlation curves show the same , equilibration towards no correlation at very long ranges.

      As highlighted in Figure 5Ai, long-range negative correlations (grey segments) predominantly connect distant TUs of the same colour. This is quantified in Figure 5Bi: restricting to same-colour TUs shows that at large genomic separations the correlation is almost entirely negative, with small fluctuations at distances just below 3000 kbp where sampling is sparse; we therefore avoid further interpretation of this regime.

      “These results illustrate how the sequence of TUs on a string can strikingly affect formation of mixed clusters; they also provide an explanation of why activities of human TUs within genomic regions of hundreds of kbp are positively correlated [60].” This is a very nice insight.

      We thank the Reviewer for the very supportive comment.

      “To quantify the extent to which TFs of different colours share clusters, we introduce a demixing coefficient, θ<sub>dem</sub> (defined in Fig. 1).” This is not defined in Fig. 1 or anywhere else here in the main text.

      We thank the Referee for pointing this out. For a given cluster, the demixing coefficient is defined as

      where n is the number of colors, i indexes each color present in the model, and x<sub>i,max</sub> the largest fraction of TFs of the same i-th color in a single TF cluster.

      The demixing coefficient is defined in the Methods section; therefore, we have replaced defined in Fig. 1 with see Methods for definition.

      “Mixing is facilitated by the presence of weakly-binding beads, as replacing them with non-interacting ones increases demixing and reduces long-range negative correlations (Figure S3). Therefore, the sequence of strong and weak binding sites along strings determines the degree of mixing, and the types of small-world network that emerge. If eQTLs also act transcriptionally in the way we suggest [11], we predict that down-regulating eQTLs will lie further away from their targets than up-regulating ones.” Going into these side topics and minke points here is super distracting and waters down the message. Maybe first deal with the main conclusions on mixed vs demixed clusters in dependence on the strong and specific binding site patterns, before dealing with other additional points like the role of weak binding sites.

      Thank you for the suggestion. We now changed the paragraph to highlight the main results. The new paragraph is as follows. “These results on activity correlation and TF cluster composition suggest that, if eQTLs act transcriptionally as expected [7], down-regulating eQTLs are likely to be located further from their target genes than up-regulating ones. In addition, it is important to note that mixing is promoted by the presence of weakly binding beads; replacing these with non-interacting ones leads to increased demixing and a reduction in long-range negative correlations (Figure S3). More generally, our findings indicate that the presence of multiple TF colors offers an effective mechanism to enrich and fine-tune transcriptional regulation.”

      “…provides a powerful pathway to enrich and modulate transcriptional regulation.” Before going into the possible meaning and implications of the results, please discuss the results themselves first.

      See previous point.

      Figure 5B. Does activation typically coincide with spatial compaction of the binding sites into a small space or within the confines of a condensate? My guess would be that colocalization of the other color in a small space is what leads to the mixing effect?

      As the Reviewer correctly noted, the activity of a given TU is indeed influenced by the presence of nearby TUs of the same color, since their proximity facilitates the recruitment of additional TFs and enhances the overall transcriptional activity. In this context, the mixing effect is certainly affected by the 1D arrangement of TUs along the chromatin fiber. As emphasized in the revised manuscript, when domains of same-color TUs are present (as in the 6-pattern string), the degree of demixing is greater compared to the case where TUs of different colors alternate and large domains are absent (as in the 1-pattern string). This difference in the demixing parameter as a function of the 1D TU arrangement is clearly visible in Fig. S2B.

      “…euchromatic regions blue, and heterochromatic ones grey.” Please also explain what these color monomers mean in terms of non specific interactions with the TFs.

      Generally, in our simulation approach we assume euchromatin regions to be more open and accessible to transcription factors, whereas heterochromatin corresponds to more compacted chromatin segments [9]. To reflect this, we introduce weak, non-specific interactions between euchromatin and TFs, while heterochromatin interacts with TFs only thorugh steric effects. To clarify this point, we have now slightly revised the caption of Fig.6.

      “More quantitatively, Spearman’s rank correlation coefficient is 3.66 10<sup>−1</sup>, which compares with 3.24 10<sup>−1</sup> obtained previously using a single-colour model [11].” This comparison does not tell me whether the improvement in model performance justifies an additional model component. There are other, likelihood based approaches to assess whether a model fits better in a relevant extent by adding a free model parameter. Can these be used for a more conclusive comparison? Besides, a correlation of 0.36 does not seem so good?

      We understand the Reviewer’s concern that the observed increase in the activity correlation may not appear to provide strong evidence for the improvement of the newly introduced model. However, within the context of polymer models developed to study realistic gene transcription and chromatin organization, this type of correlation analysis is a widely accepted approach for model validation. Experimental data commonly used for such validation include Hi-C maps, FISH experiments, and GRO-seq data [10,11]. The first two are typically employed to assess how accurately the model reproduces the 3D folding of chromatin; a comparison between experimental and simulated Hi-C maps is provided in the Supplementary Information (Fig. S5), showing a Pearson correlation of 0.7. GRO-seq or RNA-seq data, on the other hand, are used to evaluate the model’s ability to predict gene transcription levels. To date, the highest correlation for transcriptional activity data has been achieved by the HiP-HoP model at a resolution of 1 kbp [10], reporting a Spearman correlation of 0.6. Therefore, the correlation obtained with our 2-color model represents a good level of agreement when compared with the more complex HiP-HoP model. In this context, the observed increase in correlation—from 0.324 to 0.366—can be regarded as a modest yet meaningful improvement.

      “…consequently, use of an additional color provides a statisticallysignificant improvement (p-value < 10<sup>−6</sup>, 2-sided t-test).” I do not follow this argument. Given enough simulation repeats, any improvement, no matter how small, will lead to statistically significant improvements.

      We agree that this sentence could be misleading. We have now rephrased it in a clearer manner specifying that each of the two correlation values is statistically significant alone, while before we were wrongly referring to the significance of the improvement.

      “Additionally, simulated contact maps show a fair agreement with Hi-C data (Figure S5), with a Pearson correlation r ∼ 0.7 (p-value < 10<sup>−6</sup>, 2-sided t-test).” Nice!

      We thank the Reviewer for the positive comment.

      “Because we do not include heterochromatin-binding proteins, we should not however expect a very accurate reproduction of Hi-C maps: we stress that here instead we are interested in active chromatin, transcription and structure only as far as it is linked to transcription.” Then why do you not limit your correlation assessment to only these regions to show that these are very well captured by your model?

      We thank the Reviewer for this insightful comment. Indeed, we could have restricted our investigation to active chromatin regions, as done in our previous works [11,12]. However, our intention in this section of the manuscript was to clarify that the current model is relatively simple and therefore not expected to achieve a very high level of agreement between experimental and simulated Hi-C maps. Another important limitation of the two color model described in the section is the absence of active loop extrusion mediated by SMC proteins, which is known to play a central role in establishing TADs boundaries. Consequently, even if our analysis were limited to active chromatin regions, the agreement with experimental Hi-C maps would still remain lower than that obtained with more comprehensive models, such as HiP-HoP, that we use later in the last section of the paper. We have now added a comment in the revised manuscript explicitly noting the lack of active loop extrusion in our 2-color model.

      “We also measure the average value of the demixing coefficient, θ<sub>dem</sub> (Materials and Methods). If θ<sub>dem</sub> = 1, this means that a cluster contains only TFs of one colour and so is fully demixed; if θ<sub>dem</sub> = 0, the cluster contains a mixture of TFs of all colors in equal number, and so is maximally mixed.” Repetitive.

      We have now rephrased the sentence in a more concise way.

      “…notably, this is similar to the average number of productivelytranscribing pols seen experimentally in a transcription factory [6].” That seems a bit fast and loose. The number of Polymerases can differ depending on state, type of factory, gene etc. and vary between anything from to a few hundreds of Polymerase complexes depending on definition of factory, and what is counted as active. Also, one would think that polymerases only make up a small part of the overall protein pool that constitutes a condensate, so it is unclear whether this is a pertinent estimate.

      Here we refer to the average size of what is normally referred to as a PolII factory, not a generic nuclear condensate. These are the clusters which arise in our simulations. These structures emerge through microphase separation and have been well characterised, for instance see [13] for a recent review. For these structures while there is a distribution the average is well defined and corresponds to a size of about 100 nm, which is very much in line with the size of the clusters we observe, both in terms of 3D diameter and number of participating proteins. Because of the size, the number of active complexes which can contribute cannot be significantly more than ∼ 10. These estimates are, we note, very much in line with super-resolution measurements of SAF-A clusters [14], which are associated with active transcription and hence it is reasonable to assume they colocalise with RNA and polymerase clusters.

      “Conversely, activities of similar TUs lying far from each other on the genetic map are often weakly negatively correlated, as the formation of one cluster sequesters some TFs to reduce the number available to bind elsewhere.” This point is interesting, and I strongly suspect that this indeed happening. But I don’t think it was shown in the analysis of the simulation results in sufficient clarity. We need direct assessment of this sequestration, currently it’s only indirectly inferred.

      Indeed, this is the mechanism underlying the emergence of negative long-range correlations among TU activity values. As the Reviewer correctly pointed out, the competition for a finite number of TFs was only indirectly inferred in the original manuscript. To address this, we have now included a new figure explicitly illustrating this effect. In Fig. S12, we show the kymograph of active TUs (left panel), as in Fig. 2E(i) of the main text, alongside a new kymograph depicting the number of green TFs within a sphere of radius 10σ centered on each green TU (right panel). For simplicity, we focus here only on green TUs and TFs. It can be observed that, during the initial part of the simulation, green TFs are localized near genomic position ∼ 2000(right panel), where green TUs are transcriptionally active (left panel). Toward the end of the simulation, TUs near genomic position ∼ 500 become active, coinciding with the relocation of TFs to this region and the depletion of the previous one.

      In the definition for the demixing coefficient (equation 1), what does the index i stand for?

      Here i is an index denoting each of the colors present in the model. We have now specified the meaning of i after Eq. 1.

      Reviewer 3 (Public Review):

      In this work, the authors present a chromatin polymer model with some specific pattern of transcription units (TUs) and diffusing TFs; they simulate the model and study TFclustering, mixing, gene expression activity, and their correlations. First, the authors designed a toy polymer with colored beads of a random type, placed periodically (every 30 beads, or 90kb). These colored beads are considered a transcription unit (TU). Same-colored TUs attract with each other mediated by similarly colored diffusing beads considered as TFs. This led to clustering (condensation of beads) and correlated (or anti-correlation) ”gene expression” patterns. Beyond the toy model, when authors introduce TUs in a specific pattern, it leads to emergence of specialized and mixed cluster of different TFs. Human chromatin models with realistic distribution of TUs also lead to the mixing of TFs when cluster size is large.

      Strengths.

      This is a valuable polymer model for chromatin with a specific pattern of TUs and diffusing TF-like beads. Simulation of the model tests many interesting ideas. The simulation study is convincing and the results provide solid evidence showing the emergence of mixed and demixed TF clusters within the assumptions of the model.

      Weaknesses.

      Weakness of the work: The model has many assumptions. Some of the assumptions are a bit too simplistic. Concerns about the work are detailed below:

      We thank the Referee for this overall positive evaluation.

      We thank the Referee for this important observation. The way we The authors assume that when the diffusing beads (TFs) are near a TU, the gene expression starts. However, mammalian gene expression requires activation by enhancer-promoter looping and other related events. It is not a simple diffusion-limited event. Since many of the conclusions are derived from expression activity, will the results be affected by the lack of looping details?

      We do not need to assume promoter-enhancer contact, this emerges naturally through the bridging-induced phase separation and indeed is a key strength of our model. Even though looping is not assumed as key to transcriptional initiation, in practice the vast majority of events in which a TF is near a TU are associated with the presence of a cluster where regulatory elements are looped. So transcription in our case is associated with the bridging-induced phase separation, and there is no lack of looping, looping is naturally associated with transcription, and this is an emergent property of the model (not an assumption), which is an important feature of our model. Accordingly, both contact maps and transcriptional activity are well predicted by our model, both in the version described here and in the more sophisticated single-colour HiP-HoP model [10] (an important ingredient of which is the bridging-induced phase separation).

      Authors neglect protein-protein interactions. Without proteinprotein interactions, condensate formation in natural systems is unlikely to happen.

      We thank the Reviewer for pointing out the absence of protein-protein interactions in our simulations. While we acknowledge this limitation, we would like to emphasize that experimental studies have not observed nuclear proteins forming condensates at physiological concentrations in the absence of DNA or chromatin. For example, studies such as Ryu et al. [15] and Shakya et al. [16] show that protein-protein interactions alone are insufficient to drive condensate formation in vivo. Instead, the presence of a substrate, such as DNA or chromatin, is essential to favor and stabilize the formation of protein clusters.

      In our simulations, we propose that protein liquid-liquid phase separation (LLPS) is driven by the presence of both strong and weak attractions between multivalent protein complexes and the chromatin filament. As stated in our manuscript, the mechanism leading to protein cluster formation is the bridging induced attraction. This mechanism involves a positive feedback loop, where protein binding to chromatin induces a local increase in chromatin density, which then attracts more proteins, further promoting cluster formation.

      While we acknowledge that adding protein-protein interactions could be incorporated into our simulations, we believe this would need to be a weak interaction to remain consistent with experimental data. Additionally, incorporating such interactions would not alter the conclusions of our study.

      What is described in this paper is a generic phenomenon; many kinds of multivalent chromatin-binding proteins can form condensates/clusters as described here. For example, if we replace different color TUs with different histone modifications and different TFs with Hp1, PRC1/2, etc, the results would remain the same, wouldn’t they? What is specific about transcription factor or transcription here in this model? What is the logic of considering 3kb chromatin as having a size of 30 nm? See Kadam et al. (Nature Communications 2023). Also, DNA paint experimental measurement of 5kb chromatin is greater than 100 nm (see work by Boettiger et al.).

      We thank the Reviewer for this important observation, which we now address. To begin, we consider the toy model introduced in the first part of the manuscript, where TUs are randomly positioned rather than derived from epigenetic data. As the Reviewer points out, in this simplified context, our results reflect a generic phenomenon: the composition of clusters depends primarily on their size, independent of the specific types of proteins involved. However, the main goal of our work is to gain insights into apparently contradictory experimental findings, which show that some transcription factories consist of a single type of transcription factors, while other contain multiple types. This led us to focus on TF clusters and their role in transcriptional regulation and co-regulation of distant genes. Therefore, in the second part of the manuscript, we use DNase I hypersensitive site (DHS) data to position TUs based on predicted TF binding sites, providing a more biological framework. In both the toy model and the more realistic HiP-HoP model, we observe a size-dependent transition in cluster composition. However, we refrain from generalizing these results to clusters composed of other protein complexes, such as HP1 and PRC, as their binding is governed by distinct epigenetic marks (e.g. H3K927me3 and H3K27me3), which exhibit different genomic distributions compared to DHS marks.

      Finally, the mapping of 3kb to 30nm is an estimate which does not significantly impact our conclusions. The relationship between genomic distance (in kbp) and spatial distance (in nm) is highly dependent on the degree of chromatin compaction, which can vary across cell types and genomic context. As such, providing an exact conversion is challenging [17]. For example, in a previous work based on the HiP-HoP model [12] we compared simulated and experimental FISH measurements and found that 1kbp typically corresponds to 15 − 20nm, implying that 3kbp could span 60nm. Nevertheless, we emphasize that varying this conversion factor does not affect the core results or conclusions of our study. We have now included a clarification in the revised SI to highlight this point.

      Recommendations for the authors:

      Other points.

      Figure 1(D) caption says 2.25σ = 1.6 nanometer. Is this a typo? Sigma is 30nm.

      Yes, it was. As 1σ ∼ 30nm, we have 2.25σ = 2.25 · 30 nm = 67.2 nm ∼ 6.7 × 10<sup>−8</sup>m. We have now corrected the caption.

      Page 6, column 2nd, 3rd para, it is written that θ<sub>dem</sub> (”defined in Fig.1”). There is no θ<sub>dem</sub> defined in Fig.1, is there? I can see it defined in Methods but not in Fig. 1.

      Correct, we replaced (defined in Fig.1) with (see Methods for definition).

      Page 6, column 2, 4th para: what does “correlations overlap and correlations diverge mean”?

      With reference to the plots from Fig. 5B, correlation overlap and diverge simply refers to the fact that same-colour (red curves) and different-colour (blue curves) correlation trends may or may not overlap on each other. We have now clarified this point.

      What is the precise definition of correlation in Fig 5B (Y-axis)?

      In Fig.5B, correlation means Pearson correlation. We have now specified this point in the revised text and in the caption of Fig.5.

      References

      (1) S. A. Quinodoz, J. W. Jachowicz, P. Bhat, N. Ollikainen, A. K. Banerjee, I. N. Goronzy, M. R. Blanco, P. Chovanec, A. Chow, Y. Markaki et al., “Rna promotes the formation of spatial compartments in the nucleus,” Cell, vol. 184, no. 23, pp. 5775–5790, 2021.

      (2) R. A. Beagrie, A. Scialdone, M. Schueler, D. C. Kraemer, M. Chotalia, S. Q. Xie, M. Barbieri, I. de Santiago, L.-M. Lavitas, M. R. Branco et al., “Complex multi-enhancer contacts captured by genome architecture mapping,” Nature, vol. 543, no. 7646, pp. 519–524, 2017.

      (3) R. A. Beagrie, C. J. Thieme, C. Annunziatella, C. Baugher, Y. Zhang, M. Schueler, A. Kukalev, R. Kempfer, A. M. Chiariello, S. Bianco et al., “Multiplex-gam: genome-wide identification of chromatin contacts yields insights overlooked by hi-c,” Nature Methods, vol. 20, no. 7, pp. 1037–1047, 2023.

      (4) L. Liu, B. Zhang, and C. Hyeon, “Extracting multi-way chromatin contacts from hi-c data,” PLOS Computational Biology, vol. 17, no. 12, p. e1009669, 2021.

      (5) R.-S. Nozawa, L. Boteva, D. C. Soares, C. Naughton, A. R. Dun, A. Buckle, B. Ramsahoye, P. C. Bruton, R. S. Saleeb, M. Arnedo et al., “Saf-a regulates interphase chromosome structure through oligomerization with chromatin-associated rnas,” Cell, vol. 169, no. 7, pp. 1214–1227, 2017.

      (6) E. A. Boyle, Y. I. Li, and J. K. Pritchard, “An expanded view of complex traits: from polygenic to omnigenic,” Cell, vol. 169, no. 7, pp. 1177–1186, 2017.

      (7) C. Brackley, N. Gilbert, D. Michieletto, A. Papantonis, M. Pereira, P. Cook, and D. Marenduzzo, “Complex small-world regulatory networks emerge from the 3d organisation of the human genome,” Nat. Commun., vol. 12, no. 1, pp. 1–14, 2021.

      (8) R. B. Brem and L. Kruglyak, “The landscape of genetic complexity across 5,700 gene expression traits in yeast,” Proceedings of the National Academy of Sciences, vol. 102, no. 5, pp. 1572– 1577, 2005.

      (9) M. Chiang, C. A. Brackley, D. Marenduzzo, and N. Gilbert, “Predicting genome organisation and function with mechanistic modelling,” Trends in Genetics, vol. 38, no. 4, pp. 364–378, 2022.

      (10) M. Chiang, C. A. Brackley, C. Naughton, R.-S. Nozawa, C. Battaglia, D. Marenduzzo, and N. Gilbert, “Genome-wide chromosome architecture prediction reveals biophysical principles underlying gene structure,” Cell Genomics, vol. 4, no. 12, 2024.

      (11) A. Buckle, C. A. Brackley, S. Boyle, D. Marenduzzo, and N. Gilbert, “Polymer simulations of heteromorphic chromatin predict the 3d folding of complex genomic loci,” Mol. Cell, vol. 72, no. 4, pp. 786–797, 2018.

      (12) G. Forte, A. Buckle, S. Boyle, D. Marenduzzo, N. Gilbert, and C. A. Brackley, “Transcription modulates chromatin dynamics and locus configuration sampling,” Nature Structural & Molecular Biology, vol. 30, no. 9, pp. 1275–1285, 2023.

      (13) P. R. Cook and D. Marenduzzo, “Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations,” Nucleic acids research, vol. 46, no. 19, pp. 9895–9906, 2018.

      (14) M. Marenda, D. Michieletto, R. Czapiewski, J. Stocks, S. M. Winterbourne, J. Miles, O. C. Flemming, E. Lazarova, M. Chiang, S. Aitken et al., “Nuclear rna forms an interconnected network of transcription-dependent and tunable microgels,” BioRxiv, pp. 2024–06, 2024.

      (15) J.-K. Ryu, C. Bouchoux, H. W. Liu, E. Kim, M. Minamino, R. de Groot, A. J. Katan, A. Bonato, D. Marenduzzo, D. Michieletto et al., “Bridging-induced phase separation induced by cohesin smc protein complexes,” Science advances, vol. 7, no. 7, p. eabe5905, 2021.

      (16) A. Shakya, S. Park, N. Rana, and J. T. King, “Liquid-liquid phase separation of histone proteins in cells: role in chromatin organization,” Biophysical journal, vol. 118, no. 3, pp. 753–764, 2020.

      (17) A.-M. Florescu, P. Therizols, and A. Rosa, “Large scale chromosome folding is stable against local changes in chromatin structure,” PLoS computational biology, vol. 12, no. 6, p. e1004987, 2016.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      In this manuscript, Aghabi et al. present a comprehensive characterization of ZFT, a metal transporter located at the plasma membrane of the eukaryotic parasite Toxoplasma gondii. The authors provide convincing evidence that ZFT plays a crucial role in parasite fitness, as demonstrated by the generation of a conditional knockdown mutant cell line, which exhibits a marked impact on mitochondrial respiration, a process dependent on several iron-containing proteins. Consistent with previous reports, the authors also show that disruption of mitochondrial metabolism leads to conversion into the persistent bradyzoite stage. The study then employed advanced techniques, such as inductively coupled plasma-mass spectrometry (ICP-MS) and X-ray fluorescence microscopy (XFM), to demonstrate that ZFT depletion results in reduced parasite-associated metals, particularly iron and zinc. Additionally, the authors show that ZFT expression is modulated by the availability of these metals, although defects in the transporter could not be compensated for by exogenous addition of iron or zinc. 

      While the manuscript does not directly investigate the transport function of ZFT through biochemical assays, the authors indirectly support the notion that ZFT can transport zinc by demonstrating its ability to compensate for a lack of zinc transport in a yeast heterologous system. Furthermore, phenotypic analyses suggest defects in iron availability, particularly with regard to Fe-S mitochondrial proteins and mitochondrial function. Overall, the manuscript provides a solid, well-rounded argument for ZFT's role in metal transport, using a combination of complementary approaches. Although direct biochemical evidence for the transporter's substrate specificity and transport activity is lacking, the converging evidence, including changes in metal concentrations upon ZFT depletion, yeast complementation data, and phenotypic changes linked to iron deficiency, presents a convincing case. Some aspects of the results may appear somewhat unbalanced, particularly since iron transport could not be confirmed through heterologous complementation, while zinc-related phenotypes in the parasites have not been thoroughly explored (which is challenging given the limited number of zinc-dependent proteins characterized in Toxoplasma). Nevertheless, given that metal acquisition remains largely uncharacterized in Toxoplasma, this manuscript provides an important first step in identifying a metal transporter in these parasites, and the data presented are generally convincing and insightful. 

      We thank the reviewer for their assessment and would like to highlight that we now add direct biochemical characterisation in the new Figure 8, supporting our hypothesis and confirming iron transport by this protein.

      Reviewer #2 (Public review): 

      Summary: 

      The intracellular pathogen Toxoplasma gondii scavenges metal ions such as iron and zinc to support its replication; however, mechanistic studies of iron and zinc uptake are limited. This study investigates the function of a putative iron and zinc transporter, ZFT. In this paper, the authors provide evidence that ZFT mediates iron and zinc uptake by examining the regulation of ZFT expression by iron and zinc levels, the impact of altered ZFT expression on iron sensitivity, and the effects of ZFT depletion on intracellular iron and zinc levels in the parasite. The effects of ZFT depletion on parasite growth are also investigated, showing the importance of ZFT function for the parasite. 

      Strengths: 

      A key strength of the study is the use of multiple complementary approaches to demonstrate that ZFT is involved in iron and zinc uptake. Additionally, the authors build on their finding that loss of ZFT impairs parasite growth by showing that ZFT depletion induces stage conversion and leads to defects in both the apicoplast and mitochondrion. 

      Weaknesses: 

      (1) Excess zinc was shown not to alter ZFT expression, but a cation chelator (TPEN) did lead to decreased expression. While TPEN is often used to reduce zinc levels, does it have any effect on iron levels? Could the reduction in ZFT after TPEN treatment be due to a reduction in the level of iron or another cation?

      WE thank the reviewers for this comment, we agree that TPEN is a fairly unspecific cation chelator so to determine if its effects are due to removal of zinc or other cations we treated with TPEN and either zinc or iron. Co-incubation of TPEN and zinc prevented ZFT depletion, while TPEN+FAC had no effect compared to TPEN alone (new Figure 6h and i), strongly suggesting the effects on ZFT abundance are linked to zinc and not just iron.  

      (2) ZFT expression was found to be dynamic depending on the size of the vacuole, based on mean fluorescence intensity measurements. Looking at protein levels by Western blot at different times during infection would strengthen this finding. 

      We show here that ZFT expression is highly dynamic, depending both the iron status of the host cell and the number of parasites/vacuole. However, validating this finding by western would be complex due to the highly unsynchronised nature of parasite replication and the large number (5x10<sup>6</sup> - 1x10<sup>7</sup>cells) of parasites required to visualise ZFT. Further, we show that ZFT is apparently internalised prior to degradation. For this reason, we have not attempted to validate this finding by western blotting at this time.

      (3) ZFT localization remained at the parasite periphery under low iron conditions. However, in the images shown in Figure S1c, larger vacuoles (containing 4-8 parasites) are shown for the untreated conditions, and single parasite-containing vacuoles are shown for the low iron condition. As ZFT localization is predominantly at the basal end of the parasite in larger PV and at the parasite periphery for smaller vacuoles, it would be better to compare vacuoles of similar size between the untreated and low-iron conditions.

      The reviewer brings up a good point, the concentration of iron chelator that we used here does not enable parasite replication, making an assessment of changes in localisation challenging. To address this, have new data using a much lower concentration of chelator (20 mM), which is still expected to impact the parasites (Hanna et al, 2025), but allows for replication. In this low iron environment, ZFT localisation remained significantly more peripheral (Fig. S1d,e), supporting our hypothesis that ZFT localisation is iron dependent, independent of vacuolar stage.

      Reviewer #3 (Public review): 

      Summary:

      Aghabi et al set out to characterize a T. gondii transmembrane protein with a ZIP domain, termed ZFT. The authors investigate the consequences of ZFT downregulation and overexpression for parasite fitness. Downregulation of ZFT causes defects in the parasite's endosymbiotic organelles, the apicoplast and the mitochondrion. Specifically, lack of ZFT causes a decrease in mitochondrial respiration, consistent with its role as an iron transporter. This impact on the mitochondria appears to trigger partial differentiation to bradyzoites. The authors furthermore demonstrate that expression of TgZFT can rescue a yeast mutant lacking its zinc transporter and perform an array of direct metal ion measurements, including X-ray fluorescence microscopy and inductively coupled mass spectrometry (ICP-MS). These reveal reduced metal ions in parasites depleted in ZFT. Overall, the data by Aghabi et al. reveal that ZFT is a major metal ion transporter in T. gondii, importing iron and zinc for diverse essential processes. 

      Strengths:

      This study's strength lies in the thorough characterization of the transporter. The authors combine a number of techniques to measure the impact of ZFT depletion, ranging from the direct measurement of metal ions to determining the consequences for the parasite's metabolism (mitochondrial respiration), as well as performing a yeast mutant complementation. This work is very thorough and clearly presented, leaving little doubt about this protein's function. 

      Weaknesses:

      This study offers no major novel insights into the biology of T. gondii. The transporter was already annotated as a zinc transporter (ToxoDB), was deemed essential (PMID: 27594426), and localized to the plasma membrane (PMID: 33053376). This study mostly confirms and validates these previous datasets. The authors identify three other proteins with a ZIT domain. Particularly, the role of TGME49_225530 is intriguing, as it is likely fitness-conferring (score: -2.8, PMID: 27594426) and has no subcellular localization assigned. Characterizing this protein as well, revealing its localization, and identifying if and how these transporters coordinate metal ion transport would have been worthwhile. 

      We agree that the work presented here validates the previous datasets, and if that was all we had done, we agree that the biological insights would be limited. However, we have gone significantly beyond the predictions, demonstrating dynamic localisation changes, iron-mediated regulation, the lack of substrate-based complementation and validating transport activity of both zinc and iron. Although in silico predictions and screens can be informative, it remains important to validate biological functions experimentally. While we agree that characterisation of TGME49_225530 (as well as the other two annotated ZIP proteins) would be interesting, and will certainly form part of our future plans, it is significantly beyond the scope of the presented manuscript.

      Another weakness is the data related to the impact of ZFT downregulation on the apicoplast in Figure 4. The authors show that downregulation of ZFT causes an increase in elongated apicoplasts (Figure 4d). The subsequent panels seem to show that the parasites present a dramatic growth defect at that time point. This growth arrest can directly explain the elongated apicoplast, but does not allow any conclusion about an impact on the organelle. In any case, an assessment of 'delayed death' as presented in Figure 4c seems futile, since the many other processes affected by zinc and iron depletion likely cause a rapid death, masking any potential delayed death.

      To address this point, we agree that given the importance of iron and zinc to the parasite that we cannot differentiate the death of the parasite due to apicoplast defects from death from other causes and we have modified the discussion to reflect this, as below.

      “However, given the delayed phenotype typically seen upon apicoplast disruption, we cannot determine if this is a direct effect of ZFT, or a downstream consequence of metal depletion”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Specific Comments: 

      (1) The background on the typical sequence features that would identify Toxoplasma ZIP homologues should be expanded and clarified. While these proteins are likely quite divergent and may lack many conserved features, the manuscript currently does not provide enough detail to assess how similar (or different) TgZIPs are from well-characterized family members. Additionally, the justification for focusing on TGGT1_261720 (ZFT) over TGGT1_225530, as stated in the first paragraph of the results section, seems unclear. There is no predictive data supporting a potential plasma membrane localization for TGGT1_225530 (yet this cannot be excluded), and TGGT1_225530 appears to have more canonical metal-binding motifs. I believe that the fact that only TGGT1_261720 is iron-regulated should be sufficient justification for its selection, and this point could be emphasized more clearly. Furthermore, the discussion mentions a leucine residue that may be associated with broad substrate specificity, but this is not addressed in the initial comparative sequence analysis. These residues and the HK motif are not actually addressed in the Gyimesi et al. reference currently mentioned; thus this could be clarified and updated with references (such as PMID: 31914589) that provide more recent insights into key residues involved in metal selectivity in ZIP transporters.

      We thank you for this comment, to address these points:

      We agree that the iron-mediated regulation is sufficient for our focus on ZFT and have clarified the text to reflect this, as described above.

      We have also updated the references as suggested, our apologies for this oversight.

      We have further expanded the discussion, especially with reference to our new results using heterologous expression in oocytes (please see above).

      (2) Figure 1D, Figure 2A, C, H, Figure 3D, Figure 6F, H, corresponding text and paragraph 2 of the Discussion: It seems that most of the "non-specific bands" annotated in Figure 1D, which are lower molecular weight products, are not present in the parental cell line, suggesting they may not be non-specific after all. These bands also vary depending on the cell line (e.g., promoter used, see Figures 2H and 3D) or experimental conditions (e.g., iron excess or depletion). Given the dynamic localization of ZFT during intracellular development, it may be worth exploring whether these lower molecular weight bands represent degraded forms of TgZFT, possibly corresponding to the basally-clustered signal observed by immunofluorescence, with only the full-length protein associating with the plasma membrane. This possibility should be investigated or at least discussed further.

      While the lower bands are not present in the parental, we do see them in other HA-tagged lines, especially when the expression of the tagged protein is low, seen below (Author response image 1). We don’t currently have an explanation for these, but we can confirm that they do not change in abundance in parallel with the full length protein, supporting our hypothesis that these bands are an artefact of the anti-HA antibody in our system. Although ZFT is clearly degraded (e.g. Fig. 1g), we currently do not believe these bands are ZFT c-terminal degradation products.

      Author response image 1.

      Western blot of ZFT-3HA<sub>zft</sub> and another HA-tagged unrelated cytosolic protein, demonstrating that the lower bands are most likely nonspecific.

      (3) It is unfortunate that ZFT could not complement a yeast iron transporter mutant cell line, as this would have provided a strong argument for ZFT's role in iron transport. The manuscript does not provide much detail about the Δfet2/3 yeast mutant line. Fet3 is the ferroxidase subunit, while Ftr1 is the permease subunit of the high-affinity iron transport complex in yeast. Fet2, however, appears to be Saccharomyces cerevisiae's VPS41 homolog. Therefore, is Δfet2/3 the most appropriate mutant to use, or would another mutant line (e.g., ΔFtr1) be a better choice? Additionally, while Figure 7 suggests a decrease in metal uptake upon ZFT depletion, it would be useful to test whether overexpression of ZFT leads to enhanced metal incorporation, perhaps using a FerroOrange assay. 

      We thank the reviewer for their comments, which we have answered below:

      The Δfet2/3 yeast mutant was a typo and has been corrected, or apologies, we did use the  Δfet3/4 mutant line, based on previous successful experiments involving plant metal transporters (e.g  (DiDonato et al., 2004)).

      Unfortunately, we were unable to perform the FerroOrange assay in the overexpression line as this line is endogenously fluorescent in the same channel as FerroOrange.

      However, as detailed above we have now added significant new data, confirming our hypothesis that ZFT is an iron/zinc transporter through heterologous expression in Xenopus oocytes in the new figure 8. This provides direct evidence of transport of iron, and evidence that zinc can inhibit this transport, consistent with our hypothesis.  

      (4) The annotation of the blot in Figure 2H suggests that overexpressed ZFT-TY can only be detected in the absence of heat denaturation. However, this is not addressed in the text. Does heat denaturation also affect the detection of ZFT-3HA or the lower molecular weight products? This should be clarified in the manuscript. 

      Interestingly, ZFT is detectable after boiling at 95° C for 5 minutes when expressed at endogenous (or near endogenous) levels in the ZFT-3HA<sub>sag1</sub> and ZFT-3HA<sub>zft</sub> tagged parasite lines. However, overexpression of ZFT leads to a loss of detection via western blot when boiled, although the protein is detectable without heat denaturation.

      A possible explanation for this is that overexpression of protein may cause ZFT to miss-fold, making the protein more prone to aggregation following boiling, rendering the protein insoluble and unable to enter the gel. Moreover, heat aggregation can sometimes mask the epitope tags on the protein that is required for the antibody to be recognised, possibly explaining by ZFT is undetectable when overexpressed and exposed to boiling conditions, as has previously been observed for other transmembrane proteins (e.g. (Tsuji, 2020)).

      We have clarified this in the results section, although we do not have a full explanation for this, we consider it important to share for others who may be looking at expression of these proteins.

      (5) Figure 3G: It might be helpful to include an uncropped gel profile to allow readers to visualize that the main product does indeed correspond to a potential dimeric form in the native PAGE. 

      This has now been added in Figure S3e, thank you for this suggestion.

      (6) The investigation of the impact of ZFT depletion on the apicoplast could be improved. The authors suggest that ZFT knockdown inhibits apicoplast replication based on a modest increase in elongated organelles, but the term "delayed death" is not appropriate in that case, as it is typically linked to a loss of the organelle. This is not observed here and is also illustrated by the unchanged CPN60 processing profile. So, clearly, there seems to be no strong morphological effect on the apicoplast early on after ZFT depletion. On the other hand, the authors dismiss any impact on TgPDH-E2 lipoylation (which is iron-dependent) based on the fact that the lipoylated form of the protein is still detected by Western blot. However, closer inspection of the blot in Figure 4B suggests that the intensity of the annotated TgPDH-E2 signal is reduced compared to the -ATc condition (although there might be differences in protein loading, as indicated by the control) or even with the mitochondrial 2-oxoglutarate dehydrogenase-E2, whose lipoylation is presumably iron-independent (see PMID: 16778769). This experiment should be repeated, and the results quantified properly in case something was missed, and the duration of depletion conditions perhaps extended further. Of note, it would also be worthwhile to revisit size estimations, as the displayed profiles seem inconsistent with the typical sizes of lipoylated proteins detected with the anti-lipoyl antibody (e.g., ~100 kDa for PDH-E2, ~60 kDa for branched-chain 2-oxo acid dehydrogenase, and ~40 kDa 2-oxoglutarate dehydrogenase).

      We thank the reviewer for this comment. We agree that there is no strong defect on the apicoplast in the first lytic cycle and we have modified the language to remove reference to delayed death, as given the magnitude of changes associated with loss of iron and zinc, we cannot be certain about the role of the apicoplast.

      Based on this suggestion, we have now quantified the levels of lipoylation of PDH-E2, BDCK-E2 and OGDH-E2 and now include this in Figure S4b, c, d. Supporting our other results, we do not see a significant change in PDH-E2 lipolyation upon ZFT knockdown. However, although OGDH-E2 lipoylation is unchanged (Figure S4c) interestingly we do see a significant increase in BDCK-E2 lipoylation (Figure S4d). This process is not expected to be directly iron related, as mitochondrial lipoylation is through scavenging rather than synthesis however, speaks to the larger mitochondrial disruption that we see. We now consider this further in the discussion.

      For the sizes, we thank the reviewer for bringing this up, our apologies this was due to an error in the annotation, and we have now corrected this in the figure.

      (7) In the third paragraph of the discussion, the authors mention the inability to complement ZFT loss by adding exogenous metals. One argument is the potential lack of metal access to the parasitophorous vacuole (PV). Although largely unexplored, this point could be expanded further in the discussion, as the issue of metal transport to the parasite involves not only the parasite plasma membrane but also the PV membrane. Additionally, the authors mention the absence of functional redundancy in transporters, but it would be helpful to discuss potential stage-specific or differential expression of other ZIP candidates. Transcriptomic data available on Toxodb.org could provide useful insights into this, and experimental approaches, such as RT-PCR, could be used to assess the expression of these candidates in the absence of ZFT. 

      On the issue of metals crossing the PV membrane, we agree that while we do not currently know mechanisms of metal transport within the infected host cell, we do have experimental confirmation that the concentration and form of the metals that we are using can impact the parasites. We show that metal treatment inhibits parasites growth (e.g. Figure 3k-n, Figure 6a-d) and we can detect the increased metals through our experiments using FerroOrange and FluroZine (Figure 7a, c). In these experiments, parasites were treated intracellularly and so we can confirm that, regardless of the mechanism, iron and zinc can reach the parasite. While entry of metals across the PV is an intriguing question, it is beyond the scope of the present work which focuses on the role of the selected transporter.

      We agree that a more detailed discussion of the other ZIP transporters is warranted. We have extended this section of the discussion although for now, we cannot determine the role of the other ZIP transporters in Toxoplasma.

      (8) In the discussion, the authors mention that « Inhibition of respiration has previously been linked to bradyzoite conversion ». To strengthen their point, the authors could mention that mitochondrial Fe-S mutants, as well as mutants affecting mitochondrial translation or the mitochondrial electron transport chain, also initiate bradyzoite conversion (PMID: 34793583). This would reinforce the connection between mitochondrial dysfunction and stage conversion. 

      This is an excellent point and we have added this to the discussion as follows:

      “Inhibition of mitochondrial Fe-S biogenesis or mitochondrial respiration have both previously been linked to bradyzoite conversion (Pamukcu et al., 2021; Tomavo and Boothroyd, 1995), however we do not yet know the signalling factors linking iron, zinc or mitochondrial function to bradyzoite differentiation”.

      (9) As a general comment on manuscript formatting, providing page and line numbers would significantly improve the manuscript's readability and allow reviewers to more easily reference specific sections. This would help address the minor issues of typos (e.g., multiple occurrences of "promotor"). I suggest a careful read-through to correct these issues. 

      We thank the reviewer for this comment and in the resubmitted version we have corrected these issues. 

      Reviewer #2 (Recommendations for the authors): 

      (1) In the alignment (Figure 1a), the BPZIP sequence is from which organism (genus, species)? It would be helpful to include this information in the figure legend.

      Apologies for this oversight, this figure and section have been reworked and the species name (Bordetella bronchiseptica) added.

      (2) In reference to Figure 1a, the authors state, "Interestingly, all parasite ZIP-domain proteins examined have a HK motif at the M2 metal binding". I was wondering if by "all" the authors mean Toxoplasma and Plasmodium falciparum (shown in Figure 1a) or did the authors also look at other apicomplexan parasites such as Cryptosporidium or Neospora? Is this a general feature of apicomplexan parasites? 

      We looked at this, and the HK motif in the M2 binding site is conserved in Neospora Cryptosporidium, and even the digenic gregarine Porospora cf. gigantea. However, in the more distantly related Chromera we find a HH motif at the same position. This suggests that the HK motif is present in the Apicomplexa, but not conserved in the free-living Alveolata. Although we cannot speculate on the role of this motif currently, its role in metal import in Apicomplexa does deserve future scrutiny. To reflect this finding we have modified Figure 1a and the text.

      (3) In Figure 1e, to better visualize the ZFT-3HA staining at the basal pole, it would be better to omit the DAPI staining from the merged image. It is difficult to see the ZFT staining in the image of the large vacuole.

      We have removed the DAPI from this image to improve clarity.

      (4) Based on the "delayed-death" phenotype of the apicoplast, it is not surprising that no defects were observed in CPN60 processing or protein lipoylation. Have the authors considered measuring these phenotypes after a further round of growth (as was done for visualizing apicoplast morphology)? 

      We agree that changes in apicoplast function are often only seen in the second round of replication. However, here we wanted to check if ZFT depletion led to immediate changes in function of the organelle, which was not the case. It is highly likely that after the second round, we would see significant defects in the apicoplast function, however given the immediate importance of iron and zinc to many processes within the parasite, we believe that these experiments would be complicated to interpret.

      (5) Depleting ZFT led to a reduction in expression levels for the mitochondrial Fe-S protein SDHB but not for a cytosolic Fe-S protein. Is it expected that less intracellular iron (via depleted ZFT) would differentially affect mitochondrial versus cytosolic Fe-S proteins? 

      Previous studies (e.g., Maclean et al., 2024; Renaud et al., 2025) have shown that upon direct inhibition of the cytosolic Fe-S pathway, ABCE1 is fairly stable and levels can persist for 2-3 days post treatment. However, our recent work has shown that rapid and acute depletion of iron directly (though treatment with a chelator) can lead to ABCE1 levels decreasing within 24h (Hanna et al., 2025). In the case of ZFT knockdown, due to the more gradual reduction in iron levels seen (e.g. Figure 7j) we believe the parasites are prioritising key Fe-S pathways (e.g. essential proteostasis through ABCE1), probably while remodelling metabolism (as seen in our Seahorse assays). However, there are many proteins expected to be directly impacted by iron and zinc restriction that these parasites experience, and different protein classes are expected to behave differently in these conditions.

      Reviewer #3 (Recommendations for the authors): 

      (1) Is the effect on the plaque size between T7S4-ZFT (-aTc) in regular and 'high iron' conditions significant? The authors show convincingly that the plaque size is smaller due to the swapped promoter and the resulting overexpression of ZFT. But is the effect aggravated in high iron? This would be expected if excess iron were the problem.

      The plaque sizes are significantly smaller in the T7S4-ZFT line under high iron compared to the untreated condition, and compared to the parental untreated line. However, if we normalise plaque size to untreated conditions for both lines, there is not a significant change in plaque size in high iron between the parental and T7S4-ZFT. This is possibly due to the concentration of iron used (200 mM), which may not be optimal to see this effect, or the time taken for plaque assays (6-7 days), which may allow the excess iron to be stored by the host cells, changing the effective concentration of parasite exposure.

      (2) I struggle to understand the intracellular growth assay in Figure 5b. Here, T7S4-ZFT parasites show 25 % of vacuoles with more than 8 parasites (labelled 8+). But such large vacuoles are not observed in the parental strain. It appears as if the inducible strain grows faster even though it was earlier shown to have a fitness defect (see Figure 3j). Can you please clarify?

      This is a result of rapid growth of the parental line, some vacuoles in this line lysed and initiated a new round of replication at this time point while we saw no evidence at any timepoint that ZFT-depleted parasites were able to lyse the host cell. However, the initial (24-48h post ATc addition) replication rate of the ZFT KD remains similar to the parental. In this panel, we wanted to emphasize that the major phenotype we see upon ZFT depletion is vacuole disorganisation, which we believe is linked to the start of differentiation into bradyzoites.

      (3) Did the authors perform an IFA in addition to the Western blot to localize the 2nd Ty-tagged ZFT copy? It seems important to validate that the protein correctly localizes to the plasma membrane. 

      We have done so and now include these data in Figure S2b. Overexpression of ZFT-Ty localises to internal structures (probably vesicles) with some signal at the periphery, however, this limited expression at the periphery is sufficient to mediate the phenotypes that we see.

      (4) First sentence of the abstract and introduction: The authors speak of metabolism and cellular respiration as though they are two different processes. Is respiration not part of metabolism? 

      This is an excellent point, we wanted to distinguish mitochondrial respiration  from general cellular metabolism, but this was not clear. We have now changed this in the introduction to the below:

      “Iron, and other transition metals such as zinc, manganese and copper, are essential nutrients for almost all life, playing vital roles in biological processes such as DNA replication, translation, and metabolic processes including mitochondrial respiration (Teh et al., 2024)”

      (5) 2nd paragraph of the introduction: toxoplasmosis is written capitalized but should be lower case.

      This has been corrected.

      (6) Figure 4j legend: change 'shits parasites to a more quiescent stage' to 'shifts parasites'.

      This has been corrected, our apologies.

      (7) Please correct the following sentence: 'These data demonstrate ZFT depletion leads to the expression of the bradyzoite-specific markers BAG1 and DBL.' DBL is not expressed by the parasite. It is a lectin that binds to the sugars in the cyst wall.

      We have now modified this in the text. The sentence now reads: “These data show that ZFT depletion leads to the expression of the bradyzoite marker BAG1 and the production of the cyst wall, as detected by DBL”.

      (8) In the section on yeast complementation with TgZFT, the authors write: 'Based on this success, we also attempted to complement...'. Please consider changing 'Success' to something more neutral.

      We have modified the text to now read: “Based on these results, we also attempted to complement”…

      (9) In the discussion, the authors write: 'We see a delayed phenotype on the apicoplast, suggesting that metal import is also required in this organelle, although no apicoplast metal transporters have yet been identified.' Please consider the study Plasmodium falciparum ZIP1 Is a Zinc-Selective Transporter with Stage-Dependent Targeting to the Apicoplast and Plasma Membrane in Erythrocytic Parasites (PMID: (38163252).

      We thank the reviewer for the note and have modified the text to include this and the reference. Please see below:

      “Iron is known to be required in the apicoplast (Renaud et al., 2022), zinc also may be required, as the fitness-conferring Plasmodium zinc transporter ZIP1 is transiently localised to the apicoplast (Shrivastava et al., 2024), although the functional relevance of this localisation has not yet been established”.

      (10) The authors write: 'Iron is known to be required in the apicoplast (Renaud et al., 2022), although a potential role for zinc in this organelle has not yet been established.' The role for zinc in the apicoplast may not have been shown formally, but surely among its hundreds of proteins, and those involved in replication and transcription, there are some that depend on zinc...?

      Yes, we agree it would make sense, however multiple searches using ToxoDB and the datasets from Chen et al (2025) were unable to find any apicoplast-localised proteins with zinc-binding domains. We cannot exclude that zinc is in the apicoplast, and the results from Plasmodium (Shrivastava et al., 2024) may suggest that is, however currently we do not have any evidence for its role within this organelle.

      References

      DiDonato, R.J., Roberts, L.A., Sanderson, T., Eisley, R.B., Walker, E.L., 2004. Arabidopsis Yellow Stripe-Like2 (YSL2): a metal-regulated gene encoding a plasma membrane transporter of nicotianamine-metal complexes. Plant J 39, 403–414. https://doi.org/10.1111/j.1365-313X.2004.02128.x

      Hanna, J.C., Shikha, S., Sloan, M.A., Harding, C.R., 2025. Global translational and metabolic remodelling during iron deprivation in Toxoplasma gondii. https://doi.org/10.1101/2025.08.11.669662

      Maclean, A.E., Sloan, M.A., Renaud, E.A., Argyle, B.E., Lewis, W.H., Ovciarikova, J., Demolombe, V., Waller, R.F., Besteiro, S., Sheiner, L., 2024. The Toxoplasma gondii mitochondrial transporter ABCB7L is essential for the biogenesis of cytosolic and nuclear iron-sulfur cluster proteins and cytosolic translation. mBio 15, e00872-24. https://doi.org/10.1128/mbio.00872-24

      Pamukcu, S., Cerutti, A., Bordat, Y., Hem, S., Rofidal, V., Besteiro, S., 2021. Differential contribution of two organelles of endosymbiotic origin to iron-sulfur cluster synthesis and overall fitness in Toxoplasma. PLoS Pathog 17, e1010096. https://doi.org/10.1371/journal.ppat.1010096

      Renaud, E.A., Maupin, A.J.M., Berry, L., Bals, J., Bordat, Y., Demolombe, V., Rofidal, V., Vignols, F., Besteiro, S., 2025. The HCF101 protein is an important component of the cytosolic iron–sulfur synthesis pathway in Toxoplasma gondii. PLoS Biol 23, e3003028. https://doi.org/10.1371/journal.pbio.3003028

      Shrivastava, D., Jha, A., Kabrambam, R., Vishwakarma, J., Mitra, K., Ramachandran, R., Habib, S., 2024. Plasmodium falciparum ZIP1 Is a Zinc-Selective Transporter with Stage-Dependent Targeting to the Apicoplast and Plasma Membrane in Erythrocytic Parasites. ACS Infect. Dis. 10, 155–169. https://doi.org/10.1021/acsinfecdis.3c00426

      Teh, M.R., Armitage, A.E., Drakesmith, H., 2024. Why cells need iron: a compendium of iron utilisation. Trends in Endocrinology & Metabolism 35, 1026–1049. https://doi.org/10.1016/j.tem.2024.04.015 Tomavo, S., Boothroyd, J.C., 1995. Interconnection between organellar functions, development and drug resistance in the protozoan parasite, Toxoplasma gondii. International Journal for Parasitology 25, 1293–1299. https://doi.org/10.1016/0020-7519(95)00066-B.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      We thank Reviewer #1 for the careful reading of our manuscript and for the constructive comments. We have provided responses to each of the comments below.

      We greatly appreciate Reviewer #1’s accurate public review of our study on the kinesin motor using the DNA origami nanospring (NS). With respect to the strengths, we fully agree with Reviewer #1’s comments. Regarding the weakness, we would like to respond as follows.

      It is true that, unlike optical tweezers, our method does not provide real-time data display. Optical tweezers enable real-time observation and manipulation of kinesin molecules at arbitrary time points. Achieving real-time observation and manipulation is indeed an important challenge for the future development of the NS technique. On the other hand, Iwaki et al. (our co-corresponding author) has already investigated dynamic properties of motor proteins under load, such as step size and force–velocity relationship of myosin VI using NS. We are now preparing high spatiotemporal resolution microscopy experiments on the KIF1A system to measure its step size and force–velocity relationship, which inherently require such resolution.

      Reviewer #2 Public Review

      We appreciate the constructive comments of Reviewer #2, which have strengthened both the presentation and interpretation of our results.

      We would like to thank Reviewer #2 for providing a highly accurate assessment of the strengths of our experiments. Regarding the weaknesses, we would like to respond as follows. First, Iwaki et al. (our co-corresponding author) have already succeeded in observing the stepping motion of myosin VI using the nanospring (NS) in their previous work. We are also currently preparing high spatiotemporal resolution microscopy experiments to observe the stepping motion of KIF1A in our system. Second, while it is true that the NS does not follow Hooke’s law, it is possible to design and construct NSs with an appropriate dynamic range by tuning the spring constant to match the forces exerted by protein molecules. Finally, we agree that our first observation of the stall plateau in KIF1A using the NS is a meaningful achievement. However, with respect to the suggestion that “increasing validity requires also studying kinesin-1,” we have a somewhat different perspective. The validity of the NS method has already been thoroughly examined in the previous work on myosin VI by Iwaki et al., where results were compared with those obtained using optical tweezers. Moreover, the focus of this manuscript is on KAND caused by KIF1A mutations. From this perspective, although we appreciate the suggestion, we consider it important to keep the present study focused on KIF1A and its implications for KAND.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The authors detect the attachments that occur during a processive run by KIF1A by monitoring the suppression of the angular fluctuations of the fluorescent signal and plot this, for example, in Figure 3a as the Length of the NS (which presumably is a readout of force) vs time. This interval includes the time when the KIF1A is actively moving along the MT and when it is stalled. It would be interesting to know the actual stall time of the motor in order to be able to calculate a detachment rate constant. For attachment periods such as the first example highlighted in pink in Figure 3a, the stall time is pretty much equal to the attachment time since the motor is moving so fast and the stall period is so long. However, for short attachment times such as the fifth pink interval shown in this same figure or the traces with the mutant KIF1As in Figure 4 this is not so. Can the authors institute a program to identify the periods where the motor has stretched the NS spring to the point where it stalls, and then calculate this time in order to do an exponential fit to the "dwell time distribution"?

      By introducing another criterion (see Methods, “Rate of relative increase in NS’s length”), the attachment duration was separated into the two time regions noted by the reviewer. After reanalyzing all the data, we evaluated only the stall duration this time. As a result, the estimated stall-force values became more reliable and accurate. The dwell time analysis of was performed and included in the supplementary material for WT KIF1A, for which sufficient data were available.

      (2) The histogram of stall events in Figure 3b is quite broad. Please discuss.

      The newly added distributions from individual molecules (Fig. 3b) show that the variety in the stall force distribution is not due to multiple molecules, but is primarily an intrinsic property of single KIF1A molecules reflecting the complex kinetics of KIF1A under load, including occasional backward steps and reattachments. In addition, because the nanospring is a non-linear spring, a disadvantage is that even small fluctuations in extension can result in a substantial deviation in the measured stall force. These points have been added to the Discussion section.

      (3) Figure 3c, it is clear that for attachment times greater than 5s the attachment duration is independent of the Lstall, but this is not so clear for the short attachment durations. Some of this may relate to the fact that you're measuring attachment durations and not stall or dwell times as described in my first comment. Do you feel this is due to less precision in measuring the "attachment duration" during the short attachments, or just simply that more data is needed here? I assume that you do not want to imply that there is a load-dependence of the attachment durations here? Perhaps an expanded view of the data set from 0-10 seconds would clarify. 

      As described in our response to comment (1), the stall durations were separated from the attachment durations. This improved the measurement accuracy and revealed that and are uncorrelated (Fig. 3c). We appreciate this constructive comment.

      Reviewer #2 (Recommendations for the authors):

      (1) Off-axis forces are described as 'upward', 'perpendicular', and 'horizontal'. Consider referring to off-axis force, and if necessary, defining the direction of the force(s) relative to the axis of the immobilised MT. If necessary, a cartoon of XYZ axes might be added to F1c? 

      An XZ axis was added to the schematic in Fig. 1c.

      (2) If I understand correctly, stall forces are calculated by averaging the entire region in which the angular fluctuation is reduced below a threshold. In cases like the 3rd and 7th events on the trace in F1a, this will reduce the average. Perhaps consider separately averaging the later time points in each stall event? Perhaps also consider correlating the angular fluctuation signals and the spring length signal? Some fluctuations during stall plateaus might indicate slip back and re-engage events? 

      Instead of separately averaging the later time points in each stall event, we separated the stall force duration from the overall attachment duration (Fig. 3). This allowed us to obtain more accurate stall force values. The relationship between the NS length and the angular fluctuation during KIF1A slip-back events differed among individual stall events, and no clear trend was observed. Two representative examples are shown in the Author response image 1.

      Author response image 1.

      (3) Please describe all relevant methods fully instead of referencing previous work. For example, nanospring preparation refers readers to reference 21 (which in turn references an earlier paper).

      We revised the Methods section to include the procedures described in the previous reference, and we added the sequence information of the DNA origami to the supplementary information.

      (4) Were any experiments tried at reduced ATP concentration?

      (5) Were any data obtained from WT KIF5B? For kinesin-1, stall plateau forces of >7 pN are obtained.

      This study focused on comparing the stall forces of wild-type and KAND-related mutant KIF1A molecules under physiological ATP conditions, as our main goal was to characterize the disease-relevant phenotypes. Experiments at reduced ATP concentrations and with WT KIF5B are indeed important future directions but are beyond the scope of the present study. These follow-up experiments are currently in progress.

      (6) In Figure 1b, consider showing the attachment to the mutant KIF5B, and reversing the orientation so it corresponds to Figure 1c.

      KIF1A and KIF5B share the same binding method, so to indicate that the schematic in Fig. 1b represents both, we replaced ‘KIF1A’ with ‘Kinesin’.

      (7) In Figure 3d, add force axis. In general, please re-check all force axes. In Supplement S3, the stall plateau labels appear well above their corresponding axis ticks. In Figure 4, several mutants appear to be stalling at well over 5 pN, yet Table 1 gives a much lower value. Presumably, this reflects averaging effects?

      We added the force axis to Fig. 3d. Besides, we corrected Fig. S3 and Fig. 4 because there were errors in the conversion from length to force. As the reviewer pointed out, the apparent discrepancy between the force values in Fig. 4 and Table 1 arises mainly from averaging effects.

    1. Author response:

      General Statements

      In this manuscript we characterize an exquisitely reproducible model of iPSC differentiation into neuroepithelial cells, use it to mechanistically study cell shape changes and planar cell polarity signaling activation during this transition, then apply it to identify patient-specific cell deficiencies in both forward and reverse genetic screens as a power tool for patient-stratification in personalized medicine. To our knowledge, we provide the first evidence of a human pathogenic mutation directly impairing apical constriction: an evolutionarily conserved behavior of epithelial cells which is the subject of intense research. 

      We are very pleased with the balanced and rigorous reviews generated through Review Commons, which we have already used to improve our manuscript. Reviewer 1 highlights that our study “is significant not only for verifying the cell behaviors necessary for neural tube closure in a human iPSC model, but also for establishing a robust assay for the functional testing of NTD-associated sequence variants.” Reviewer 2 agrees that “results are solid and convincing, the data are quantitative, and the manuscript is well written”, and that our “derivation of patient lines from amniotic fluid and execution of experiments before birth is a remarkable demonstration that points toward precision-medicine applications, while motivating rescue strategies and additional clean genetic models.” Reviewer 3 is “enthusiastic about this work and believe it represents a significant step forward in the effort to establish precision medicine approaches for diagnoses of the patient-specific causative cellular defects underlying human neural tube closure defects.” 

      Below, we have replied to each of the reviewers’ comments.

      Description of the planned revisions

      R2.2. Lines 156-166. The authors claim that changes in gene expression precede morphological changes. I am not convinced this is supported by their data. Fig. 1g (epithelial thickness) and Fig. 1k (PAX6 expression) seem to have similar dynamics. The authors can perform a cross-correlation between the two plots to see which Δt gives maximum correlation. If Δt < 0, then it would suggest that gene expression precedes morphology, as they claim. Fig. 1j shows that NANOG drops before the morphological changes, but loss of NANOG is not specific to neural differentiation and therefore should not be related to the observed morphological changes.

      We are happy to do this analysis fully in revision. Our initial analysis performing crosscorrelation between apical area and CDH2 protein in one line shows the highest crosscorrelation at Δt = -1, suggesting neuroepithelial CDH2 increases before apical area decreases. In contrast, the same analysis comparing apical area versus PAX6 shows Δt = 0, suggesting concurrence. This analysis will be expanded to include the other markers we quantified and the manuscript text amended accordingly. We are keen to undertake additional experiments to test whether these cells swap their key cadherins – CDH1 and CDH2 - before they begin to undergo morphological changes (see the response to Reviewer 3’s minor comment 1 immediately below).

      R3.1(Minor) There seems to be a critical window at day 5 of the differentiation protocol, both in terms of cell morphology and the marker panel presented in Figure 1i. Do the authors have any data spanning the hours from day 5 to 6? If not, I don't think they need to generate any, but do I think this is a very interesting window worthy of further discussion for a couple of reasons. First, several studies of mouse neural tube closure have shown that various aspects of cell remodeling are temporally separable. For example, between Grego-Bessa et al 2016 and Brooks et al 2020 we can infer that apicobasal elongation rapidly increases starting at E8.5, whereas apical surface area reduction and constriction are apparent somewhat earlier at E8.0. I think it would be interesting to see if this separability is conserved in humans. Second, is there a sense of how the temporal correlation between the pluripotent and early neural fate marker data presented here corroborate or contradict the emerging set of temporally resolved RNA seq data sets of mouse development at equivalent early neural stages?

      Cell shape analysis between days 5 and 6 has now been added (see the response to point 2.1 below). As the reviewer predicted, this is a transition point when apical area begins to decrease and apicobasal elongation begins to increase.

      We also thank the reviewer for this prompt to more closely compare our data to the previous mouse publications, which we have added to the discussion. The Grego-Bessa 2016 paper appears to show an increase in thickness between E7.75 and E8.5, but these are not statistically compared. Previous studies showed rapid apicobasal elongation during the period of neural fold elevation, when neuroepithelial cells apically constrict. This has now been added to the discussion: 

      Discussion: “In mice, neuroepithelial apicobasal thickness is spatially-patterned, with shorter cells at the midline under the influence of SHH signalling[14,77,78]. Apicobasal thickness of the cranial neural folds increases from ~25 µm at E7.75 to ~50 µm at E8.5[79]: closely paralleling the elongation between days 2 and 8 of differentiation in our protocol. The rate of thickening is non-uniform, with the greatest increase occurring during elevation of the neural folds[80], paralleled in our model by the rapid increase in thickness between days 4-6 as apical areas decrease. Elevation requires neuroepithelial apical constriction and these cells’ apical area also decreases between E7.75 and E8.5 in mice[79], but we and others have recently shown that this reduction is both region and sex-specific[14,81]. Specifically, apical constriction occurs in the lateral (future dorsal) neuroepithelium: this corresponds with the identity of the cells generated by the dual SMAD inhibition model we use[56]. More recently, Brooks et al[82] showed that the rapid reduction in apical area from E8-E8.5 is associated with cadherin switching from CDH1 (E-cadherin) to CDH2 (N-cadherin). This is also directly paralleled in our human system, which shows low-level co-expression of CDH1 and CDH2 at day 4 of differentiation, immediately before apical area shrinks and apicobasal thickness increases.”

      Prompted by the in vivo data in Brooks et al (2025)[82], we are keen to further explore the timing of CDH1/CDH2 switching versus apical constriction with new experimental data in revisions.

      R3.2(Minor) 2) Can the authors elaborate a bit more on what is known regarding apicobasal thickening and pseudo-stratification and how their work fits into the current understanding in the discussion? This is a very interesting and less well studied mechanism critical to closure, which their model is well suited to directly address. I am thinking mainly of the Grego-Bessa at al., 2016 work on PTEN, though interestingly the work of Ohmura et al., 2012 on the NUAK kinases also shows reduced tissue thickening (and apical constriction) and I am sure I have missed others. Given that the authors identify MED24 as a likely candidate for the lack of apicobasal thickening in one of their patient derived lines, is there any evidence that it interacts with any of the known players?

      We have now added further discussion on the mechanisms by which the neuroepithelium undergoes apicobasal elongation. Nuclear compaction is likely to be necessary to allow pseudostratification and apicobasal elongation. The reviewer’s comment has led us to realise that diminished chromatin compaction is a potential outcome of MED24 down-regulation in our GOSB2 patient-derived line. Figure 4D suggests the nuclei of our MED24 deficient patientderived line are less compacted than control equivalents and we propose to quantify nuclear volume in more detail to explore this possibility.

      Additionally, we have already expanded our discussion as suggested by the reviewer:

      Discussion: “Mechanistic separability of apical constriction and apicobasal elongation is consistent with biomechanical modelling of Xenopus neural tube closure showing that both are independently required for tissue bending[61]. Nonetheless, neuroepithelial apical constriction and apicobasal elongation are co-regulated in mouse models: for example, deletion of Nuak1/2[83], Cfl1[84], and Pten[79] all produce shorter neuroepithelium with larger apical areas. Neuroepithelial cells of the GOSB2 line described here, which has partial loss of MED24, similarly produces a thinner neuroepithelium with larger apical areas. Although apical areas were not analysed in mouse models of Med24 deletion, these embryos also have shorter and non-pseudostratified neuroepithelium.

      Our GOSB2 line – which retains readily detectable MED24 protein – is clearly less severe than the mouse global knockout, and the clinical features of the patient from which this line was derived are milder than the phenotype of Med24 knockout embryos[68]. Mouse embryos lacking one of Med24’s interaction partners in the mediator complex, Med1, also have thinner neuroepithelium and diminished neuronal differentiation but successfully close their neural tube[85]. As general regulators of polymerase activity, MED proteins have the potential to alter the timing or level of expression of many other genes, including those already known to influence pseudostratification or apicobasal elongation. MED depletion also causes redistribution of cohesion complexes[86] which may impact chromatin compaction, reducing nuclear volume during differentiation.”

      R3.3(Minor) 3) Is there any indication that Vangl2 is weakly or locally planar polarized in this system? Figure 2F seems to suggest not, but Supplementary Figure 5 does show at least more supracellular cable like structures that may have some polarity. I ask because polarization seems to be one of the properties that differs along the anteroposterior axis of the neural plate, and I wonder if this offers some insight into the position along the axis that this system most closely models?

      VANGL2 does not appear to be planar polarised in this system. This is similar to the mouse spinal neuroepithelium, in which apical VANGL2 is homogenous but F-actin is planar polarised (Galea et al Disease Models and Mechanisms 2018). We do observe local supracellular cablelike enrichments of F-actin in the apical surface of iPSC-derived neuroepithelial cells:

      Author response image 1.

      Preliminary identification of apical supracellular cables suggestive of local polarity. Top: F-actin staining shown in inverted grey LUT highlighting enrichment along directionally-polarised cell borders (blue arrows). Bottom: Staining orientation (blue ~ X axis, red ~ Y axis) based on OrientationJ analysis illustrating localised organisation of F-actin enrichment.

      We propose to compare the length of F-actin cables and coherency of their orientation at the start and end of neuroepithelial differentiation, and in wild-type versus VANGL2mutant epithelia.

      Description of the revisions that have already been incorporated in the transferred manuscript

      Reviewer #1:

      Major points

      (1) It is mentioned throughout the manuscript that 3 plates were evaluated per line. I believe these are independently differentiated plates. This detail is critical concerning rigor and reproducibility. This should be clearly stated in the Methods section and in the first description of the experimental system in the Results section for Figure 1.

      These experimental details have now been clarified. Unless otherwise stated, all findings were confirmed in three independently differentiated plates from the same line or at least one differentiation from each of three lines. 

      Methods: Unless otherwise stated, for each iPSC line three independently differentiated plates were generated and analysed, with each plate representing a separate differentiation experiment performed on different days.

      (2) For the patient-specific lines - how many lines were derived per patient?

      This has now been clarified in the methods. Microfluidic reprogramming of a small number of amniocytes produces one line per patient representing a pool of clones. Subcloning from individual cells would not be possible within the timeframe of a pregnancy. 

      Methods: For patient-specific iPSC lines, one independent iPSC line was obtained per patient following microfluidic mmRNA reprogramming.

      (3) Was the Vangl2 variant introduced by prime editing? Base editing? The details of the methods are sparse.

      We have now expanded these details:

      Methods: “VANGL2 knock-in lines were generated using CRSIPR-Cas9 homology directed repair editing by Synthego (SO-9291367-1). The guide sequence was AUGAGCGAAGGGUGCGCAAG and the donor sequence was CAATGAGTACTACTATGAGGAGGCTGAGCATGAGCGAAGGGTGTGCAAGAGGAGGGCCAGGTGGGTCCCTGGGGGAGAAGAGGAGAG.

      Sequence modification was confirmed by Sanger sequencing before delivery of the modified clones, and Sanger sequencing was repeated after expansion of the lines (Supplementary Figure 5) as well as SNP arrays (Illumina iScan, not shown) confirming genomic stability.”

      Author response image 2.

      Snapshot of Illumina iScan SNP array showing absence of chromosomal duplications or deletions in the CRISPR-modified VANGL2-knockin lines or their congenic control.

      (4) Suggested text changes.

      Some additional suggestions for improvement.

      The abstract could be more clearly written to effectively convey the study's importance. Here are some suggestions

      Line 26: Insert "apicobasal" before "elongation" - the way it is written, I initially interpreted it as anterior-posterior elongation.

      Line 29: Please specify that the lines refer to 3 different established parent iPSC lines with distinct origins and established using different reprogramming methods, plus 2 control patient-derived lines. - The reproducibility of the cell behaviors is impressive, but this is not captured in the abstract.

      Line 32: add that this mutation was introduced by CRISPR-Cas9 base/prime editing.

      The last sentence of the abstract states that the study only links apical constriction to human NTDs, but also reveals that neural differentiation and apical-basal elongation were found. The introduction could also use some editing.

      Line 71: insert "that pulls actin filaments together" after "power strokes" Line 73: "apically localized," do you mean "mediolaterally" or "radially"?

      Line 75: Can you specify that PCP components promote "mediolaterally orientated" apical constriction Lines 127: Specify that NE functions include apical basal elongation and neurodifferentiation are disrupted in patient-derived models

      All have now been corrected.

      Reviewer #2:

      Major comments:

      (1) Figure 1. The authors use F-actin to segment cell areas. Perhaps this could be done more accurately with ZO-1, as F-actin cables can cross the surface of a single cell. In any case, the authors need to show a measure of segmentation precision: segmented image vs. raw image plus a nuclear marker (DAPI, H2B-GFP), so we can check that the number of segmented cells matches the number of nuclei.

      We used ZO-1 to quantify apical areas of the VANGL2-konckin lines in Figure 3. Segmentation of neuroepithelial apical areas based on F-actin staining is commonplace in the field (e.g. in the Brooks et al 2022 paper cited by another reviewer), and is generally robust because the cell junctions are much brighter than any apical fibres not associated with the apical cortex. However, we accept that at earlier stages of differentiation there may be more apical fibres when cells are cuboidal. We have therefore repeated our analysis of apical area using ZO-1 staining as suggested, analysing a more temporally-detailed time course in one iPSC line. This new analysis confirms our finding of lack of apical area change between days 2-4 of differentiation, then progressive reduction of apical area between days 4-8, further validating our system. Including nuclear images is not helpful because of the high nuclear index of pseudostratified epithelia (e.g. see Supplementary Figure 7) which means that nuclei overlap along the apicobasal axis. Individual nuclei cannot be related to their apical surface in projected images.

      (3) Figure 2d. The laser ablation experiment in the presence of ROCK inhibitor is clear, as I can easily see the cell outlines before and after the experiment. In the absence of ROCK inhibitor, the cell edges are blurry, and I am not convinced the outline that the authors drew is really the cell boundary. Perhaps the authors can try to ablate a larger cell patch so that the change in area is more defined.

      The outlines on these images are not intended to show cell boundaries, but rather link landmarks visible at both timepoints to calculate cluster (not cell) change in area. This is as previously shown in Galea et al Nat Commun 2021 and Butler et al J Cell Sci 2019. We have now amended the visualisation of retraction to make representation of differences between conditions more intuitive. 

      (4) Figure 2d. Do the cells become thicker after recoil?

      This is unlikely because the ablated surface remains in the focal plane. Unfortunately, we are unable to image perpendicularly to the direction of ablation to test whether their apical surface moves in Z even by a very small amount. This has now been clarified in the results:

      Results: “The ablated surface remained within the focal plane after ablation, indicating minimal movement along the apical-basal axis.”

      (6) Lines 403-415. The authors report poor neural induction and neuronal differentiation in GOSB2. As far as I understand, this phenotype does not represent the in vivo situation. Thus, it is not clear to what extent the in vitro 2D model describes the human patient.

      The GOSB2 iPSC line we describe does represent the in vivo situation in Med24 knockout mouse embryos, but is clearly less severe because we are still able to detect MED24 protein expressed in this line. We do not have detailed clinical data of the patient from which this line was obtained to determine whether their neurological development is normal. However, it is well established that some individuals who have spina bifida also have abnormalities in supratentorial brain development. It is therefore likely that abnormalities in neuron differentiation/maturation are concomitant with spina bifida. Our findings in the GOSB2 line complement earlier studies which also identified deficiencies in the ability of patient-derived lines to form neurons, but were unable to functionally assess neuroepithelial cell behaviours we studied. This has now been clarified in the discussion:

      Discussion: “Neuroepithelial cells of the GOSB2 line described here, which has partial loss of MED24, similarly produces a thinner neuroepithelium with larger apical areas. Although apical areas were not analysed in mouse models of Med24 deletion, these embryos also have shorter and non-pseudostratified neuroepithelium. 

      Our GOSB2 line – which retains readily detectable MED24 protein – is clearly less severe than the mouse global knockout, and the clinical features of the patient from which this line was derived are milder than the phenotype of Med24 knockout embryos[68].

      Mouse embryos lacking one of Med24’s interaction partners in the mediator complex, Med1, also have thinner neuroepithelium and diminished neuronal differentiation but successfully close their neural tube[85].”

      (7) The experimental feat to derive cell lines from amniotic fluid and to perform experiments before birth is, in my view, heroic. However, I do not feel I learned much from the in vitro assays. There are many genetic changes that may cause the in vivo phenotype in the patient. The authors focus on MED24, but there is not enough convincing evidence that this is the key gene. I would like to suggest overexpression of MED24 as a rescue experiment, but I am not sure this is a single-gene phenotype. In addition, the fact that one patient line does not differentiate properly leads me to think that the patient lines do not strengthen the manuscript, and that perhaps additional clean mutations might contribute more.

      We appreciate the reviewer’s praise of our personalised medicine approach and fully agree that neural tube defects are rarely monogenic. The patient lines we studied were not intended to provide mechanistic insight, but rather to demonstrate the future applicability of our approach to patient care. Our vision is that every patient referred for fetal surgery of spina bifida will have amniocytes (collected as part of routine cystocentesis required before surgery) reprogrammed and differentiated into neuroepithelial cells, then neural progenitors, to help stratify their postnatal care. One could also picture these cells becoming an autologous source for future cellbased therapies if they pass our reproducible analysis pipeline as functional quality control. This has now been clarified in the discussion:

      Discussion: “The multi-genic nature of neural tube defect susceptibility, compounded by uncontrolled environmental risk factors (including maternal age and parity[102]), mean that patient-derived iPSC models are unlikely to provide mechanistic insight. They do provide personalised disease models which we anticipate will enable functional validation of genetic diagnoses for patients and their parents’ recurrence risk in future pregnancies, and may eventually stratify patients’ postnatal care. We also envision this model will enable quality control of patient-derived cells intended for future autologous cell replacement therapies, as is being developed in post-natal spinal cord injury[103]. Thus, the highly reproducible modelling platform we evaluate – which is robust to differences in iPSC reprogramming method, sex and ethnicity – represents a valuable tool for future mechanistic insights and personalised disease modelling applications.”

      Significance:

      In addition, the model was unsuccessful in one of the two patient-derived lines, which limits generalizability and weakens claims of patient-specific predictive value.

      We disagree with the reviewer that “the model was unsuccessful in one of the two patientderived lines”. The GOSB1 line demonstrated deficiency of neuron differentiation independently of neuroepithelial biomechanical function, whereas the GOSB2 line showed earlier failure of neuroepithelial function. We also do not, at this stage, make patient-specific predictive claims: this will require longer-term matching of cell model findings with patient phenotypes over the next 5-10 years.  

      Reviewer #3:

      Major comments

      (1) One of my few concerns with this work is that the relative constriction of the apical surface with respect to the basal surface is not directly quantified for any of the experiments. This worry is slightly compounded by the 3D reconstructions Figure 1h, and the observation that overall cell volume is reduced and cell height increased simultaneously to area loss. Additionally, the net impact of apical constriction in tissues in vivo is to create local or global curvature change, but all the images in the paper suggest that the differentiated neural tissues are an uncurved monolayer even missing local buckles. I understand that these cells are grown on flat adherent surfaces limiting global curvature change, but is there evidence of localized buckling in the monolayer? While I believe-along with the authors-that their phenotypes are likely failures in apical constriction, I think they should work to strengthen this conclusion. I think the easiest way (and hopefully using data they already have) would be to directly compare apical area to basal area on a cell wise basis for some number of cells. Given the heterogeneity of cells, perhaps 30-50 cells per condition/line/mutant would be good? I am open to other approaches; this just seems like it may not require additional experiments.

      As the reviewer observes, our cultures cannot bend because they are adhered on a rigid surface. The apical and basal lengths of the cultures will therefore necessarily be roughly equal in length. Some inwards bending of the epithelium is expected at the edges of the dish, but these cannot be imaged. The live imaging we show in Figure 2 illustrates that, just as happens in vivo, apical constriction is asynchronous. This means not all cells will have ‘bottle’ shapes in the same culture. We now illustrate the evolution of these shapes in more detail in Supplementary Figure 1.

      Additionally, the reviewer’s comment motivated us to investigate local buckles in the apical surface of our cultures when their apical surfaces are dilated by ROCK inhibition. We hypothesised that the very straight apical surface in normal cultures is achieved by a balance of apical cell size and tension with pressure differences at the cell-liquid interface. Consistent with our expectation, the apical surface of ROCK-inhibited cultures becomes wrinkled (Supplementary figure 4). The VANGL2-KI lines do not develop this tortuous apical surface (as shown in Figure 3), which is to be expected given their modification is present throughout differentiation unlike the acute dilation caused by ROCK inhibition.

      This new data complements our visualisation of apical constriction in live imaging, apical accumulation of phospho-myosin, and quantification of ROCK-dependent apical tension as independent lines of evidence that our cultures undergo apical constriction. 

      (2) Another slight experimental concern I have regards the difference in laser ablation experiments detailed in Figure 3h-i from those of Figure 2d-e. It seems like WT recoil values in 3h-I are more variable and of a lower average than the earlier experiments and given that it appears significance is reached mainly by impact of the lower values, can the authors explain if this variability is expected to be due to heterogeneity in the tissue, i.e. some areas have higher local tension? If so, would that correspond with more local apical constriction?

      There is no significant difference in recoil between the control lines in Figures 2 and 3, albeit the data in Figure 3 is more variable (necessitating more replicates: none were excluded). We also showed laser ablation recoil data in Supplementary Figure 10, in which we did identify a graphing error (now corrected, also no significant difference in recoil from the other control groups as shown in Author response image 3).

      Author response image 3.

      Recoil following laser ablation is not significantly different between different experiments. X axis labels indicate the figure panel each set of ablation data is shown in. Points represent an independent differentiation dish.

      (4)(Minor) I think some of the commentary on the strengths and limitations of the model found in the Results section should be collated and moved to the discussion in a single paragraph. For example, this could also briefly touch on/compare to some of the other models utilizing hiPSCs (These are mentioned briefly in the intro, but this comparison could be elaborated on a bit after seeing all the great data in this work).

      These changes have now been made:

      Discussion: “Some of these limitations, potentially including inclusion of environmental risk factors, can be addressed by using alternative iPSC-derived models[93,94]. For example, if patients have suspected causative mutations in genes specific to the surface (non-neural) ectoderm, such as GRHL2/3, 3D models described by Karzbrun et al[49] or Huang et al[95] may be informative. Characterisation of surface ectoderm behaviours in those models is currently lacking. These models are particularly useful for high-throughput screens of induced mutations[95], but their reproducibility between cell lines, necessary to compare patient samples to non-congenic controls, remains to be validated. Spinal cell identities can be generated in human spinal cord organoids, although these have highly variable morphologies[96,97]. As such, each iPSC model presents limitations and opportunities, to which this study contributes a reductionist and highly reproducible system in which to quantitatively compare multiple neuroepithelial functions.”

      (5) While the authors are generally good about labeling figures by the day post smad inhibition, in some figures it is not clear either from the images or the legend text. I believe this includes supplemental figures 2,5,6,8, and 10 (apologies if I simply missed it in one or more of them)

      These have now been added.

      (6) The legend for Figure 2 refers to a panel that is not present and the remaining panel descriptions are off by a letter. I'm guessing this is a versioning error as the text itself seems largely correct, but it may be good to check for any other similar errors that snuck in

      This has now been corrected.

      (7) The cell outlines in Figure 3d are a bit hard to see both in print and on the screen, perhaps increase the displayed intensity?

      This has now been corrected.

      Description of analyses that authors prefer not to carry out

      R2.5. Figure 3. The authors mention their previous study in which they show that Vangl2 is not cell-autonomously required for neural closure. It will be interesting to study whether this also the case in the present human model by using mosaic cultures.

      The reviewer is correct that this is one of the exciting potential future applications of our model, which will first require us to generate stable fluorescently-tagged lines (to identify those cells which lack VANGL2). We will also need to extensively analyze controls to validate that mixing fluo-tagged and untagged lines does not alter the homogeneity of differentiation, or apical constriction, independently of VANGL2 deletion. As such, the reviewer is suggesting an altogether new project which carries considerable risk and will require us to secure dedicated funding to undertake.

      R3.8(Minor) The authors show a fascinating piece of data in Supplementary Figure 1, demonstrating that nuclear volume is halved by day 8. Do they have any indication if the DNA content remains constant (e.g., integrated DAPI density)? I suppose it must, and this is a minor point in the grand scheme, but this represents a significant nuclear remodeling and may impact the overall DNA accessibility.

      We agree with the reviewer that the reduction in nuclear volume is important data both because it informs understanding of the reduction in total cell volume, and because it suggests active chromatin compaction during differentiation. Unfortunately, the thicker epithelium and superimposition of nuclei in the differentiated condition means the laser light path is substantially different, making direct comparisons of intensity uninterpretable. Additionally, the apical-most nuclei will mostly be in G2/M phase due to interkinetic nuclear migration. As such, the comparison of DAPI integrated density between epithelial morphologies would not be informative (Author response image 4).

      Author response image 4.

      Lateral views of DAPI-stained nuclei on Days 2 and 8 of differentiation. Note the rapid loss of staining intensity below the apical pseudo-row of nuclei on Day 8. This intensity change is likely due to the apical nuclei being in G2/M phase and therefore having more DNA, and rapid loss of 405nm wavelength signal at depth.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This work addresses a key question in cell signalling: how does the membrane composition affect the behaviour of a membrane signalling protein? Understanding this is important, not just to understand basic biological function but because membrane composition is highly altered in diseases such as cancer and neurodegenerative disease. Although parts of this question have been addressed on fragments of the target membrane protein, EGFR, used here, Srinivasan et al. harness a unique tool, membrane nanodisks, which allow them to probe full-length EGFR in vitro in great detail with cutting-edge fluorescent tools. They find interesting impacts on EGFR conformation in differently charged and fluid membranes, explaining previously identified signalling phenotypes.

      Strengths:

      The nanodisk system enables full-length EGFR to be studied in vitro and in a membrane with varying lipid and cholesterol concentrations. The authors combine this with single-molecule FRET utilising multiple pairs of fluorophores at different places on the protein to probe different conformational changes in response to EGF binding under different anionic lipid and cholesterol concentrations. They further support their findings using molecular dynamics simulations, which help uncover the full atomistic detail of the conformations they observe.

      Weaknesses:

      Much of the interpretation of the results comes down to a bimodal model of an 'open' and 'closed' state between the intracellular tail of the protein and the membrane. Some of the data looks like a bimodal model is appropriate, but its use is not sufficiently justified (statistically or otherwise) in this work in its current form. The experiments with varying cholesterol in particular appear to suggest an alternate model with longer fluorescent lifetimes. More justification of these interpretations of the central experiment of this work would strengthen the paper.

      We thank the reviewer for highlighting the strengths of the study, including the use of nanodiscs, single-molecule FRET, and MD simulations to probe full-length EGFR in controlled membrane environments.

      We agree that statistical justification is important for interpreting the distributions. To address this, we performed global fits of the data with both two- and three-Gaussian models and evaluated them using the Bayesian Information Criterion (BIC), which balances the model fit with a penalty for additional parameters. The three-Gaussian model gave a substantially lower BIC, indicating statistical preference for the more complex model. However, we also assessed the separability of the Gaussian components using Ashman’s D, which quantifies whether peaks are distinct. This analysis showed that two Gaussians (µ = 2.64 and 3.43 ns) are not separable, implying they represent one broad distribution rather than two states.

      Author response table 1.

      Both the two- and three-Gaussian models include a low-value component (µ = ~1.3 ns), but the apparent improvement of the three-Gaussian model arises only from splitting the central population into two overlapping Gaussians. Thus, while the BIC favors the three-Gaussian model statistically, Ashman’s D demonstrates that the central peak should not be interpreted as bimodal. Therefore, when all the distributions are fit globally, the data are best explained as two Gaussians, one centered at ~1.3 ns and the other at ~2.7 ns, with cholesterol-dependent shifts reflecting changes in the distribution of this population rather than the emergence of a separate state. Finally, we acknowledge that additional conformations may exist, but based on this analysis a bimodal model describes the populations captured in our data and so we limit ourselves to this simplest framework.

      We have clarified this in the revised manuscript by adding a section in the Methods (page 26) titled Model Selection and Statistical Analysis, which describes the results of the global two- versus three-Gaussian fits evaluated using BIC and Ashman’s D. Additional details of these analyses are also provided in response to Reviewer #1, Question 8 (Recommendations for the authors).

      Reviewer #2 (Public review):

      Summary:

      Nanodiscs and synthesized EGFR are co-assembled directly in cell-free reactions. Nanodiscs containing membranes with different lipid compositions are obtained by providing liposomes with corresponding lipid mixtures in the reaction. The authors focus on the effects of lipid charge and fluidity on EGFR activity.

      Strengths:

      The authors implement a variety of complementary techniques to analyze data and to verify results. They further provide a new pipeline to study lipid effects on membrane protein function.

      We thank the reviewer for noting the strengths of our approach, particularly the use of complementary techniques and the development of a new pipeline to study lipid effects on membrane protein function.

      Weaknesses:

      Due to the relative novelty of the approach, a number of concerns remain.

      (1) I am a little skeptical about the good correlation of the nanodisc compositions with the liposome compositions. I would rather have expected a kind of clustering of individual lipid types in the liposome membrane, in particular of cholesterol. This should then result in an uneven distribution upon nanodisc assembly, i.e., in a notable variation of lipid composition in the individual nanodiscs. Could this be ruled out by the implemented assays, or can just the overall lipid composition of the complete nanodisc fraction be analyzed?

      We monitored insertion of anionic lipids into nanodiscs by performing zeta potential measurements, which report on surface charge, and cholesterol insertion by Laurdan fluorescence, which reports on membrane order. Both assays provide information at the ensemble level, not single-nanodisc resolution. We clarified this in the Methods section (see below).

      Cholesterol clustering is well documented in ternary systems with saturated lipids and sphingolipids [Veatch, Biophys J., 2003; Risselada, PNAS, 2008]. However, in unsaturated POPC-cholesterol mixtures such as those used here, cholesterol primarily alters bilayer order and large-scale segregation is not typically observed.  The addition of POPS to the POPC-cholesterol mixture perturbs cholesterol-induced ordering, lowering the likelihood of cholesterol-rich domains [Kumar, J. Mol. Graphics Modell., 2021].

      Lipid heterogeneity between nanodiscs would be expected to give rise to heterogeneity in hydrodynamic properties, including potentially broadening the dynamic light scattering (DLS) distributions. However, the full width at half maximum (FWHM) values from the DLS measurements (see Author response table 2) do not indicate a broadening with cholesterol. Statistical testing (Mann-Whitney U test for non-normal data) showed no significant difference between samples with and without cholesterol (p = 0.486; n = 4 per group). While the sample size is small making firm conclusions challenging, these results suggest that large-scale heterogeneity is unlikely.

      Author response table 2.

      In the case of POPS lipids, clustering of POPS in EGFR embedded nanodiscs is a recognized property of receptor-lipid interactions. Molecular dynamics simulations have shown that POPS, although constituting only 30% of the inner leaflet, accounts for ~50% of the lipids directly contacting EGFR [Arkhipov, Cell, 2013], underscoring that anionic lipids are preferentially recruited to the receptor’s immediate environment.

      For nanodiscs containing cholesterol and anionic lipids, our smFRET experiments were designed to isolate the effect of EGF binding. The nanodisc population is the same in the ± EGF conditions as EGF was introduced just prior to performing sm-FRET experiments, and not during nanodisc assembly. Thus, for a given lipid composition, any observed differences between ligand-free and ligand-bound states reflect conformational changes of EGFR.

      Methods, page 23, “Zeta potential measurements to quantify surface charge of nanodiscs: Data analysis was processed using the instrumental Malvern’s DTS software to obtain the mean zeta-potential value. This ensemble measurement reports the average surface charge of the nanodisc population, verifying incorporation of anionic POPS lipids.”

      Methods, page 23, “Fluorescence measurements with Laurdan to confirm cholesterol insertion into nanodiscs: The excitation spectrum was recorded by collecting the emission at 440 nm and emission spectra was recorded by exciting the sample at 385 nm. Laurdan fluorescence provides an ensemble readout of membrane order and confirms cholesterol incorporation into the nanodisc population. While laurdan does not resolve the composition of individual nanodiscs, prior work has shown that POPC–cholesterol mixtures are miscible without forming cholesterol-rich domains[91,92], thus the observed ordering changes likely reflect the intended input cholesterol content at the ensemble level.”

      (91) Veatch, S. L. & Keller, S. L. Separation of liquid phases in giant vesicles of ternary mixtures of phospholipids and cholesterol. Biophysical journal, 85(5), 3074-3083 (2003).

      (92) Risselada, H. J. & Marrink, S. J. The molecular face of lipid rafts in model membranes. Proceedings of the National Academy of Sciences 105(45), 17367–17372 (2008).

      (2) Both templates have been added simultaneously, with a 100-fold excess of the EGFR template. Was this the result of optimization? How is the kinetics of protein production? As EGFR is in far excess, a significant precipitation, at least in the early period of the reaction, due to limiting nanodiscs, should be expected. How is the oligomeric form of the inserted EGFR? Have multiple insertions into one nanodisc been observed?

      We thank the reviewer for these insightful questions. Yes, the EGFR:ApoA1∆49 template ratio of 100:1 was empirically determined through optimization experiments now shown in the revised Supplementary Fig. 3. Cell-free reactions were performed across a range of EGFR:ApoA1∆49 template ratios (1:2 to 1:200) and sampled at different time points (2-19 hours). As shown in the gels, EGFR expression increased with higher template ratios and longer reaction times up to ~9 hours, while ApoA1 expression became clearly detectable only after 6 hours. Based on these results, we selected an EGFR:ApoA1∆49 ratio of 100:1 and 8-hour reaction time as the optimal condition, which yielded sufficient full-length EGFR incorporated into nanodiscs for ensemble and single-molecule experiments.

      In cell-free systems, protein yield does not scale directly with DNA template concentration, as translation efficiency is limited by factors such as ribosome availability and co-translational membrane insertion [Hunt, Chem. Rev., 2024; Blackholly, Front. Mol. Biosci., 2022]. Consistent with this, we observed that ApoA1∆49 is produced at higher levels than EGFR despite the lower DNA input (Supplementary Fig. 2b). Providing an excess EGFR template prevents the reaction from becoming limited by scaffold availability and helps compensate for the fact that, as a large multi-domain receptor, EGFR expression can yield truncated as well as full-length products. This strategy ensures that sufficient full-length receptors are available for nanodisc incorporation. We will clarify this in the Methods section (see below).

      We observed little to no visible precipitation under the reported cell-free conditions, likely due to the following reasons: (i) EGFR and ApoA1∆49 are co-expressed in the cell-free reaction, and ApoA1∆49 assembles into nanodiscs concurrently with receptor translation, providing an immediate membrane sink (ii) ApoA1∆49 is expressed at high levels, maintaining disc concentrations that keep the reaction in a soluble regime.

      The sample contains donor-labeled EGFR (snap surface 594) together with acceptor-labeled lipids (cy5-labeled PE doped in the nanodisc). We assess the oligomerization state of EGFR in nanodiscs using single-molecule photobleaching of the donor channel. Snap surface 594 is a benzyl guanine derivative of Atto 594 that reacts with the SNAP tag with near-stoichiometry efficiency [Sun, Chembiochem, 2011]. Most molecules (~75%) exhibited a single photobleaching step, consistent with incorporation of a single EGFR per nanodisc [Srinivasan, Nat. Commun., 2022]. A minority of traces (~15%) showed two photobleaching steps and about ~10% of traces showed three or more photobleaching steps, consistent with occasional multiple insertions. For all smFRET analysis, we restricted the dataset to single-step photobleaching traces, ensuring measurements were performed on monomeric EGFR.

      Methods, page 20, “Production of labeled, full-length EGFR nanodiscs: Briefly, the E.Coli slyD lysate, in vitro protein synthesis E.Coli reaction buffer, amino acids (-Methionine), Methionine, T7 Enzyme, protease inhibitor cocktail (Thermofisher Scientific), RNAse inhibitor (Roche) and DNA plasmids (20ug of EGFR and 0.2ug of ApoA1∆49) were mixed with different lipid mixtures. The DNA template ratio of EGFR:ApoA1∆49 = 100:1 was empirically chosen by testing different ratios on SDS-PAGE gels and selecting the condition that maximized full-length EGFR expression in DMPC lipids (Supplementary Fig. 3).”

      (3) The IMAC purification does not discriminate between EGFR-filled and empty nanodiscs. Does the TEM study give any information about the composition of the particles (empty, EGFR monomers, or EGFR oligomers)? Normalizing the measured fluorescence, i.e., the total amount of solubilized receptor, with the total protein concentration of the samples could give some data on the stoichiometry of EGFR and nanodiscs.

      Negative-stain TEM was performed to confirm nanodisc formation and morphology, but this method does not resolve whether a given disc contains EGFR. To directly assess receptor stoichiometry, we instead relied on single-molecule photobleaching of snap surface 594-labeled EGFR (see response to Point 2). These experiments showed that the majority of nanodiscs contain a single receptor, with a minority containing two receptors. For all smFRET analyses, we restricted data to single-step photobleaching traces, ensuring measurements were performed on monomeric EGFR.

      We did not normalize EGFR fluorescence to total protein concentration because the bulk protein fraction after IMAC purification includes both receptor-loaded and empty nanodiscs. The latter contribute to ApoA1∆49 mass but do not contain receptors and including them would underestimate receptor occupancy. Importantly, the presence of empty nanodiscs does not affect our measurements as photobleaching and single-molecule FRET analyses selectively report only on receptor-containing nanodiscs. This clarification has been added to the Methods.

      Methods, page 26, “Fluorescence Spectroscopy: Traces with a single photobleaching step for the donor and acceptor were considered for further analysis. Regions of constant intensity in the traces were identified by a change-point algorithm95. Donor traces were assigned as FRET levels until acceptor photobleaching. The presence of empty nanodiscs does not influence these measurements, as photobleaching and single-molecule FRET analyses selectively report on receptor-containing nanodiscs.”

      (4) The authors generally assume a 100% functional folding of EGFR in all analyzed environments. While this could be the case, with some other membrane proteins, it was shown that only a fraction of the nanodisc solubilized particles are in functional conformation. Furthermore, the percentage of solubilized and folded membrane protein may change with the membrane composition of the supplied nanodiscs, while non-charged lipids mostly gave rather poor sample quality. The authors normalize the ATP binding to the total amount of detectable EGFR, and variations are interpreted as suppression of activity. Would the presence of unfolded EGFR fractions in some samples with no access to ATP binding be an alternative interpretation?

      We agree that not all nanodisc-embedded EGFR molecules may be fully functional and that the fraction of folded protein could vary with lipid composition. In our ATP-binding assay, EGFR detection relies on the C-terminal SNAP-tag fused to an intrinsically disordered region. Successful labeling requires that this segment be translated, accessible, and folded sufficiently to accommodate the SNAP reaction, which imposes an additional requirement compared to the rigid, structured kinase domain where ATP binds. Misfolded or truncated EGFR molecules would therefore likely fail to label at the C-terminus. These factors strongly imply that our assay predominantly reports on receptor molecules that are intact and well folded.

      Additionally, our molecular dynamics simulations at 0% and 30% POPS support the experimental ATP-binding measurements (Fig. 2c, d). This consistency between both the experimental and simulated evidence, including at 0% POPS where reduced receptor folding might be expected, suggests that the observed lipid-dependent changes are more likely due to modulation of the functional receptor rather than receptor misfolding. We have clarified these points by adding the following

      Results, page 7, “Role of anionic lipids in EGFR kinase activity: In the presence of EGF, increasing the anionic lipid content decreased the number of contacts from 71.8 ± 1.8 to 67.8 ± 2.4, indicating increased accessibility, again in line with the experimental findings. Because detection of EGFR relies on labeling at the C-terminus and ATP binding requires an intact kinase domain, the ATPbinding assay is for receptors that are properly folded and competent for nucleotide binding. The consistency between experimental results and MD simulations suggests that the observed lipiddependent changes are more likely due to modulation of functional EGFR than to artifacts from misfolding.”

      Reviewer #1 (Recommendations for the authors):

      The experimental program presented here is excellent, and the results are highly interesting. My enthusiasm is dampened by the presentation in places which is confusing, especially Figure 3, which contains so many of the results. I also have some reservations about the bimodal interpretation of the lifetime data in Figure 3.

      We thank the reviewer for their positive assessment of our experimental approach and results. In the revised version, we have improved figure organization and readability by adding explicit labels for lipid composition and EGF presence/absence in all lifetime distributions, moving key supplementary tables into main text, and reorganizing the supplementary figures as Extended Data Figures following eLife’s format. Figures and tables now appear in the order in which they are referenced in the text to further improve readability.

      Regarding the bimodal interpretation of the lifetime distribution, we have performed global fits of the data with both two- and three-Gaussian models and evaluated them using the Bayesian Information Criterion (BIC) and Ashman’s D analysis, which supported the bimodal interpretation. Details of this analysis are provided in our response to comment (8) below and included in the manuscript.

      Specific comments below:

      (1) Abstract -"Identifying and investigating this contribution have been challenging owing to the complex composition of the plasma membrane" should be "has".

      We have corrected this error in the revised manuscript.

      (2) Results - p4 - some explanation of what POPC/POPS are would be helpful.

      We have added the text below discussing POPC and POPS.

      Results, page 4, “POPC is a zwitterionic phospholipid forming neutral membranes, whereas POPS carries a net negative charge and provides anionic character to the bilayer[56]. Both PC and PS lipids are common constituents of mammalian plasma membranes, with PC enriched in the outer leaflet and PS in the inner leaflet[22].”

      (22) Lorent, J. H., Levental, K. R., Ganesan, L., Rivera-Longsworth, G., Sezgin, E., Doktorova, M., Lyman, E. & Levental, I. Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape. Nature Chemical Biology 16, 644–652 (2020).

      (56) Her, C., Filoti, D. I., McLean, M. A., Sligar, S. G., Ross, J. A., Steele, H. & Laue, T. M. The charge properties of phospholipid nanodiscs. Biophysical journal 111(5), 989–998 (2016).

      (3) Figure 2b - it would be easier to compare if these were plotted on top of each other. Are we at saturating ATP binding concentration or below it? Also, please put a key to say purple - absent and orange +EGF on the figure. I am also confused as to why, with no EGF, ATP binding is high with 0% POPS, but low when EGF is present, but that then reverses with physiological lipid content.

      While we agree that a direct comparison would be easier, the ATP-binding experiments for the ± EGF conditions were actually performed independently on separate SDS-PAGE gels, which unfortunately precludes such a comparison. We have added a color key to clarify the -EGF and +EGF datasets.

      The experiments were carried out at 1 µM of the fluorescently labeled ATP analogue (atto647Nγ ATP). Reported kinetic measurements for the isolated EGFR kinase domain indicate an K<sub>m</sub> of 5.2 µM suggesting that our experimental concentration is below, but close to the saturating range ensuring sensitivity to changes in accessibility of the binding site rather than saturating all available receptors.

      We have revised the manuscript to clarify these details by including the following text:

      Results, page 6, “To investigate how the membrane composition impacts accessibility, we measured ATP binding levels for EGFR in membranes with different anionic lipid content. 1 µM of fluorescently-labeled ATP analogue, atto647N-γ ATP, which binds irreversibly to the active site, was added to samples of EGFR nanodiscs with 0%, 15%, 30% or 60% anionic lipid content in the absence or presence of EGF.”

      Methods, page 24, “ATP binding experiments: Full-length EGFR in different lipid environments was prepared using cell-free expression as described above. 1μM of snap surface 488 (New England Biolabs) and atto647N labeled gamma ATP (Jena Bioscience) was added after cell-free expression and incubated at 30 °C , 300 rpm for 60 minutes. 1μM of atto647N-γ ATP was used, corresponding to a concentration near the reported Km of 5.2 µM for ATP binding to the isolated EGFR kinase domain[93], ensuring sensitivity to lipid-dependent changes in ATP accessibility.”

      (ii) Nucleotide binding is suppressed under basal conditions, likely to ensure that the catalytic activity is promoted only upon EGF stimulation.

      The molecular dynamics simulations at 0% and 30% POPS further support this interpretation, showing that anionic lipids modulate the accessibility of the ATP-binding site in a manner consistent with experimental trends (Fig. 2c and 2d).

      We have clarified these points in the main text with the following additions:

      Results, page 6, “In the presence of EGF, ATP binding overall increased with anionic lipid content with the highest levels observed in 60% POPS bilayers. In the neutral bilayer, ligand seemed to suppress ATP binding, indicating anionic lipids are required for the regulated activation of EGFR.”

      Results, page 7, “In the absence of EGF, increasing the anionic lipid content from 0\% POPS to 30% POPS increased the number of ATP-lipid contacts 58.6±0.7 to 74.4±1.2, indicating reduced accessibility, consistent with the experimental results and suggesting anionic lipids are required for ligand-induced EGFR activity.”

      (93) Yun, C. H., Mengwasser, K. E., Toms, A. V., Woo, M. S., Greulich, H., Wong, K. K., Meyerson,M. & Eck, M.J. The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP. PNAS, 105(6), 2070–2075 (2008).

      (4) Figure 2d - how was the 16A distance arrived at?

      We thank the reviewer for pointing this out. The 16 Å cutoff was chosen based on the physical dimensions of the ATP analogue used in the experiments. Specifically, the largest radius of the atto647N-γ ATP molecule is ~16.9 Å, which defines the maximum distance at which lipid atoms could sterically obstruct access of ATP to the binding pocket. Accordingly, in the simulations, contacts were defined as pairs of coarse-grained atoms between lipid molecules and the residues forming the ATP-binding site (residues 694-703, 719, 766-769, 772-773, 817, 820, and 831) separated by less than 16 Å.

      We have rewritten the rationale for selecting the 16 Å cutoff in the Methods section to improve clarity.

      Methods, page 28, “Coarse-grained, Explicit-solvent Simulations with the MARTINI Force Field: We analyzed our simulations using WHAM[108,109] to reweight the umbrella biases and compute the average values of various metrics introduced in this manuscript. Specifically, we calculated the distance between Residue 721 and Residue 1186 (EGFR C-terminus) of the protein. To quantify the accessibility of the ATP-binding site, we calculated the number of contacts between lipid molecules and the residues forming the ATP-binding pocket (residues 694-703, 719, 766-769, 772-773, 817, 820, and 831)[110]. Close contact between the bilayer and these residues would sterically hinder ATP binding; thus, the contact number serves as a proxy for ATP-site accessibility. The cutoff distance for defining a contact was set to 16 Å, corresponding to the largest molecular radius of the fluorescent ATP analogue (atto647N-γ ATP, 16.96 Å111). Accordingly, we defined a contact as a pair of coarse-grained atoms, one from the lipid membrane and one from the ATP binding site, within a mutual distance of less than 16 Å.”

      (5) Figure 2e-h - I think a bar chart/violin plot/jitter plot would make it easier to compare the peak values. The statistics in the table should just be quoted in the text as value +/- error from the 95% confidence interval. The way it is written currently is confusing, as it implies that there is no conformational change with the addition of EGF in neutral lipids, but there is ~0.4nm one from the table. I don't understand what you mean by "The larger conformational response of these important domains suggests that the intracellular conformation may play a role in downstream signaling steps, such as binding of adaptor proteins"?

      We thank the reviewer for these suggestions. For the smFRET lifetime distributions (Figure 2j, k; previously Figure 2e, f), we have now included jitter plots of the donor lifetimes in the Supplementary Figure 11 to facilitate direct visual comparison of the median and distribution widths for each lipid composition and ±EGF conditions. The distance distributions for the ATP to C-terminus in Figure 2e, f (previously Figure 2g, h) were obtained from umbrella-sampling simulations that calculate free-energy profiles rather than raw, unbiased distance values. Because the sampling is guided by biasing potentials, individual distance values cannot be used to construct violin or jitter plots. We therefore present the simulation data only as probability density distributions, which best reflect the equilibrium distributions derived from them.

      We have also revised the text to report the median ± 95% confidence interval, improving clarity and consistency with the statistical table.

      Results, page 9: “In the neutral bilayer (0% POPS), the distributions in the absence of EGF peaks at 8.1 nm (95% CI: 8.0–8.2 nm) and in the presence of EGF peaks at 8.6 nm (95% CI: 8.5–8.7 nm) (Table 1, Supplementary Table 1). In the physiological regime of 30% POPS nanodiscs, the peak of the donor lifetime distribution shifts from 9.1 nm (95% CI: 8.9–9.2 nm) in the absence of EGF to 11.6 nm (95% CI: 11.1–12.6 nm) in the presence of EGF (Table 1, Supplementary Table 1), which is a larger EGF-induced conformational response than in neutral lipids.”

      Finally, we have rephrased the sentence in question for clarity. The revised text now reads:

      Results, page 9: “The larger conformational response observed in the presence of anionic lipids suggests that these lipids enhance the responsiveness of the intracellular domains to EGF, potentially ensuring interactions between C-terminal sites and adaptor proteins during downstream signaling.”

      (6) "r, highlighting that the charged lipids can enhance the conformational response even for protein regions far away from the plasma membrane" - is it not that the neutral membrane is just very weird and not physiological that EGFR and other proteins don't function properly?

      We agree with the reviewer that completely neutral (0% POPS) membranes are not physiological and likely do not support the native organization or activity of EGFR. We have revised the text to clarify that the 30% POPS condition represents a more native-like lipid environment that restores or stabilizes the expected conformational response, rather than "enhancing" it. The revised sentence now reads:

      Results, page 10: “Both experimental and computational results show a larger EGF-induced conformational change in the partially anionic bilayer, consistent with the notion that a partially anionic lipid bilayer provides a more native environment that supports proper receptor activation, compared to the non-physiological neutral membrane.”

      (7) "snap surface 594 on the C-terminal tail as the donor and the fluorescently-labeled lipid (Cy5) as the acceptor (Supplementary Fig. 2, 11)." Why not refer to Figure 3a here to make it easier to read?

      We have added the reference to Figure 3a, and we thank the Reviewer for the suggestion.

      (8) Figure 3 - the bimodality in many of these plots is dubious. It's very clear in some, i.e. 0% POPS +EGF, but not others. Can anything be done to justify bimodality better?

      We agree that statistical justification is important for interpreting lifetime distributions. To address this, we performed global fits of the data with both two- and three-Gaussian models and evaluated them using the Bayesian Information Criterion (BIC), which balances the model fit with a penalty for additional parameters. The three-Gaussian model gave a substantially lower BIC, indicating statistical preference for the more complex model. However, we also assessed the separability of the Gaussian components using Ashman’s D, which quantifies whether peaks are distinct. This analysis showed that two of the Gaussians are not separable, implying they represent one broad distribution rather than two discrete states. Therefore, when all the distributions are fit globally, the data are best described as two Gaussians, one centered at ~1.3 ns and the other at ~2.7 ns, with cholesterol-dependent shifts reflecting changes in the distribution of this population rather than the emergence of a separate state. We better justified our choice of model by incorporating the results of the global two- vs three-Gaussian fits with BIC and Ashman’s D analysis in the revised manuscript.

      Methods, page 27: “Model Selection and Statistical Analysis

      Global fitting of lifetime distributions was performed across all experimental conditions using maximum likelihood estimation. Both two-Gaussian and three-Gaussian distribution models were evaluated as described previously.62 Model performance was compared using the Bayesian Information Criterion (BIC),[101] which balances model likelihood and complexity according to

      BIC = -2 ln L + k ln n

      where L is the likelihood, k is the number of free parameters, and n is the number of singlemolecule photon bunches across all experimental conditions. A lower BIC value indicates a statistically better model[101]. The separation between Gaussian components was subsequently assessed using the Ashman’s D where a score above 2 indicates good separation[102]. For two Gaussian components with means µ1, µ2 and standard deviations σ1, σ2,

      where Dij represents the distance metric between Gaussian components i and j. All fitted parameters, likelihood values, BIC scores, and Ashman’s D values are summarized in Supplementary Table 5.”

      (101) Schwarz, G. Estimating the dimension of a model. The Annals of Statistics, 461–464 (1978).

      (102) Ashman, K. M., Bird, C. M. & Zepf, S. E. Detecting bimodality in astronomical datasets. The Astronomical Journal 108(6), 2348–2361 (1994).

      (9) Figure 3c - can you better label the POPS/POPC on here?

      We thank the reviewer for this suggestion. In the revised manuscript, Figure 3b (previously Figure 3c) has been updated to label the lipid composition corresponding to each smFRET distribution to make the comparison across conditions easier to follow.

      (10) Figure 3g - it looks like cholesterol causes a shift in both the peaks, such that the previous open and closed states are not the same, but that there are 2 new states. This is key as the authors state: "Remarkably, high anionic lipids and cholesterol content produce the same EGFR conformations but with opposite effects on signaling-suppression or enhancement." But this is only true if there really are the same conformational states for all lipid/cholesterol conditions. Again, the bimodal models used for all conditions need to be justified.

      We appreciate the reviewer’s insightful comment. We agree that the interpretation of the lifetime distributions depends on whether cholesterol and anionic lipids modulate existing conformational states or create new ones. To test this, we performed global fits of all distributions using the two- and three-Gaussian models and compared them using the Bayesian Information Criterion (BIC) and Ashman’s D, the results of which are described in detail in response to (8) above.

      Both fitting models, two- and three-Gaussian, identified the same short lifetime component (µ = 1.3 ns), suggesting this reflects a well separated conformation. While the three-Gaussian model gave a lower BIC, Ashman’s D analysis indicated that the two of the three components (µ = 2.6 ns and 3.4 ns) are not statistically separable, suggesting they represent a single broad conformational population rather than distinct states. If instead these two components reflected distinct states present under different conditions, Ashman’s D analysis would have found the opposite result. This supports our interpretation that high cholesterol and high anionic lipid content produce similar conformation ensembles with opposite effects on signaling output.

      Finally, we acknowledge that additional conformations may exist, but based on this analysis a bimodal model describes the populations captured in our data and so we limit ourselves to this simplest framework. We have clarified this rationale in the revised manuscript and added the results of the BIC and Ashman’s D analysis to support this interpretation.

      (11) Why are we jumping about between figures in the text? Figure 1d is mentioned after Figure 2. Also, DMPC is shown in the figures way before it is described in the text. It is very confusing. Figure 3 is so compact. I think it should be spread out and only shown in the order presented in the text. Different parts of the figure are referred to seemingly at random in the text. Why is DMPC first in the figure, when it is referred to last in the text?

      Following the Reviewer’s comment, we have revised the figure order and layout to improve readability and ensure consistency with the text. The previous Figures 1d-f which introduce the single-molecule fluorescence setup are now Figure 2g-i, positioned immediately before the first single-molecule FRET experiments (Fig 2j, k). The DMPC distribution in Figure 3 has been moved to the Supplementary Information (Supplementary Fig. 17), where it is shown alongside POPC, as these datasets are compared in the section “Mechanism of cholesterol inhibition of EGFR transmembrane conformational response”. The smFRET distributions in Figure 3 are now presented in the same sequence as they are discussed in the text, and the figure has been spread out for better clarity.

      (12) Throughout, I find the presentation of numerical results, their associated error, and whether they are statistically significantly different from each other confusing. A lot of this is in supplementary tables, but I think these need to go in the main text.

      To improve clarity and ensure that key quantitative results are easily accessible, we have moved the relevant supplementary tables to the main text. Specifically, the following tables have been incorporated into the main manuscript:

      (i) Median distance between the ATP binding site and the EGFR C-terminus, or between membrane and EGFR C-terminus from smFRET measurements (previously supplementary table 1 is now main table 1)

      (ii) Median distance between the membrane and the EGFR C-terminus in different anionic lipid environments (previously supplementary table 4 is now main table 2)

      (iii) Median distance between the membrane and the EGFR C-terminus in different cholesterol environments (previously supplementary table 8 and 12 is now combined to be main table 3)

      (13) Supplementary figures - in general, there is a need to consider how to combine or simplify these for eLife, as they will have to become extended data figures.

      We thank the reviewer for this helpful suggestion. In the revised manuscript, we have reorganized the supplementary figures into extended data figures in accordance with eLife’s format. Specifically:

      - Supplementary Figs. 1–7 are now grouped as Extended Data Figures for Figure 1 in the main text. They are now Figure 1 - figure supplements 1–7.

      - Supplementary Fig. 8–11 is now Extended Data Figure associated with Figure 2. It is now Figure 2 - figure supplements 1–4.

      - Supplementary Figs. 12–17 are now grouped as Extended Data Figures for Figure 3. They are now Figure 3 - figure supplements 1–6.

      (14) Supplementary Figure 2 - label what the two bands are in the EGFR and pEGFR sets at the bottom of panel c.

      We thank the reviewer for this comment. The two bands shown in the EGFR and pEGFR blots in Supplementary Fig. 2d (previously Supplementary Fig. 2c) corresponds to replicate samples under identical conditions. We have now clarified this in the figure legend and labeled the lanes as “Rep 1” and “Rep 2” in the revised figure and modified the figure legend.

      Supplementary Figure 2, page 31: “(d) Western blots were performed on labelled EGFR in nanodiscs. Anti-EGFR Western blots (left) and anti-phosphotyrosine Western blots (right) tested the presence of EGFR and its ability to undergo tyrosine phosphorylation, respectively, consistent with previous experiments on similar preparations[18, 54, 55]. The two lanes in each blot correspond to replicate samples under identical conditions.”

      (15) Supplementary Figures 3+4 - a bar chart/boxplot or similar would be easier for comparison here.

      In the revised version, we have replaced the histograms with jitter plots showing the nanodisc size distributions for each condition in supplementary figures 4 and 5 (previously supplementary figures 3 and 4). The plots display individual measurements with a horizontal line indicating the mean size (mean ± standard deviation values provided in the caption).

      (16) Supplementary Figures 10, 12, 13, 15, 16 - I would jitter these.

      We have incorporated jitter plots for the relevant datasets in Supplementary Figures 11, 13, 15, 16 and 17 (previously supplementary figures 10, 12 13, 15 and 16) to provide a clearer visualization of the data distributions and median values.

      Reviewer #2 (Recommendations for the authors):

      (1) Reactions were performed in 250 µL volumes. What is the average yield of solubilized EGFR in those reactions? Are there differences in the EGFR solubilization with the various lipid mixtures?

      The amount of solubilized EGFR produced in each 250 µL cell-free reaction was below the reliable detection limit for quantitative absorbance assays. At these protein levels, little to no EGFR precipitation was observed for all lipid compositions. Although exact yields could not be determined, fluorescence-based detection confirmed the presence of functional, nanodiscincorporated EGFR suitable for smFRET and ensemble fluorescence experiments. We observed variability in total yield between independent reactions within the same lipid composition, which is common for cell-free systems, but no consistent trend attributable to lipid composition.

      (2) Figure S2: It would be better to have a larger overview of the particles on a grid to get a better impression of sample homogeneity.

      TEM images showing a larger field of view have been added for each lipid composition in Supplementary Figures 4 and 5.

      (3) Figure 2b: It appears that there is some variation in the stoichiometry of ApoA1 and EGFR within the samples. Have equal amounts of each sample been analyzed? Are there, in addition, some precipitates of EGFR? It would further be good to have a negative control without expression to get more information about the additional bands in Figure S2b. As they do not appear in the fluorescent gel, it is unlikely that they represent premature terminations of EGFR.

      The fluorescence intensity from the bound ATP analogue (Atto 647N-ATP) and from the snap surface 488 label, which binds stoichiometrically to the SNAP tag at the EGFR C-terminus, was measured for each sample. The relative amount of ATP binding was quantified for each sample by normalizing to the EGFR content (Figure 2b). This normalization accounts for the different amounts of EGFR produced in each condition.

      We did not observe any visible precipitation under the reported cell-free conditions, likely due to the following reasons:

      (i) EGFR and ApoA1 are co-expressed in the cell-free reaction, and ApoA1 assembles into nanodiscs concurrently with receptor translation, providing an immediate membrane sink

      (ii) ApoA1 is expressed at high levels, maintaining disc concentrations that keep the reaction in a soluble regime.

      A control cell-free reaction containing only ApoA1∆49 (1 µg) and no EGFR template, analyzed after affinity purification, showed a single prominent band at ~ 25 kDa (gel image below), corresponding to ApoA1, along with faint background bands typical of Ni-NTA purification from cell-lysates. These weak, non-specific bands likely arise from co-purification of endogenous E.coli proteins.  

      The ApoA1∆49-only control gel has now been included as part of the supplementary figure 2.

      (4) Figure S2c: It would be better to show the whole lanes to document the specificity of the antibodies. Anti-Phosphor antibodies are frequently of poor selectivity. In that case, a negative control with corresponding tyrosine mutations would be helpful.

      We have updated Figure S2d (previously Figure S2c) to include the full gel lanes to better illustrate the specificity of both the total EGFR and phospho-EGFR (Y1068) antibodies. The results show a single clear band at the expected molecular weight for EGFR, conforming antibody specificity.

      (5) The Results section already contains quite some discussion. I would thus recommend combining both sections.

      We thank the reviewer for the suggestion. We have now created a results and discussion section to better reflect the content of these paragraphs, with the previous discussion section now a subsection focused on implications of these results.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study identifies a mechanism responsible for the accumulation of the MET receptor in invadopodia, following stimulation of Triple-negative breast cancer (TNBC) cells with HGF. HGF-driven accumulation and activation of MET in invadopodia causes the degradation of the extracellular matrix, promoting cancer cell invasion, a process here investigated using gelatin-degradation and spheroid invasion assays.

      Mechanistically, HGF stimulates the recycling of MET from RAB14-positive endosomes to invadopodia, increasing their formation. At invadopodia, MET induces matrix degradation via direct binding with the metalloprotease MT1-MMP. The delivery of MET from the recycling compartment to invadopodia is mediated by RCP, which facilitates the colocalization of MET to RAB14 endosomes. In this compartment, HGF induces the recruitment of the motor protein KIF16B, promoting the tubulation of the RAB14-MET recycling endosomes to the cell surface. This pathway is critical for the HGF-driven invasive properties of TNBC cells, as it is impaired upon silencing of RAB14.

      Strengths:

      The study is well-organized and executed using state-of-the-art technology. The effects of MET recycling in the formation of functional invadopodia are carefully studied, taking advantage of mutant forms of the receptor that are degradation-resistant or endocytosis-defective.

      Data analyses are rigorous, and appropriate controls are used in most of the assays to assess the specificity of the scored effects. Overall, the quality of the research is high.

      The conclusions are well-supported by the results, and the data and methodology are of interest for a wide audience of cell biologists.

      We sincerely thank the reviewer for his/her positive feedback and for considering our study to be well executed and rigorous. The valuable suggestions and comments will certainly improve the understanding of the role of the RAB14-RCP-KIF16B axis in MET trafficking and breast cancer invasion. Below we have addressed each of the concerns and suggestions point to point raised by the reviewer.

      Weakness:

      The role of the MET receptor in invadopodia formation and cancer cell dissemination has been intensively studied in many settings, including triple-negative breast cancer cells. The novelty of the present study mostly consists of the detailed molecular description of the underlying mechanism based on HGF-driven MET recycling. The question of whether the identified pathway is specific for TNBC cells or represents a general mechanism of HGF-mediated invasion detectable in other cancer cells is not addressed or at least discussed

      We thank the reviewer for raising this point. We want to clarify that in TNBCs, the lack of the hormonal receptor progesterone receptor, estrogen receptor, and HER2 makes the overexpression of EGFR and MET crucial in terms of prognosis and treatment (PMID: 27655711, 25368674). Hence study of MET signalling and trafficking is more relevant for TNBCs compared to other cancer cells. We will add an explanation in the discussion section in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Khamari and colleagues investigate how HGF-MET signaling and the intracellular trafficking of the MET receptor tyrosine kinase influence invadopodia formation and invasion in triple-negative breast cancer (TNBC) cells. They show that HGF stimulation enhances both the number of invadopodia and their proteolytic activity. Mechanistically, the authors demonstrate that HGF-induced, RAB4- and RCP-RAB14-KIF16B-dependent recycling routes deliver MET to the cell surface specifically at sites where invadopodia form. Moreover, they report that MET physically interacts with MT1-MMP - a key transmembrane metalloproteinase required for invadopodia function- and that these two proteins co-traffic to invadopodia upon HGF stimulation.

      Although the HGF-MET axis has previously been implicated in invadopodia regulation (e.g., by Rajadurai et al., Journal of Cell Science 2012), studies directly linking ligand-induced MET trafficking with the spatial regulation of MT1-MMP localization and activity have been lacking.

      Overall, the manuscript addresses a relevant and timely topic and provides several novel insights. However, some sections require clearer and more concise writing (details below). In addition, the quality, reliability, and robustness of several data sets need to be improved.

      Strengths:

      A key strength of the study is the novel demonstration that HGF-mediated, RAB4- and RAB14-dependent recycling of MET delivers this receptor, together with MT1MMP, to invadopodia -highlighting a previously unrecognized mechanism, regulating the formation and proteolytic function of these invasive structures. Another strong point is the breadth of experimental approaches used and the substantial amount of supporting data. The authors also include an appropriate number of biological replicates and analyze a sufficiently large number of cells in their imaging experiments, as clearly described in the figure legends.

      We greatly appreciate the positive assessment we have from the reviewer, who also acknowledged the novelty and relevance of our study. Below, we have carefully addressed the comments/concerns raised regarding this study and will strengthen the reliability and robustness by revisiting the data, providing additional analyses where required, and clarifying methodological details.

      Weakness:

      (1) Inappropriate stimulation times for endocytosis and recycling assays. The experiments examining MET endocytosis and recycling following HGF stimulation appear to use inappropriate incubation times. After ligand binding, RTKs typically undergo endocytosis within minutes and reach maximal endosomal accumulation within 5-15 minutes. Although continuous stimulation allows repeated rounds of internalization, the temporal dynamics of MET trafficking should be examined across shorter time points, ideally up to 1 hour (e.g., 15, 30, and 60 minutes). The authors used 2-, 3-, or 6-hour HGF stimulation, which, in my opinion, is far too long to study ligandinduced RTK trafficking.

      We understand the reviewer’s concern regarding the HGF stimulation time point for endocytosis and recycling. We want to highlight that to study the recycling/surface delivery of MET in response to HGF, we performed TIRF microscopy-based imaging, where images were taken within 1h of HGF addition (Fig. 2I). Additionally, we will incorporate surface biotinylation to show the recycling of MET as suggested in comment -7. Moreover, we have observed the effect of HGF on gelatin degradation and invadopodia formation after 3h of HGF stimulation. We were curious to know where MET resides with prolonged ligand stimulation. Hence, to study the localization of MET to invadopodia or the endocytic markers, the cells were stimulated with HGF for 2-3 hours. 

      (2) Low efficiency of MET silencing in Figure S1I. The very low MET knockdown efficiency shown in Figure S1I raises concerns. Given the potential off-target effects of a single shRNA and the insufficient silencing level, it is difficult to conclude whether the reduction in invadopodia number in Figure 1F is genuinely MET-dependent. The authors later used siRNA-mediated silencing (Figure S5C), which was more effective. Why was this siRNA not used to generate the data in Figure 1F? Why did the authors rely on the inefficient shRNA C#3?

      We understand the concern raised by the reviewer. We want to emphasize that we have employed three different approaches to investigate the effect of MET silencing/inhibition on invadopodia formation. (i) A MET kinase inhibitor, PHA665752, which shows reduced invadopodia formation. (Fig. 1D, E). (ii) Silencing with shRNA: Since the level of silencing of MET with the shRNA was not sufficient, cells were stained with MET as a readout for MET silencing, and images of the cells with depleted MET expression were captured, and invadopodia numbers were quantified (Fig. 1F). (iii) Using the SMARTpool siRNA of MET, we have shown the MT1-MMP containing invadopodia in Fig S5E, which shows another evidence of the role of MET in invadopodia activity. An additional graph showing invadopodia formation derived from the siRNA-mediated MET silencing will be added to the revised figure.

      (3) Missing information on incubation times and inconsistencies in MET protein levels. The figure legends do not indicate how long the cells were incubated with HGF or the MET inhibitor PHA665752 before immunoblotting. This information is crucial, particularly because both HGF and PHA665752 cause a substantial decrease in the total MET protein level. Notably, such a decrease is absent in MDA-MB-231 cells treated with HGF in the presence of cycloheximide (Figure S2F). The authors should comment on these inconsistencies. Additionally, the MET bands in Figure S1J appear different from those in Figure S1C, and MET phosphorylation seems already high under basal conditions, with no further increase upon stimulation (Figure S1J). The authors should address these issues. 

      We apologise for the unintentional omission of experimental detailing about HGF or drug incubation time, which will be incorporated into the figure legend appropriately. The blot will be replaced with a more appropriate representative image.

      Regarding the decreased MET level in the drug-treated condition: literature suggests that the MET inhibitor PHA665752 also promotes MET degradation, corroborating our result shown in Fig. S1J (PMID: 15788682, 18327775). Further in Fig. S1J, the relative phosphorylation of MET when compared to the total MET level in the HGF-treated condition is higher. We will add the quantification in the revised manuscript to add more clarity.

      Next, in the fig. S1C, the rabbit anti-MET (CST, D1C2 XP) antibody has been used, which binds to a c-terminal motif of MET and identifies both the 170kDa as well as 140kDa protein representing the uncleaved and cleaved form of MET. In Fig. S1J, the mouse antiMET (CST, L6E7) antibody has been used, which binds to an N-terminal motif of MET and recognizes only the 140kDa protein.

      (4) Insufficient representation and randomization of microscopic data. For microscopy, only single representative cells are shown, rather than full fields containing multiple cells. This is particularly problematic for invadopodia analysis, as only a subset of cells forms these structures. The authors should explain how they ensured that image acquisition and quantification were randomized and unbiased. The graphs should also include the percentage of cells forming invadopodia, a standard metric in the field. Furthermore, some images include altered cells - for example, multinucleated cells - which do not accurately represent the general cell population.

      We thank the reviewer for raising this point. The single-cell images are shown for clarity and to visualize the subcellular features; however, the conclusions are made based on the quantitative analysis of multiple cells collected from multiple frames (at least 30 frames per condition). Here, we would like to highlight that the image acquisition has been done over random fields in a coverslip. In the graphs shown in Fig. 1B, 1C, 4F, S1F, S1H, S5J’ it can be seen that there are frames where there is no degradation or invadopodia formed, which has also been taken into account. For a better representation of the population of cellforming invadopodia, a graph showing the percentage of cells forming invadopodia will be added to the figure.

      (5) Use of a single siRNA/shRNA per target. As noted earlier, using only one siRNA or shRNA carries the risk of off-target effects. For every experiment involving gene silencing (MET, RAB4, RAB14, RCP, MT1-MMP), at least two independent siRNAs/shRNAs should be used to validate the phenotype.

      We would like to clarify that we are using SMARTPool siRNA, which contains 4 individual siRNAs for the target gene. Literature suggests that using a pool of siRNA has reduced offtarget effects compared to using single oligos for gene silencing (PMID: 14681580, 33584737, 24875475).

      While SMARTpool siRNA minimizes the off-target effect, it does not eliminate the possibility of it. To confirm that the observed phenotypes are specifically attributable to the genes investigated in this study, we will perform additional experiments using two independent siRNAs targeting RCP and RAB14. RAB4 is known to be associated with MET trafficking (PMID: 21664574, 30537020), and we have taken RAB4 as a positive control. Hence, we feel the suggested experiment is not required to support the conclusion made regarding RAB4.

      For MET, we have used shRNA and an inhibitor to show the effect of MET inhibition/perturbation in the invadopodia-associated activity, which validates the observations of siRNA-mediated gene silencing.

      We have shown the effect of MT1-MMP depletion on invadopodia formation using a CRISPR-based gene knock-out study, and another study from our group has shown the effect using siRNA (PMID: 31820782), which supports our MT1-MMP KO cell observation.    

      (6) Insufficient controls for antibody specificity. The specificity of MET, p-MET, and MT1-MMP staining should be demonstrated in cells with effective gene silencing. This is an essential control for immunofluorescence assays.

      MET immunofluorescence staining in the MET-depleted condition has been provided in Fig. 1F, and an immunoblot for the siRNA-mediated gene silencing has been provided in Fig. S5C. We will add the entire field of view to show the MET silencing in Fig. 1F.

      The inhibition of MET kinase activity using PHA665752 abolished the MET phosphorylation, as shown in Fig S1J. In line with Joffre et.al. Fig 3C, S2I shows increased Tyr 1234/1235 phosphorylation of M1250T MET mutant (PMID: 21642981). Further, studies have shown the specificity of the antibody by immunoblotting and immunofluorescence using MET inhibitors (PMID: 21973114, 41009793).

      For the MT1-MMP immunoblot showing significant depletion in MT1-MMP protein level by the SMARTpool siRNA has been provided in Fig. S5L. Further MT1-MMP silencing has been validated by immunofluorescence in the following studies. PMID: 22291036, 21571860, 20505159.

      (7) Inadequate demonstration of MET recycling. MET recycling should be directly demonstrated using the same approaches applied to study MT1-MMP recycling. The current analysis - based solely on vesicles near the plasma membrane - is insufficient to conclude that MET is recycled back to the cell surface.

      We appreciate the reviewer’s suggestion for an alternative approach to show MET trafficking. We aim to demonstrate MET trafficking using a biochemical approach, which will be included in the revised version. 

      (8) Insufficient evidence for MET-MT1-MMP interaction. The interaction between MET and MT1-MMP should be validated by immunoprecipitation of endogenous proteins, particularly since both are endogenously expressed in the studied cell lines.

      We thank the reviewer for pointing out the lack of MET-MT1-MMP interaction at the endogenous level. We have carried out the immunoprecipitation of endogenous MET to validate the interaction with MT1-MMP. However, we could not capture the interaction of these proteins at endogenous levels. We hypothesize that the interaction between MT1MMP and MET may be weak in nature, with a high K<sub>d</sub> value, and accordingly, it was difficult to precipitate the endogenous MT1-MMP by MET. The immunoblot will be added to the revised manuscript and discussed.

      (9) Inconsistent use of cell lines and lack of justification. The authors use two TNBC cell lines: MDA-MB-231 and BT-549, without providing a rationale for this choice. Some assays are performed in MDA-MB-231 and shown in the main figures, whereas others use BT-549, creating unnecessary inconsistency. A clearer, more coherent strategy is needed (e.g., present all main findings in MDA-MB-231 and confirm key results in BT549 in supplementary figures).

      MDA-MB-231 and BT-549 are two well-characterized TNBC cell lines, which are being used extensively to study breast cancer cell invasion. These two cell lines also show overexpression of MET, making them suitable model cell lines for our study. 

      MDA-MB-231 has less transfection efficiency compared to BT-549. Additionally, MET is also a difficult gene to transfect, making it hard to perform experiments in MDA-MB-231 with MET overexpression. Though most of the experiments have been performed in both cell lines, a few of the studies have been performed only in the BT-549 cells. Further, we have focused on displaying the different approaches taken to validate an observation in the main figure, which led to showing the data in distinct cell lines.

      Also, showing observations in different cell lines is a practice that has been followed by multiple authors in the past. (PMID:  39751400, 41079612, 25049275, 22366451)

      (10) Inconsistency in invadopodia numbers under identical conditions. The number of invadopodia formed in Figure 1E is markedly lower than in Figure 1C, despite identical conditions. The authors should explain this discrepancy.

      We sincerely thank the reviewer for pointing out the inconsistency in invadopodia numbers across 2 experiments. Fig. 1C has 2 conditions: UT and the HGF-treated condition. The Untreated condition has the serum-free media without any stimulation. Whereas we have added vehicle (DMSO) in Fig. 1D, E, since the drug is resuspended in DMSO. This difference in the treatment is likely to be responsible for the decreased numbers of invadopodia in Fig. 1E.

      (11) Questionable colocalization in some images. In some figures - for example, Figure 2G - the dots indicated by arrows do not convincingly show colocalization. The authors should clarify or reanalyze these data.

      We thank the reviewer for the valuable comment. The apparent lack of convincing colocalization is likely due to the relatively lower fluorescence intensity of MET at these structures. We will add the line intensity plots for the indicated puncta to show the intensity of both channels in the figure.

      To quantify the colocalization of two channels, we have used the automated image analysis software motiontracking (motiontracking.mpi-cbg.de), which has been detailed in the method section. Motiontracking considers only those objects to be colocalized if there is an overlapping area of more than 35% between the two channels. Lastly, the apparent colocalization is corrected for random colocalization, which is the random permutation of object colocalization. This makes object-based colocalization more reliable than intensitybased colocalization. 

      (12) Abstract, Introduction, and  Discussion require substantial rewriting. a) The abstract should be accessible to a broader audience and should avoid using abbreviations and protein names without context. b) The introduction should better describe the cellular processes and proteins investigated in this study. c) The discussion currently reads more like an extended summary of results. It lacks deeper interpretation, comparison with existing literature, and consideration of the broader implications of the findings.

      We thank the reviewer for this suggestion. We will modify the abstract, introduction, and discussion as per the suggestion.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, the authors explore a novel concept: GPCR-mediated regulation of miRNA release via extracellular vesicles (EVs). They perform an EV miRNA cargo profiling approach to investigate how specific GPCR activations influence the selective secretion of particular miRNAs. Given that GPCRs are highly diverse and orchestrate multiple cellular pathways - either independently or collectively - to regulate gene expression and cellular functions under various conditions, it is logical to expect alterations in gene and miRNA expression within target cells.

      Strengths:

      The novel idea of GPCRs-mediated control of EV loading of miRNAs.

      Weaknesses:

      Incomplete findings failed to connect and show evidence of any physiological parameters that are directly related to the observed changes. The mechanical detail is lacking.

      We appreciate the reviewer's acknowledgment of the novelty of this study. We agree with the reviewer that further mechanistic insights would strengthen the manuscript. The mechanisms by which miRNA is sorted into EVs remain poorly understood. Various factors, including RNAbinding protein, sequence motifs, and cellular location, can influence this sorting process(Garcia-Martin et al., 2022; Liu & Halushka, 2025; Villarroya-Beltri et al., 2013; Yoon et al., 2015). Ago2, a key component of the RNA-induced silencing complexes, binds to miRNA and facilitates miRNA sorting. Ago2 has been found in the EVs and can be regulated by the cellular signaling pathway.  For instance, McKenzie et al. demonstrated that KRAS-dependent activation of MEK-ERK can phosphorylate Ago2 protein, thereby regulating the sorting of specific miRNAs into EVs(McKenzie et al., 2016). In the differentiated PC12 cells, Gαq activation leads to the formation of Ago2-associated granules, which selectively sequester unique transcripts(Jackson et al., 2022). Investigating GPCR, G protein, and GPCR signaling on Ago2 expression, location, and phosphorylation states could provide valuable insights into how GPCRs regulate specific miRNAs within EVs. We have expanded these potential mechanisms and future research in the discussion section (page 16-17).

      The manuscript falls short of providing a comprehensive understanding. Identifying changes in cellular and EV-associated miRNAs without elucidating their physiological significance or underlying regulatory mechanisms limits the study's impact. Without demonstrating whether these miRNA alterations have functional consequences, the findings alone are insufficient. The findings may be suitable for more specialized journals.

      Thank you for the feedback. We acknowledge that validating the target genes of the top candidate miRNAs is an important next step. In response to the reviewer's concerns, we have expanded the discussion of future research in the manuscript (page 19-20). Although this initial study is primarily descriptive, it establishes a novel conceptual link between GPCR signaling and EV-mediated communication.

      Furthermore, a critical analysis of the relationship between cellular miRNA levels and EV miRNA cargo is essential. Specifically, comparing the intracellular and EV-associated miRNA pools could reveal whether specific miRNAs are preferentially exported, a behavior that should be inversely related to their cellular abundance if export serves a beneficial function by reducing intracellular levels. This comparison is vital to strengthen the biological relevance of the findings and support the proposed regulatory mechanisms by GPCRs.

      We appreciate the valuable suggestions from the reviewer. EV miRNA and cell miRNAs may exhibit distinct profiles as miRNAs can be selectively sorted into or excluded from EVs(Pultar et al., 2024; Teng et al., 2017; Zubkova et al., 2021). Investigating the difference between cellular miRNA levels and EV miRNA cargo would provide insight into the mechanism of miRNA sorting and the functions of miRNAs in the recipient cells. The expression of the cellular miRNAs is a highly dynamic process. To accurately compare the miRNA expression levels, profiling of EV miRNA and cellular miRNA should be conducted simultaneously. However, as an exploratory study, we were unable to measure the cellular miRNAs without conducting the entire experiment again.

      Reviewer #2 (Public review):

      Summary:

      This study examines how activating specific G protein-coupled receptors (GPCRs) affects the microRNA (miRNA) profiles within extracellular vesicles (EVs). The authors seek to identify whether different GPCRs produce unique EV miRNA signatures and what these signatures could indicate about downstream cellular processes and pathological processes.

      Methods:

      (1) Used U2OS human osteosarcoma cells, which naturally express multiple GPCR types.

      (2) Stimulated four distinct GPCRs (ADORA1, HRH1, FZD4, ACKR3) using selective agonists.

      (3) Isolated EVs from culture media and characterized them via size exclusion chromatography, immunoblotting, and microscopy.

      (4) Employed qPCR-based miRNA profiling and bioinformatics analyses (e.g., KEGG, PPI networks) to interpret expression changes.

      Key Findings:

      (1) No significant change in EV quantity or size following GPCR activation.

      (2) Each GPCR triggered a distinct EV miRNA expression profile.

      (3) miRNAs differentially expressed post-stimulation were linked to pathways involved in cancer, insulin resistance, neurodegenerative diseases, and other physiological/pathological processes.

      (4) miRNAs such as miR-550a-5p, miR-502-3p, miR-137, and miR-422a emerged as major regulators following specific receptor activation.

      Conclusions:

      The study offers evidence that GPCR activation can regulate intercellular communication through miRNAs encapsulated within extracellular vesicles (EVs). This finding paves the way for innovative drug-targeting strategies and enhances understanding of drug side effects that are mediated via GPCR-related EV signaling.

      Strengths:

      (1) Innovative concept: The idea of linking GPCR signaling to EV miRNA content is novel and mechanistically important.

      (2) Robust methodology: The use of multiple validation methods (biochemical, biophysical, and statistical) lends credibility to the findings.

      (3) Relevance: GPCRs are major drug targets, and understanding off-target or systemic effects via EVs is highly valuable for pharmacology and medicine.

      Weaknesses:

      (1) Sample Size & Scope: The analysis included only four GPCRs. Expanding to more receptor types or additional cell lines would enhance the study's applicability.

      We are encouraged that the reviewer recognized the novelty, methodological rigor, and significance of our work. We recognize the limitations of our current model system and emphasize the need to test additional GPCR families and cell lines in the future studies, as detailed in the discussion section (Page 19, second paragraph).

      (2) Exploratory Nature: This study is primarily descriptive and computational. It lacks functional validation, such as assessing phenotypic effects in recipient cells, which is acknowledged as a future step.

      We appreciate the feedback. We recognize the importance of validating the function of the top candidate miRNAs in the recipient cells, and this will be included in future studies (page 19-20).  

      (3) EV heterogeneity: The authors recognize that they did not distinguish EV subpopulations, potentially confounding the origin and function of miRNAs.

      Thank you for the comment. EV isolation and purification are major challenges in EV research. Current isolation techniques are often ineffective at separating vesicles produced by different biogenetic pathways. Furthermore, the lack of specific markers to differentiate EV subtypes adds to this complexity. We recognize that the presence of various subpopulations can complicate the interpretation of EV cargos. In our study, we used a combined approach of ultrafiltration followed by size-exclusion chromatography to achieve a balance between EV purity and yield. We adhere to the MISEV (Minimal Information for Studies of Extracellular Vesicles 2023) guidelines by reporting detailed isolation methods, assessing both positive and negative protein markers, and characterizing EVs by electron microscopy to confirm vesicle structure, as well as nanoparticle tracking analysis to verify particle size distribution(Welsh et al., 2024). By following these guidelines, we can ensure the quality of our study and enhance the ability to compare our findings with other studies.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Suggestions for Future Research:

      (1) Functionally validate top candidate miRNAs in recipient cells.

      We acknowledge that validating the target genes of the top candidate miRNAs is a crucial next step. In response to the reviewer's concerns, we have included this in the discussion as future research in the manuscript (page 19-20).

      (2) Investigate other GPCR families and repeat in primary or disease-relevant cell lines.

      The inclusion of different GPCRs and cell lines is suggested as an area for further investigation in the discussion. (Page 19).

      (3) Apply similar approaches in in vivo models or patient samples to assess clinical relevance.

      In response to the reviewer's concerns, we have included this in the discussion as future research in the manuscript (page 19-20).

      References

      Garcia-Martin, R., Wang, G., Brandão, B. B., Zanotto, T. M., Shah, S., Kumar Patel, S., Schilling, B., & Kahn, C. R. (2022). MicroRNA sequence codes for small extracellular vesicle release and cellular retention. Nature, 601(7893), 446-451. https://doi.org/10.1038/s41586021-04234-3  

      Jackson, L., Rennie, M., Poussaint, A., & Scarlata, S. (2022). Activation of Gαq sequesters specific transcripts into Ago2 particles. Sci Rep, 12(1), 8758. https://doi.org/10.1038/s41598022-12737-w  

      Liu, X.-M., & Halushka, M. K. (2025). Beyond the Bubble: A Debate on microRNA Sorting Into Extracellular Vesicles. Laboratory Investigation, 105(2), 102206. https://doi.org/10.1016/j.labinv.2024.102206  

      McKenzie, A. J., Hoshino, D., Hong, N. H., Cha, D. J., Franklin, J. L., Coffey, R. J., Patton, J. G., & Weaver, A. M. (2016). KRAS-MEK Signaling Controls Ago2 Sorting into Exosomes. Cell  Rep, 15(5), 978-987. https://doi.org/10.1016/j.celrep.2016.03.085  

      Pultar, M., Oesterreicher, J., Hartmann, J., Weigl, M., Diendorfer, A., Schimek, K., Schädl, B., Heuser, T., Brandstetter, M., Grillari, J., Sykacek, P., Hackl, M., & Holnthoner, W. (2024).Analysis of extracellular vesicle microRNA profiles reveals distinct blood and lymphatic endothelial cell origins. J Extracell Biol, 3(1), e134. https://doi.org/10.1002/jex2.134  

      Teng, Y., Ren, Y., Hu, X., Mu, J., Samykutty, A., Zhuang, X., Deng, Z., Kumar, A., Zhang, L., Merchant, M. L., Yan, J., Miller, D. M., & Zhang, H.-G. (2017). MVP-mediated exosomal sorting of miR-193a promotes colon cancer progression. Nature Communications, 8(1), 14448. https://doi.org/10.1038/ncomms14448  

      Villarroya-Beltri, C., Gutiérrez-Vázquez, C., Sánchez-Cabo, F., Pérez-Hernández, D., Vázquez, J., Martin-Cofreces, N., Martinez-Herrera, D. J., Pascual-Montano, A., Mittelbrunn, M., & Sánchez-Madrid, F. (2013). Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs. Nat Commun, 4, 2980. https://doi.org/10.1038/ncomms3980

      Welsh, J. A., Goberdhan, D. C. I., O'Driscoll, L., Buzas, E. I., Blenkiron, C., Bussolati, B., Cai, H., Di Vizio, D., Driedonks, T. A. P., Erdbrügger, U., Falcon-Perez, J. M., Fu, Q. L., Hill, A. F., Lenassi, M., Lim, S. K., Mahoney, M. G., Mohanty, S., Möller, A., Nieuwland, R., . . .Witwer, K. W. (2024). Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles, 13(2), e12404. https://doi.org/10.1002/jev2.12404  

      Yoon, J. H., Jo, M. H., White, E. J., De, S., Hafner, M., Zucconi, B. E., Abdelmohsen, K., Martindale, J. L., Yang, X., Wood, W. H., 3rd, Shin, Y. M., Song, J. J., Tuschl, T., Becker, K. G., Wilson, G. M., Hohng, S., & Gorospe, M. (2015). AUF1 promotes let-7b loading on Argonaute 2. Genes Dev, 29(15), 1599-1604. https://doi.org/10.1101/gad.263749.115  

      Zubkova, E., Evtushenko, E., Beloglazova, I., Osmak, G., Koshkin, P., Moschenko, A., Menshikov, M., & Parfyonova, Y. (2021). Analysis of MicroRNA Profile Alterations in Extracellular Vesicles From Mesenchymal Stromal Cells Overexpressing Stem Cell Factor. Front Cell Dev Biol, 9, 754025. https://doi.org/10.3389/fcell.2021.754025

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer # 1 (Public review):

      Significance:

      While most MAVEs measure overall function (which is a complex integration of biochemical properties, including stability), VAMP-seqtype measurements more strongly isolate stability effects in a cellular context. This work seeks to create a simple model for predicting the response for a mutation on the "abundance" measurement of VAMPseq.

      We thank the reviewer for their evaluation of our work and for their comments and feedback below.

      Of course, there is always another layer of the onion, VAMP-seq measures contributions from isolated thermodynamic stability, stability conferred by binding partners (small molecule and protein), synthesis/degradation balance (especially important in "degron" motifs), etc. Here the authors' goal is to create simple models that can act as a baseline for two main reasons:

      (1) how to tell when adding more information would be helpful for a global model;

      (2) how to detect when a residue/mutation has an unusual profile indicative of an unbalanced contribution from one of the factors listed above.

      As such, the authors state that this manuscript is not intended to be a state-of-the-art method in variant effect prediction, but rather a direction towards considering static structural information for the VAMP-seq effects. At its core, the method is a fairly traditional asymmetric substitution matrix (I was surprised not to see a comparison to BLOSUM in the manuscript) - and shows that a subdivision by burial makes the model much more predictive. Despite only having 6 datasets, they show predictive power even when the matrices are based on a smaller number. Another success is rationalizing the VAMPseq results on relevant oligomeric states.

      We thank the reviewer for their summary of the main points of our work. Based on the suggestion by the reviewer, we have added a comparison to predictions with BLOSUM62 to our revised manuscript, noting that we have previously compared the BLOSUM62 matrix to a broader and more heterogeneous set of scores generated by MAVEs (Høie et al, 2022).

      Specific Feedback:

      Major points:

      The authors spend a good amount of space discussing how the six datasets have different distributions in abundance scores. After the development of their model is there more to say about why? Is there something that can be leveraged here to design maximally informative experiments?

      We believe that these effects arise from a combination of intrinsic differences between the systems and assay-specific effects. For example, biophysical differences between the systems, such as differences in absolute folding stabilities or melting temperatures, will play a role, as will the fact that some proteins contain multiple domains.

      Also, the sequencing-based score for an individual variant in a sort-seq experiment (such as VAMP-seq) depends both on the properties of that variant and on the composition of the entire FACS-sorted cell library. This is because cells are sorted into bins depending on the composition of the entire library, which means that library-to-library composition differences can contribute to the differences between VAMP-seq score distributions. 

      From our developed models and outliers in predictions from these, it is difficult to tell which of the several possible underlying reasons cause the differences. We have briefly expanded the discussion of these points in the manuscript, and we have moreover elaborated on this in subsequent work (Schulze et al., 2025).

      They compare to one more "sophisticated model" - RosettaddG - which should be more correlated with thermodynamic stability than other factors measured by VAMP-seq. However, the direct head-tohead comparison between their matrices and ddG is underdeveloped. How can this be used to dissect cases where thermodynamics are not contributing to specific substitution patterns OR in specific residues/regions that are predicted by one method better than the other? This would naturally dovetail into whether there is orthogonal information between these two that could be leveraged to create better predictions.

      We thank the reviewer for this suggestion and indeed had spent substantial effort trying to gain additional biological insights from variants for which MAVE scores or MAVE predictions do not match predicted ∆∆G values. One major caveat in this analysis is that the experimental MAVE scores, MAVE predictions and the predicted ∆∆G values are rather noisy, making it difficult to draw conclusions based on individual variants or even small subsets of variants.

      In our revised manuscript, we have added an analysis to discover residue substitution profiles that are predicted most accurately either by a ∆∆G model or by our substitution matrix model, thereby avoiding analysis of individual variant effect scores. 

      We find that many substitution profiles are predicted equally well by the two model types, but also that there are residues for which one method predicts substitution effects better than the other method. We have added an analysis of the characteristics of the residues and variants for which either the ∆∆G model or the substitution matrix model is most useful to rank variants. Since we only find relatively few residues for which this is the case, we do not expect a model that leverages predicted scores from both methods to perform better than ThermoMPNN across variants. 

      Perhaps beyond the scope of this baseline method, there is also ThermoMPNN and the work from Gabe Rocklin to consider as other approaches that should be more correlated only with thermodynamics.

      We acknowledge that there are other approaches to predict ∆∆G beyond Rosetta including for example ThermoMPNN and our own method called RaSP (Blaabjerg et al, eLIFE, 2023), and we have added comparisons to ThermoMPNN and RaSP in the revised manuscript. We are unsure how one would use the data from Rocklin and colleagues directly, but we note that e.g. RaSP has been benchmarked on this data and other methods have been trained on this data. We originally used Rosetta since the Rosetta model is known to be relatively robust and because it has never seen large databases during training (though we do not think that training of ThermoMPNN and RaSP would be biased towards the VAMP-seq data). We note also that we have previously compared both Rosetta calculations and RaSP with VAMP-seq data for TPMT, PTEN and NUDT15 (Blaabjerg et al, eLIFE, 2023)

      I find myself drawn to the hints of a larger idea that outliers to this model can be helpful in identifying specific aspects of proteostasis. The discussion of S109 is great in this respect, but I can't help but feel there is more to be mined from Figure S9 or other analyses of outlier higher than predicted abundance along linear or tertiary motifs.

      We agree with these points and have previously spent substantial time trying to make sense of outliers in Figure S9 and Figure S18 (Figure S8 and Figure S18 of revised manuscript). The outlier analysis was challenging, in part due to the relatively high noise levels in both experimental data and predictions, and we did not find any clear signals. Some outliers in e.g. Figure S9 are very likely the result of dataset-specific abundance score distributions, which further complicates the outlier analysis. We now note this in the revised paper and hope others will use the data to gain additional insights on proteostasis-specific effects.  

      Reviewer # 2 (Public review):

      Summary:

      This study analyzes protein abundance data from six VAMP-seq experiments, comprising over 31,000 single amino acid substitutions, to understand how different amino acids contribute to maintaining cellular protein levels. The authors develop substitution matrices that capture the average effect of amino acid changes on protein abundance in different structural contexts (buried vs. exposed residues). Their key finding is that these simple structure-based matrices can predict mutational effects on abundance with accuracy comparable to more complex physics-based stability calculations (ΔΔG).

      Major strengths:

      (1) The analysis focuses on a single molecular phenotype (abundance) measured using the same experimental approach (VAMP-seq), avoiding confounding factors present when combining data from different phenotypes (e.g., mixing stability, activity, and fitness data) or different experimental methods.

      (2) The demonstration that simple structural features (particularly solvent accessibility) can capture a significant portion of mutational effects on abundance.

      (3) The practical utility of the matrices for analyzing protein interfaces and identifying functionally important surface residues.

      We thank the reviewer for the comments above and the detailed assessment of our work.

      Major weaknesses:

      (1) The statistical rigor of the analysis could be improved. For example, when comparing exposed vs. buried classification of interface residues, or when assessing whether differences between prediction methods are significant.

      We agree with the reviewer that it is useful to determine if interface residues (or any of the residues in the six proteins) can confidently be classified as buried- or exposed-like in terms of their substitution profiles. Thus, we have expanded our approach to compare individual substitution profiles to the average profiles of buried and exposed residues to now account for the noise in the VAMP-seq data. In our updated approach, we resample the abundance score substitution profile for every residue several thousand times based on the experimental VAMP-seq scores and score standard deviations, and we then compare every resampled profile to the average profiles for buried and exposed residues, thereby obtaining residue-specific distributions of RMSD<sub>buried</sub> and RMSD<sub>exposed</sub> values. These RMSD distributions are typically narrow, since many variants in several datasets have small standard deviations. In the revised manuscript, we report a residue to have e.g. a buried-like substitution profile if RMSD<sub>buried</sub> <RMSD<sub>exposed</sub> for at least 95% of the resampled profiles. We do not recalculate average scores in substitution matrices for this analysis. 

      Moreover, to illustrate potential overlap in predictive performance between prediction methods more clearly than in our preprint, we have added confidence intervals in Fig. 2 and Fig. 3 of the revised manuscript. We note that the analysis in Fig. 2 is performed using a leave-one-protein-out approach, which we believe provides the cleanest assessment of how well the different models perform.

      (2) The mechanistic connection between stability and abundance is assumed rather than explained or investigated. For instance, destabilizing mutations might decrease abundance through protein quality control, but other mechanisms like degron exposure could also be at play.

      We agree that we have not provided much description of the relation between stability and abundance in our original preprint. In the revised manuscript, we provide some more detail as well as references to previous literature explaining the ways in which destabilising mutations can cause degradation. We have moreover performed and added additional analyses of the relationship between thermodynamic stability and abundance through comparisons of stability predictions and predictions performed with our substitution matrix models.

      (3) The similar performance of simple matrix-based and complex physics-based predictions calls for deeper analysis. A systematic comparison of where these approaches agree or differ could illuminate the relationship between stability and abundance. For instance, buried sites showing exposed-like behavior might indicate regions of structural plasticity, while the link between destabilization and degradation might involve partial unfolding exposing typically buried residues. The authors have all the necessary data for such analysis but don't fully exploit this opportunity.

      This is similar to a point made by reviewer 1, and our answer is similar. We were indeed hoping that our analyses would have revealed clearer differences between effects on thermodynamic protein stability and cellular abundance and have tried to find clear signals. One major caveat in performing the suggested analysis is that both the experimental MAVE scores, ∆∆G predictions and our simple matrix-based predictions are rather noisy, making it difficult to make conclusions based on individual variants or even small subsets of variants. 

      To address this point, we have added an analysis to discover residue substitution profiles that are predicted most accurately either by a ∆∆G model or by our substitution matrix model, thereby avoiding analysis of individual variant effect scores. We find that many substitution profiles are predicted equally well by the two model types, but we also, in particular, find solvent-exposed residues for which the substitution matrix model is the better predictor. These residues are often aspartate, glutamate and proline, suggesting that surface-level substitutions of these amino acid types often can have effects that are not captured well by a thermodynamical model, either because this model does not describe thermodynamic effects perfectly, or because in-cell effects are necessary to account for to provide an accurate description.

      (4) The pooling of data across proteins to construct the matrices needs better justification, given the observed differences in score distributions between proteins (for example, PTEN's distribution is shifted towards high abundance scores while ASPA and PRKN show more binary distributions).

      We agree with the reviewer that the differences between the score distributions are important to investigate further and keep in mind when analysing e.g. prediction outliers. However, our results show that the pooling of VAMP-seq scores across proteins does result in substitution matrices that make sense biochemically and can identify outlier residues with proteostatic functions. As we also respond to a related point by reviewer 1, the differences in score distributions likely have complex origins. In that sense, we also hope that our results can inspire experimentalists to design methods to generate data that are more comparable across proteins.

      For example, biophysical differences between the systems, such as differences in absolute folding stabilities or melting temperatures will play a role, as will the fact that some proteins contain multiple domains. Also, the sequence-based score for an individual variant in a sort-seq experiment (such as VAMP-seq) depends both on the properties of that variant and from the composition of the entire FACS-sorted cell library. This is because cells are sorted into bins depending on the composition of the entire library, which means that library-to-library composition can contribute to the differences between VAMP-seq score distributions. From our developed models and outliers in predictions from these, it is difficult to tell which of the several possible underlying reasons cause the differences.

      Thus, even when experiments on different proteins are performed using the same technique (VAMP-seq), quantifying the same phenomenon (cellular abundance) and done in similar ways (saturation mutagenesis, sort-seq using four FACS bins), there can still be substantial differences in the results across different systems. An interesting side result of our work is to highlight this including how such variation makes it difficult to learn across experiments. We now elaborate on these points in the revised manuscript.

      (5) Some key methodological choices require better justification. For example, combining "to" and "from" mutation profiles for PCA despite their different behaviors, or using arbitrary thresholds (like 0.05) for residue classification.

      We hope we have explained our methodological choices clearer in the revised paper.

      We removed the dependency of the threshold of 0.05 used for residue classification in Fig. S19 of the original manuscript; in the revised manuscript we only report a residue to have e.g. a buried-like substitution profile if RMSD<sub>buried</sub> <RMSD<sub>exposed</sub> for at least 95% of the abundance score profiles that we resampled according to VAMP-seq score noise levels, as explained above.

      With respect to combining “to” and “from” mutational profiles for PCA, we could have also chosen to analyse these two sets of profiles separately to take potentially different behaviours along the two mutational axes into account. We do not think that there should be anything wrong with concatenating the two sets of profiles in a single analysis, since the analysis on the concatenated profiles simply expresses amino acid similarities and differences in a more general manner.

      The authors largely achieve their primary aim of showing that simple structural features can predict abundance changes. However, their secondary goal of using the matrices to identify functionally important residues would benefit from more rigorous statistical validation. While the matrices provide a useful baseline for abundance prediction, the paper could offer deeper biological insights by investigating cases where simple structure-based predictions differ from physics-based stability calculations.

      This work provides a valuable resource for the protein science community in the form of easily applicable substitution matrices. The finding that such simple features can match more complex calculations is significant for the field. However, the work's impact would be enhanced by a deeper investigation of the mechanistic implications of the observed patterns, particularly in cases where abundance changes appear decoupled from stability effects.

      We agree that disentangling stability and other effects on cellular abundance is one of the goals of this work. As discussed above, it has been difficult to find clear cases where amino acid substitutions affect abundance without stability beyond for example the (rare) effects of creating surface exposed degrons. Our new analysis, in which we compare substitution matrix-based predictions to stability predictions, does offer deeper insight into the relationship between the two predictor types and hence possibly between folding stability and abundance. 

      Reviewer #3 (Public review): 

      "Effects of residue substitutions on the cellular abundance of proteins" by Schulze and Lindorff-Larsen revisits the classical concept of structure-aware protein substitution matrices through the scope of modern protein structure modelling approaches and comprehensive phenotypic readouts from multiplex assays of variant effects (MAVEs). The authors explore 6 unique protein MAVE datasets based on protein abundance (and thus stability) by utilizing structural information, specifically residue solvent accessibility and secondary structure type, to derive combinations of context-specific substitution matrices predicting variant abundance. They are clear to outline that the aim of the study is not to produce a new best abundance predictor but to showcase the degree of prediction afforded simply by utilizing information on residue accessibility. The performance of their matrices is robustly evaluated using a leave-one-out approach, where the abundance effects for a single protein are predicted using the remaining datasets. Using a simple classification of buried and solvent-exposed residues, and substitution matrices derived respectively for each residue group, the authors convincingly demonstrate that taking structural solvent accessibility contexts into account leads to more accurate performance than either a structureunaware matrix, secondary structure-based matrix, or matrices combining both solvent accessibility or secondary structure. Interestingly, it is shown that the performance of the simple buried and exposed residue substitution matrices for predicting protein abundance is on par with Rosetta, an established and specialized protein variant stability predictor. More importantly, the authors finish off the paper by demonstrating the utility of the two matrices to identify surface residues that have buried-like substitution profiles, that are shown to correspond to protein interface residues, posttranslational modification sites, functional residues, or putative degrons.

      Strengths:

      The paper makes a strong and well-supported main point, demonstrating the utility of the authors' approach through performance comparisons with alternative substitution matrices and specialized methods alike. The matrices are rigorously evaluated without introducing bias, exploring various combinations of protein datasets. Supplemental analyses are extremely comprehensive and detailed. The applicability of the substitution matrices is explored beyond abundance prediction and could have important implications in the future for identifying functionally relevant sites.

      We thank the reviewer for the supportive comments on our work. 

      Comments:

      (1) A wider discussion of the possible reasons why matrices for certain proteins seem to correlate better than others would be extremely interesting, touching upon possible points like differences or similarities in local environments, degradation pathways, posttranslation modifications, and regulation. While the initial data structure differences provide a possible explanation, Figure S17A, B correlations show a more complicated picture.

      We agree with the reviewer that biochemical and biophysical differences between the proteins might contribute to the fact that some matrices correlate better than others. We also agree that it would be very interesting to understand these differences better. While it might be possible to examine some of the suggested causes of the differences, like differences or similarities in local environments, we have generally found that noise and differences in score distributions make such analyses difficult (see also responses to reviewers 1 and 2). For now, we will defer additional analyses to future work.

      (2) The performance analysis in Figure 2D seems to show that for particular proteins "less is more" when it comes to which datasets are best to derive the matrix from (CYP2C9, ASPA, PRKN). Are there any features (direct or proxy), that would allow to group proteins to maximize accuracy? Do the authors think on top of the buried vs exposed paradigm, another grouping dimension at the protein/domain level could improve performance?

      We don’t currently know if any protein- or domain-level features could be used to further split residues into useful categories for constructing new substitution matrices, but it is an interesting suggestion. We note that every substitution matrix consists of 380 averages, and creating too many residue groupings will cause some matrix entries to be averaged over very few abundance scores, at least with the current number of scores in the pooled VAMP-seq dataset. For example, while previous work has shown different mutational effects e.g. in helices and sheets (as one would expect), we find that a model with six matrices ({buried,exposed}x{helix,sheet,other}) does not lead to improved predictions (Fig. 2C), presumably because of an unfavourable balance between parameters and data.

      (3) While the matrices and Rosetta seem to show similar degrees of correlation, do the methods both fail and succeed on the same variants? Or do they show a degree of orthogonality and could potentially be synergistic?

      These are good questions and are related to similar questions from reviewers 1 and 2. In the revised manuscript, we have added additional analyses of differences between predictions from our substitution matrix model and a stability model, and we indeed find that the two methods show a degree of orthogonality. However, since we identify only relatively few residues for which one method performs better than the other, we don’t expect a synergistic model to outperform the stability predictor across all variants in any of the six proteins.  

      Overall, this work presents a valuable contribution by creatively utilizing a simple concept through cutting-edge datasets, which could be useful in various.

      Reviewing Editor:

      As discussed in more detail below, to strengthen the assessment, the authors are encouraged to:

      (1) Include more thorough statistical analyses, such as confidence intervals or standard errors, to better validate key claims (e.g., RMSD comparisons).

      (2) Perform a deeper comparison between substitution response matrices and ΔΔG-based predictions to uncover areas of agreement or orthogonality

      (3) Clarify the relationship between structural features, stability, and abundance to provide more mechanistic insights.

      As discussed above and below, we have added new analyses and clarifications to the revised manuscript.

      Reviewer #1 (Recommendations for the authors):

      Minor points:

      Why is a continuous version of the contact number used here, instead of a discrete count of neighbouring residues? WCN values of the residues in the core domain can be affected by residues far away (small contribution but not strictly zero; if there are many of them, it adds up).

      We have previously found WCN, which quantifies residue contact numbers in a continuous manner, to be a useful input feature for a classifier that determines whether individual residues are important for maintaining protein abundance or function (Cagiada et al, 2023). We have also found WCN and the cellular abundance of single substitution variants to correlate well in individual analyses of different proteins (Grønbæk-Thygesen et al., 2024; Gersing et al., 2024; Clausen et al., 2024).

      We have calculated the WCN as well as a contact number based on discrete counts of neighbouring residues for the six proteins in our dataset. When distances between residues are evaluated in the same way (i.e. using the shortest distance between any pair of heavy atoms in the side chains), and when the cutoff value used for the discrete count is equal to the r<sub>0</sub> of the WCN function, the continuous and discrete evaluations of residue contact numbers are highly and linearly correlated, and their rank correlation with the VAMP-seq data are very similar. We only observe minor contributions from residues far away in the structure on the WCN.

      Typos in SI figure captions e.g. Figure S8-11 "All predictions were performed using using...."

      Thank you for pointing this out. We have corrected the typos in Figure S8-11 (Figure S7-S10 in the revised manuscript).

      Personally, I'd appreciate a definition of these new substitution matrices under the constraints of rASA/WCN values. It was unclear to me until I read the code but we think that the definition is averaging the substitution matrix based on the clusters they are assigned to. If so, this could be straightforwardly defined in the method section with a heaviside step function.

      We have added a definition of the “buried” and “exposed” substitution matrices as a function of rASA in the methods section (“Definitions of buried and exposed residues” and “Definition of substitution matrices”) of the manuscript, as well as a definition of how we classified residues as either buried or exposed using both rASA and WCN as input. Our final substitution matrices, as shown in e.g. Fig. 2, do not depend on the WCN; only the substitution matrix results in Figure S6 (Figure S20 in the revised manuscript) depend on both WCN and rASA.

      Reviewer #2 (Recommendations for the authors):

      The following suggestions aim to strengthen the analysis and clarify the presentation of your findings:

      (1) Specific analyses to consider:

      (1.1) Analyze buried positions where the exposed matrix performs better. Understanding these cases might reveal properties of protein core regions that show unexpected mutational tolerance.

      We agree with the reviewer that a more detailed analysis of buried residues with exposed-like substitution profiles would be very interesting.

      We note that for proteins where the VAMP-seq score distribution is shifted towards high values (as it is the case for PTEN, TPMT and CYP2C9), our identification of such residues may be a result of the score distribution differences between the six datasets. To confidently identify mutationally tolerant core regions, it would be best to (a) correct for the distribution differences prior to the analysis or (b) focus the analysis on residues that fall far below the diagonal in Figure S18.

      In additional data (which can be found at https://github.com/KULL-Centre/_2024_Schulze_abundance-analysis)) ,we provide, for each of the proteins, a list of buried residues for which RMSD<sub>exposed</sub> <RMSD<sub>buried</sub> (for more than 95% of resampled substitution profiles, as described under 1.6). We have not analysed these residues further.

      (1.2) A systematic comparison of matrix-based vs. ΔΔG-based predictions could help understand both exposed sites that behave as buried (as analyzed in the paper) and buried sites that behave as exposed (1.1), potentially revealing mechanisms underlying abundance changes.

      In our revised manuscript, we have added additional analyses to compare matrixbased and ΔΔG-based predictions, focusing on exposed sites for which one prediction method captures variant effects on abundance considerably better the other prediction method. We have not investigated buried sites with exposed-like behaviour any further in this work.

      (1.3) Explore different normalization approaches when pooling data across proteins. In particular, consider using log(abundance score): if the experimental error in abundance measurements is multiplicative (which can be checked from the reported standard errors), then log transformation would convert this into a constant additive error, making the analysis more statistically sound.

      As we answer below to point 2.2, the abundance scores are, within each dataset, min-max normalised to nonsense and synonymous variant scores, and the score scale is thus in this way consistent across the six datasets. We have explained above and in the revised manuscript that abundance score distribution differences across datasets are likely partially a result of the FACS binning of assay-specific variant libraries. Using only the VAMP-seq scores (that is, without further information about the individual experiments), we cannot correct for the influence of the sorting strategy on the reported scores. A score normalisation across datasets that places all data points on a single scale would require inter-dataset references variant scores, which we do not have. We note that in a subsequent manuscript (Schulze et al, bioRxiv, 2025) we have attempted to take system- and experimentspecific score distributions into account. We now refer to this work in the revised manuscript.

      (1.4) Consider using correlation coefficients between predicted and observed abundance profiles as an alternative to RMSD, which is sensitive to the absolute values of the scores.

      We agree with the reviewer that using correlation coefficients to compare substitution profiles might also be useful, in particular for datasets with relatively unique VAMP-seq score distributions, such as the ASPA dataset. To explore this idea, we have repeated the analysis presented in Fig. S18 using the Pearson correlation coefficient r rather than the RMSD.

      As in Fig. S18, we derive r<sub>buried</sub> and r<sub>exposed</sub> for every residue in the six proteins, specifically by calculating r between the abundance score substitution profile of every individual residue and the average abundance score substitution profiles of buried and exposed residues. VAMP-seq data for the protein for which r<sub>buried</sub> and r<sub>exposed</sub> are evaluated is omitted from the calculation of average abundance score substitution profiles, and we use only monomer structures to determine whether residues are buried or exposed. 

      We show the results of this analysis in an Author response image 1 below. In each panel of the figure, r<sub>buried</sub> and r<sub>exposed</sub> are shown for individual residues of a single protein. Blue datapoints indicate residues that are solvent-exposed in the wild-type protein structures, and yellow datapoints indicate residues that are buried in the wild-type structures. Residues for which it is not the case that r<sub>buried</sub> < r<sub>exposed</sub> or r<sub>exposed</sub><r<sub>buried</sub> in more than 95% of 1000 resampled residue substitution profiles (see explanation of resampling method above) are coloured grey. “Acc.” is the balanced classification accuracy, calculated using all non-grey datapoints, indicating how many buried residues have buried-like substitution profiles (r<sub>exposed</sub><r<sub>buried</sub>) and how many solvent-exposed residues have exposed-like substitution profiles (r<sub>buried</sub> < r<sub>exposed</sub>). The classification accuracy per protein in this figure cannot be compared to the classification accuracy of the same protein in Fig. S18, since the number of datapoints used in the accuracy calculation differ between the r- and RMSD-based analyses. 

      Author response image 1.

      Comparing the r-based approach to the RMSD-based approach (Fig. S18), it is clear that the r-based method is less robust than the RMSD-based method for noisy and incomplete datasets. For the noisiest and most mutationally incomplete VAMP-seq datasets (i.e., PTEN, TPMT and CYP2C9) (Fig. 1), there are relatively few residues for which we with high confidence can determine if the substitution profile is more buried- or more exposed-like. When the VAMP-seq data is less noisy and has high mutational completeness, the r-based method becomes more robust and may thus be relevant in potential future work on new VAMP-seq data with small error bars.

      In conclusion, we find that RMSD-based approach to compare substitution profiles is more robust than an r-based approach for several of the VAMP-seq datasets that are included in our analysis. We do believe than an approach based on the correlation coefficient, or potentially several metrics, could be relevant to use, since abundance score distributions from VAMP-seq datasets can differ significantly across datasets. So as not to increase the length of the main text of our manuscript, we have not added this analysis to the revised manuscript.

      (1.5) Consider treating missing abundance scores as zero values, as they might indicate variants with very low abundance, rather than omitting them from the analysis.

      This suggestion would be most relevant for the PTEN, TPMT and CYP2C9 datasets, which all have a relatively small average mutational depth and completeness, as shown in Fig. 1B and 1C. To assess if setting missing abundance scores as zero values would be reasonable, we have compared the distributions of predicted ΔΔG values (from RaSP and ThermoMPNN) and of predicted abundance scores (from our exposure-based substitution matrices) for variants with reported and missing VAMP-seq data. We show the result in Author response image 2, with data aggregated across the six protein systems:

      Author response image 2.

      We find that variants with and without VAMP-seq data have similar ΔΔG score distributions and similar predicted abundance score distributions, and there is thus no clear enrichment of predicted loss of abundance for variants with missing VAMP-seq scores. This suggests that missing abundance scores do not necessarily indicate very low abundance. One cause of missing data might instead be problems with library generation (Matreyek et al, 2018, 2021).

      We show in Fig. S9 (Fig. S8 of the revised manuscript) that predicted scores for variants with experimental abundance scores of 0 are often overestimated for NUDT15, ASPA and PRKN, but this is not so much a problem for PTEN, TMPT and CYP2C9, the datasets with most missing scores. The lack of an enrichment of low abundance variants from the various predictors would thus still support that missing scores do not necessarily indicate low abundance.

      (1.6) Develop a proper statistical framework for comparing buried vs exposed predictions (whether using RMSD or correlations), including confidence intervals, rather than using arbitrary thresholds.

      As explained above and in the methods section of our revised manuscript, we have expanded our approach to compare the substitution profile of a residue to the average profiles of buried and exposed residues, and our method now accounts for the noise in the VAMP-seq data, making the analysis more statistically rigorous. In our expanded approach, we compare the substitution profiles of individual residues to the average profiles for buried and exposed residues 10,000 times per residue to get a residue-specific distribution of RMSD<sub>buried</sub> and RMSD<sub>exposed</sub> values. Individual RMSD<sub>buried</sub> and RMSD<sub>exposed</sub> values are calculated by resampling abundance scores from a Gaussian distribution defined by the experimentally reported abundance score and abundance score standard deviation per variant. We now only report a residue to have e.g. a buried-like substitution profile if RMSD<sub>buried</sub> < RMSD<sub>exposed</sub> in at least 95% of our samples. We do not recalculate average scores in substitution matrices for this analysis. We have updated the plots in our manuscript, e.g. in Fig. S18 and S19 of the revised version, to indicate which residues are confidently classified as buried- or exposed-like.

      (2) Presentation improvements:

      (2.1) In Figure 4, consider removing the average abundance scores, which are not directly related to the RMSD comparison being shown.

      We have decided to keep the average abundance scores in Fig. 4 (now Fig. 5), as we find the average abundance scores useful for guiding interpretation of the RMSD values. For example, an unusually small average abundance score with a relatively small standard deviation may explain a case where RMSD<sub>buried</sub> and RMSD<sub>exposed</sub> are both large. This is for example the case for residue G185 in ASPA. 

      In our preprint, the error bars on the average abundance scores in Fig. 4 (now Fig. 5) indicated the standard deviation across the abundance scores that were used to calculate the average per position. We have removed these error bars in the revised manuscript, as we realised that these were not necessarily helpful to the reader.

      (2.2) I am assuming that abundance scores are defined as the ratio abundance_variant/abundance_wt throughout the analysis, but I don't think this has been explicitly defined. If this is correct, please state it explicitly. In such case, log(abundance_score) would have a simple interpretation as the difference in abundance between variant and wild-type.

      Abundance scores are defined throughout the manuscript as sequence-based scores that have been min-max normalised to the abundance of nonsense and synonymous variants, i.e. abundance_score = (abundance_variant abundance_nonsense)/(abundance_wt–abundance_nonsense). We have described the normalisation of scores to wild-type and nonsense variant abundance in lines 164-166 of the original manuscript. We have now added additional information about the normalisation scheme in the methods section. We note that we did not ourselves apply this normalisation to the data; the scores were reported in this manner in the original publications that reported the VAMP-seq experiments for the six proteins.

      (2.3) Consider renaming "rASA" to the more commonly used "RSA" for relative solvent accessibility.

      We have decided to keep using “rASA” throughout the manuscript.

      (2.4) The weighted contact number function used differs from the established WCN measure (Σ1/rij²) introduced by Lin et al. (2008, Proteins). This should be acknowledged and the choice of alternative weighting scheme justified.

      As we have also responded to the first minor point of reviewer 1, we have previously found WCN, as it is defined in our manuscript, to be a useful input feature for a classifier that determines whether individual residues are important for maintaining protein abundance or function (Cagiada et al, 2023). We have also previously found this type of WCN to correlate well with variant abundance of individual proteins, as measured with VAMP-seq or protein fragment complementation assays (Grønbæk-Thygesen et al., 2024; Clausen et al., 2024; Gersing et al., 2024). We acknowledge that residue contact numbers or weighted contact numbers could also be expressed in other ways and that alternative contact number definitions would likely also produce values that correlate well with VAMP-seq data. Since the WCN, as defined in our manuscript, already correlates relatively well with abundance scores, we have not explored whether alternative definitions produce better correlations.  

      (2.5) Replace the phrase "in the above" with specific references to sections or simply "above" where appropriate. Also, consider replacing many instances of "moreover" with simpler alternatives such as "also" or "in addition" to improve readability.

      We have changed several sentences according to this suggestion and hope that we have improved the readability of our manuscript.

      Reviewer #3 (Recommendations for the authors):

      (1) It should be explicitly confirmed earlier that complex structures are used for NUDT15 and ASPA when assessing rASA/WCN. Additionally, it would be interesting to see the effect that deriving the matrices using NUDT15 and ASPA monomers would have.

      We have commented on the use of NUDT15 and ASPA homodimer structures earlier in the revised manuscript (specifically already in the subsection Abundance scores correlate with the degree of residue solvent-exposure section).

      When residues are classified using monomer rather than dimer structures of NUDT15 and ASPA, there is a small effect on the resulting “buried” and “exposed” substitution matrices. Entries in this set of substitution matrices calculated using either monomer or dimer structures typically differ by less than 0.05, and only a single entry differ by more than 0.1. As expected, the “exposed” matrix tend to contain slightly larger numbers when derived from dimer structures than when derived from monomer structures, meaning that when the interface residues are included in the exposed residue category, the average abundance scores of the “exposed” matrix are lowered. For buried residues, the picture is more mixed, although the overall tendency is that the interface residues make the “buried” matrix contain smaller average abundance scores for dimer compared to monomer structures. These results generally support the use of dimer structures for the residue classification.

      We here show the differences between the substitution matrices calculated with dimer or monomer structures of NUDT15 and ASPA and using data for all six proteins in our combined VAMP-seq dataset (average_abundance_score_differece = average_abundance_score_dimers – average_abundance_score _monomers):

      Author response image 3.

      We have not explored these alternative matrices further.

      (2) While the supplemental analyses are rigorous, the abundance of various metrics being presented can be confusing, especially when they seem to differ in their result. For instance, the discussion of Figure S17 (paragraph starting 428) contains mentions of mean differences but then switches to correlations, while both are presented for all panels. The claim "The datasets thus mainly differ due to differences in substitution effects in buried environments. " is well supported by the observed mean differences, but for Pearson's correlations the average panel A ,B values of buried 0.421 vs exposed 0.427 are hardly different. Which of the metrics is more meaningful, and are both needed?

      We agree with the reviewer that the claim that “The datasets thus mainly differ due to differences in substitution effects in buried environments” is not well-supported by the r between the substitution matrices, and we have removed this claim from the text.

      Since some datasets share VAMP-seq score distribution features, while others do not, the absolute difference between scores or matrices may be relevant to check for some dataset pairs, while the r may be more relevant to check for other dataset pairs. Hence, we have included both metrics in Fig S17 (Fig S11 in the revised manuscript).

      (3) Lines 337-340 - does not feel like S7 is the topic, perhaps the authors meant Figure 2A, B? In general, the supplemental figure references are out of order and panel combinations are sometimes confusing.

      We have corrected figures references to now be correct and changed the arrangement of supplemental figures so that they now occur in the correct order. We have looked through the panel combinations with clarity in mind, and hope that the current set of main and supplementary figures balances overview and detail.

      (4) Line 363 "are also are also".

      We have corrected this typo.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      The study analyzes the gastric fluid DNA content identified as a potential biomarker for human gastric cancer. However, the study lacks overall logicality, and several key issues require improvement and clarification. In the opinion of this reviewer, some major revisions are needed:

      (1) This manuscript lacks a comparison of gastric cancer patients' stages with PN and N+PD patients, especially T0-T2 patients.

      We are grateful for this astute remark. A comparison of gfDNA concentration among the diagnostic groups indicates a trend of increasing values as the diagnosis progresses toward malignancy. The observed values for the diagnostic groups are as follows:

      Author response table 1.

      The chart below presents the statistical analyses of the same diagnostic/tumor-stage groups (One-Way ANOVA followed by Tukey’s multiple comparison tests). It shows that gastric fluid gfDNA concentrations gradually increase with malignant progression. We observed that the initial tumor stages (T0 to T2) exhibit intermediate gfDNA levels, which in this group is significantly lower than in advanced disease (p = 0.0036), but not statistically different from non-neoplastic disease (p = 0.74).

      Author response image 1.

      (2) The comparison between gastric cancer stages seems only to reveal the difference between T3 patients and early-stage gastric cancer patients, which raises doubts about the authenticity of the previous differences between gastric cancer patients and normal patients, whether it is only due to the higher number of T3 patients.

      We appreciate the attention to detail regarding the numbers analyzed in the manuscript. Importantly, the results are meaningful because the number of subjects in each group is comparable (T0-T2, N = 65; T3, N = 91; T4, N = 63). The mean gastric fluid gfDNA values (ng/µL) increase with disease stage (T0-T2: 15.12; T3-T4: 30.75), and both are higher than the mean gfDNA values observed in non-neoplastic disease (10.81 ng/µL for N+PD and 10.10 ng/µL for PN). These subject numbers in each diagnostic group accurately reflect real-world data from a tertiary cancer center.

      (3) The prognosis evaluation is too simplistic, only considering staging factors, without taking into account other factors such as tumor pathology and the time from onset to tumor detection.

      Histopathological analyses were performed throughout the study not only for the initial diagnosis of tissue biopsies, but also for the classification of Lauren’s subtypes, tumor staging, and the assessment of the presence and extent of immune cell infiltrates. Regarding the time of disease onset, this variable is inherently unknown--by definition--at the time of a diagnostic EGD. While the prognosis definition is indeed straightforward, we believe that a simple, cost-effective, and practical approach is advantageous for patients across diverse clinical settings and is more likely to be effectively integrated into routine EGD practice.

      (4) The comparison between gfDNA and conventional pathological examination methods should be mentioned, reflecting advantages such as accuracy and patient comfort.

      We wish to reinforce that EGD, along with conventional histopathology, remains the gold standard for gastric cancer evaluation. EGD under sedation is routinely performed for diagnosis, and the collection of gastric fluids for gfDNA evaluation does not affect patient comfort. Thus, while gfDNA analysis was evidently not intended as a diagnostic EGD and biopsy replacement, it may provide added prognostic value to this exam.

      (5) There are many questions in the figures and tables. Please match the Title, Figure legends, Footnote, Alphabetic order, etc.

      We are grateful for these comments and apologize for the clerical oversight. All figures, tables, titles and figure legends have now been double-checked.

      (6) The overall logicality of the manuscript is not rigorous enough, with few discussion factors, and cannot represent the conclusions drawn.

      We assume that the unusual wording remark regarding “overall logicality” pertains to the rationale and/or reasoning of this investigational study. Our working hypothesis was that during neoplastic disease progression, tumor cells continuously proliferate and, depending on various factors, attract immune cell infiltrates. Consequently, both tumor cells and immune cells (as well as tumor-derived DNA) are released into the fluids surrounding the tumor at its various locations, including blood, urine, saliva, gastric fluids, and others. Thus, increases in DNA levels within some of these fluids have been documented and are clinically meaningful. The concurrent observation of elevated gastric fluid gfDNA levels and immune cell infiltration supports the hypothesis that increased gfDNA—which may originate not only from tumor cells but also from immune cells—could be associated with better prognosis, as suggested by this study of a large real-world patient cohort.

      In summary, we thank Reviewer #1 for his time and effort in a constructive critique of our work.

      Reviewer #2 (Public review):

      Summary:

      The authors investigated whether the total DNA concentration in gastric fluid (gfDNA), collected via routine esophagogastroduodenoscopy (EGD), could serve as a diagnostic and prognostic biomarker for gastric cancer. In a large patient cohort (initial n=1,056; analyzed n=941), they found that gfDNA levels were significantly higher in gastric cancer patients compared to non-cancer, gastritis, and precancerous lesion groups. Unexpectedly, higher gfDNA concentrations were also significantly associated with better survival prognosis and positively correlated with immune cell infiltration. The authors proposed that gfDNA may reflect both tumor burden and immune activity, potentially serving as a cost-effective and convenient liquid biopsy tool to assist in gastric cancer diagnosis, staging, and follow-up.

      Strengths:

      This study is supported by a robust sample size (n=941) with clear patient classification, enabling reliable statistical analysis. It employs a simple, low-threshold method for measuring total gfDNA, making it suitable for large-scale clinical use. Clinical confounders, including age, sex, BMI, gastric fluid pH, and PPI use, were systematically controlled. The findings demonstrate both diagnostic and prognostic value of gfDNA, as its concentration can help distinguish gastric cancer patients and correlates with tumor progression and survival. Additionally, preliminary mechanistic data reveal a significant association between elevated gfDNA levels and increased immune cell infiltration in tumors (p=0.001).

      Reviewer #2 has conceptually grasped the overall rationale of the study quite well, and we are grateful for their assessment and comprehensive summary of our findings.

      Weaknesses:

      (1) The study has several notable weaknesses. The association between high gfDNA levels and better survival contradicts conventional expectations and raises concerns about the biological interpretation of the findings.

      We agree that this would be the case if the gfDNA was derived solely from tumor cells. However, the findings presented here suggest that a fraction of this DNA would be indeed derived from infiltrating immune cells. The precise determination of the origin of this increased gfDNA remains to be achieved in future follow-up studies, and these are planned to be evaluated soon, by applying DNA- and RNA-sequencing methodologies and deconvolution analyses.

      (2) The diagnostic performance of gfDNA alone was only moderate, and the study did not explore potential improvements through combination with established biomarkers. Methodological limitations include a lack of control for pre-analytical variables, the absence of longitudinal data, and imbalanced group sizes, which may affect the robustness and generalizability of the results.

      Reviewer #2 is correct that this investigational study was not designed to assess the diagnostic potential of gfDNA. Instead, its primary contribution is to provide useful prognostic information. In this regard, we have not yet explored combining gfDNA with other clinically well-established diagnostic biomarkers. We do acknowledge this current limitation as a logical follow-up that must be investigated in the near future.

      Moreover, we collected a substantial number of pre-analytical variables within the limitations of a study involving over 1,000 subjects. Longitudinal samples and data were not analyzed here, as our aim was to evaluate prognostic value at diagnosis. Although the groups are imbalanced, this accurately reflects the real-world population of a large endoscopy center within a dedicated cancer facility. Subjects were invited to participate and enter the study before sedation for the diagnostic EGD procedure; thus, samples were collected prospectively from all consenting individuals.

      Finally, to maintain a large, unbiased cohort, we did not attempt to balance the groups, allowing analysis of samples and data from all patients with compatible diagnoses (please see Results: Patient groups and diagnoses).

      (3) Additionally, key methodological details were insufficiently reported, and the ROC analysis lacked comprehensive performance metrics, limiting the study's clinical applicability.

      We are grateful for this useful suggestion. In the current version, each ROC curve (Supplementary Figures 1A and 1B) now includes the top 10 gfDNA thresholds, along with their corresponding sensitivity and specificity values (please see Suppl. Table 1). The thresholds are ordered from-best-to-worst based on the classic Youden’s J statistic, as follows:

      Youden Index = specificity + sensitivity – 1 [Youden WJ. Index for rating diagnostic tests. Cancer 3:32-35, 1950. PMID: 15405679]. We have made an effort to provide all the key methodological details requested, but we would be glad to add further information upon specific request.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      This is an excellent study by a superb investigator who discovered and is championing the field of migrasomes. This study contains a hidden "gem" - the induction of migrasomes by hypotonicity and how that happens. In summary, an outstanding fundamental phenomenon (migrasomes) en route to becoming transitionally highly significant.

      Strengths:

      Innovative approach at several levels. Migrasomes - discovered by Dr Yu's group - are an outstanding biological phenomenon of fundamental interest and now of potentially practical value.

      Weaknesses:

      I feel that the overemphasis on practical aspects (vaccine), however important, eclipses some of the fundamental aspects that may be just as important and actually more interesting. If this can be expanded, the study would be outstanding.

      We sincerely thank the reviewer for the encouraging and insightful comments. We fully agree that the fundamental aspects of migrasome biology are of great importance and deserve deeper exploration.

      In line with the reviewer’s suggestion, we have expanded our discussion on the basic biology of engineered migrasomes (eMigs). A recent study by the Okochi group at the Tokyo Institute of Technology demonstrated that hypoosmotic stress induces the formation of migrasome-like vesicles, involving cytoplasmic influx and requiring cholesterol for their formation (DOI: 10.1002/1873-3468.14816, February 2024). Building on this, our study provides a detailed characterization of hypoosmotic stressinduced eMig formation, and further compares the biophysical properties of natural migrasomes and eMigs. Notably, the inherent stability of eMigs makes them particularly promising as a vaccine platform.

      Finally, we would like to note that our laboratory continues to investigate multiple aspects of migrasome biology. In collaboration with our colleagues, we recently completed a study elucidating the mechanical forces involved in migrasome formation (DOI: 10.1016/j.bpj.2024.12.029), which further complements the findings presented here.

      Reviewer #2 (Public review):

      Summary:

      The authors' report describes a novel vaccine platform derived from a newly discovered organelle called a migrasome. First, the authors address a technical hurdle in using migrasomes as a vaccine platform. Natural migrasome formation occurs at low levels and is labor intensive, however, by understanding the molecular underpinning of migrasome formation, the authors have designed a method to make engineered migrasomes from cultured, cells at higher yields utilizing a robust process. These engineered migrasomes behave like natural migrasomes. Next, the authors immunized mice with migrasomes that either expressed a model peptide or the SARSCoV-2 spike protein. Antibodies against the spike protein were raised that could be boosted by a 2nd vaccination and these antibodies were functional as assessed by an in vitro pseudoviral assay. This new vaccine platform has the potential to overcome obstacles such as cold chain issues for vaccines like messenger RNA that require very stringent storage conditions.

      Strengths:

      The authors present very robust studies detailing the biology behind migrasome formation and this fundamental understanding was used to form engineered migrasomes, which makes it possible to utilize migrasomes as a vaccine platform. The characterization of engineered migrasomes is thorough and establishes comparability with naturally occurring migrasomes. The biophysical characterization of the migrasomes is well done including thermal stability and characterization of the particle size (important characterizations for a good vaccine).

      Weaknesses:

      With a new vaccine platform technology, it would be nice to compare them head-tohead against a proven technology. The authors would improve the manuscript if they made some comparisons to other vaccine platforms such as a SARS-CoV-2 mRNA vaccine or even an adjuvanted recombinant spike protein. This would demonstrate a migrasome-based vaccine could elicit responses comparable to a proven vaccine technology. 

      We thank the reviewer for the thoughtful evaluation and constructive suggestions, which have helped us strengthen the manuscript. 

      Comparison with proven vaccine technologies:

      In response to the reviewer’s comment, we now include a direct comparison of the antibody responses elicited by eMig-Spike and a conventional recombinant S1 protein vaccine formulated with Alum. As shown in the revised manuscript (Author response image 1), the levels of S1-specific IgG induced by the eMig-based platform were comparable to those induced by the S1+Alum formulation. This comparison supports the potential of eMigs as a competitive alternative to established vaccine platforms. 

      Author response image 1.

      eMigrasome-based vaccination showed similar efficacy compared with adjuvanted recombinant spike protein The amount of S1-specific IgG in mouse serum was quantified by ELISA on day 14 after immunization. Mice were either intraperitoneally (i.p.) immunized with recombinant Alum/S1 or intravenously (i.v.) immunized with eM-NC, eM-S or recombinant S1. The administered doses were 20 µg/mouse for eMigrasomes, 10 µg/mouse (i.v.) or 50 µg/mouse (i.p.) for recombinant S1 and 50 µl/mouse for Aluminium adjuvant.

      Assessment of antigen integrity on migrasomes:

      To address the reviewer’s suggestion regarding antigen integrity, we performed immunoblotting using antibodies against both S1 and mCherry. Two distinct bands were observed: one at the expected molecular weight of the S-mCherry fusion protein, and a higher molecular weight band that may represent oligomerized or higher-order forms of the Spike protein (Figure 5b in the revised manuscript).

      Furthermore, we performed confocal microscopy using a monoclonal antibody against Spike (anti-S). Co-localization analysis revealed strong overlap between the mCherry fluorescence and anti-Spike staining, confirming the proper presentation and surface localization of intact S-mCherry fusion protein on eMigs (Figure 5c in the revised manuscript). These results confirm the structural integrity and antigenic fidelity of the Spike protein expressed on eMigs.

      Recommendations for the authors

      Reviewer #1 (Recommendations For The Authors):

      I feel that the overemphasis on practical aspects (vaccine), however important, eclipses some of the fundamental aspects that may be just as important and actually more interesting. If this can be expanded, the study would be outstanding.

      I know that the reviewers always ask for more, and this is not the case here. Can the abstract and title be changed to emphasize the science behind migrasome formation, and possibly add a few more fundamental aspects on how hypotonic shock induces migrasomes?

      Alternatively, if the authors desire to maintain the emphasis on vaccines, can immunological mechanisms be somewhat expanded in order to - at least to some extent - explain why migrasomes are a better vaccine vehicle?

      One way or another, this reviewer is highly supportive of this study and it is really up to the authors and the editor to decide whether my comments are of use or not.

      My recommendation is to go ahead with publishing after some adjustments as per above.

      We’d like to thank the reviewer for the suggestion. We have changed the title of the manuscript and modified the abstract, emphasizing the fundamental science behind the development of eMigrasome. To gain some immunological information on eMig illucidated antibody responses, we characterized the type of IgG induced by eM-OVA in mice, and compared it to that induced by Alum/OVA. The IgG response to Alum/OVA was dominated by IgG1. Quite differently, eM-OVA induced an even distribution of IgG subtypes, including IgG1, IgG2b, IgG2c, and IgG3 (Figure 4i in the revised manuscript). The ratio between IgG1 and IgG2a/c indicates a Th1 or Th2 type humoral immune response. Thus, eM-OVA immunization induces a balance of Th1/Th2 immune responses.

      Reviewer #2 (Recommendations For The Authors):

      The study is a very nice exploration of a new vaccine platform. This reviewer believes that a more head-to-head comparison to the current vaccine SARS-CoV-2 vaccine platform would improve the manuscript. This comparison is done with OVA antigen, but this model antigen is not as exciting as a functional head-to-head with a SARS-CoV-2 vaccine.

      I think that two other discussion points should be included in the manuscript. First, was the host-cell protein evaluated? If not, I would include that point on how issues of host cell contamination of the migrasome could play a role in the responses and safety of a vaccine. Second, I would discuss antigen incorporation and localization into the platform. For example, the full-length spike being expressed has a native signal peptide and transmembrane domain. The authors point out that a transmembrane domain can be added to display an antigen that does not have one natively expressed, however, without a signal peptide this would not be secreted and localized properly. I would suggest adding a discussion of how a non-native signal peptide would be necessary in addition to a transmembrane domain.

      We thank the reviewer for these thoughtful suggestions and fully agree that the points raised are important for the translational development of eMig-based vaccines.

      (1) Host cell proteins and potential immunogenicity:

      We appreciate the reviewer’s suggestion to consider host cell protein contamination. Considering potential clinical application of eMigrasomes in the future, we will use human cells with low immunogenicity such as HEK-293 or embryonic stem cells (ESCs) to generate eMigrasomes. Also, we will follow a QC that meets the standard of validated EV-based vaccination techniques. 

      (2) Antigen incorporation and localization—signal peptide and transmembrane domain:

      We also agree with the reviewer’s point that proper surface display of antigens on eMigs requires both a transmembrane domain and a signal peptide for correct trafficking and membrane anchoring. For instance, in the case of full-length Spike protein, the native signal peptide and transmembrane domain ensure proper localization to the plasma membrane and subsequent incorporation into eMigs. In case of OVA, a secretary protein that contains a native signal peptide yet lacks a transmembrane domain, an engineered transmembrane domain is required. For antigens that do not naturally contain these features, both a non-native signal peptide and an artificial transmembrane domain are necessary. We have clarified this point in the revised discussion and explicitly noted the requirement for a signal peptide when engineering antigens for surface display on migrasomes.

    1. Author response:

      The following is the authors’ response to the original reviews

      We again thank the reviewers for their comments and recommendations. In response to the reviewer’s suggestions, we have performed several additional experiments, added additional discussion, and updated our conclusions to reflect the additional work. Specifically, we have performed additional analyses in female WT and Marco-deficient animals, demonstrating that the Marco-associated phonotypes observed in male mice (reduced adrenal weight, increased lung Ace mRNA and protein expression, unchanged expression of adrenal corticosteroid biosynthetic enzymes) are not present in female mice. We also report new data on the physiological consequences of increased aldosterone levels observed in male mice, namely plasma sodium and potassium titres, and blood pressure alterations in WT vs Marco-deficient male mice. In an attempt to address the reviewer’s comments relating to our proposed mechanism on the regulation of lung Ace expression, we additionally performed a co-culture experiment using an alveolar macrophage cell line and an endothelial cell line. In light of the additional evidence presented herein, we have updated our conclusions from this study and changed the title of our work to acknowledge that the mechanism underlying the reported phenotype remains incompletely understood. Specific responses to reviewers can be seen below.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The investigators sought to determine whether Marco regulates the levels of aldosterone by limiting uptake of its parent molecule cholesterol in the adrenal gland. Instead, they identify an unexpected role for Marco on alveolar macrophages in lowering the levels of angiotensin-converting enzyme in the lung. This suggests an unexpected role of alveolar macrophages and lung ACE in the production of aldosterone.

      Strengths:

      The investigators suggest an unexpected role for ACE in the lung in the regulation of systemic aldosterone levels.

      The investigators suggest important sex-related differences in the regulation of aldosterone by alveolar macrophages and ACE in the lung.

      Studies to exclude a role for Marco in the adrenal gland are strong, suggesting an extra-adrenal source for the excess Marco observed in male Marco knockout mice.

      Weaknesses:

      While the investigators have identified important sex differences in the regulation of extrapulmonary ACE in the regulation of aldosterone levels, the mechanisms underlying these differences are not explored.

      The physiologic impact of the increased aldosterone levels observed in Marco -/- male mice on blood pressure or response to injury is not clear.

      The intracellular signaling mechanism linking lung macrophage levels with the expression of ACE in the lung is not supported by direct evidence.

      Reviewer #2 (Public Review):

      Summary:

      Tissue-resident macrophages are more and more thought to exert key homeostatic functions and contribute to physiological responses. In the report of O'Brien and Colleagues, the idea that the macrophage-expressed scavenger receptor MARCO could regulate adrenal corticosteroid output at steady-state was explored. The authors found that male MARCO-deficient mice exhibited higher plasma aldosterone levels and higher lung ACE expression as compared to wild-type mice, while the availability of cholesterol and the machinery required to produce aldosterone in the adrenal gland were not affected by MARCO deficiency. The authors take these data to conclude that MARCO in alveolar macrophages can negatively regulate ACE expression and aldosterone production at steady-state and that MARCO-deficient mice suffer from secondary hyperaldosteronism.

      Strengths:

      If properly demonstrated and validated, the fact that tissue-resident macrophages can exert physiological functions and influence endocrine systems would be highly significant and could be amenable to novel therapies.

      Weaknesses:

      The data provided by the authors currently do not support the major claim of the authors that alveolar macrophages, via MARCO, are involved in the regulation of a hormonal output in vivo at steady-state. At this point, there are two interesting but descriptive observations in male, but not female, MARCO-deficient animals, and overall, the study lacks key controls and validation experiments, as detailed below.

      Major weaknesses:

      (1) According to the reviewer's own experience, the comparison between C57BL/6J wild-type mice and knock-out mice for which precise information about the genetic background and the history of breedings and crossings is lacking, can lead to misinterpretations of the results obtained. Hence, MARCO-deficient mice should be compared with true littermate controls.

      (2) The use of mice globally deficient for MARCO combined with the fact that alveolar macrophages produce high levels of MARCO is not sufficient to prove that the phenotype observed is linked to alveolar macrophage-expressed MARCO (see below for suggestions of experiments).

      (3) If the hypothesis of the authors is correct, then additional read-outs could be performed to reinforce their claims: levels of Angiotensin I would be lower in MARCO-deficient mice, levels of Antiotensin II would be higher in MARCO-deficient mice, Arterial blood pressure would be higher in MARCO-deficient mice, natremia would be higher in MARCO-deficient mice, while kaliemia would be lower in MARCO-deficient mice. In addition, co-culture experiments between MARCO-sufficient or deficient alveolar macrophages and lung endothelial cells, combined with the assessment of ACE expression, would allow the authors to evaluate whether the AM-expressed MARCO can directly regulate ACE expression.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) Corticosterone levels in male Marco -/- mice are not significantly different, but there is (by eye) substantially more variability in the knockout compared to the wild type. A power analysis should be performed to determine the number of mice needed to detect a similar % difference in corticosterone to the difference observed in aldosterone between male Marco knockout and wild-type mice. If necessary the experiments should be repeated with an adequately powered cohort.

      Using a power calculator (www.gigacalculator.com) it was determined that our sample size of 13 was one less than sufficient to detect a similar % difference in corticosterone as was detected in corticosterone. We regret that we unable to perform additional measurements as the author suggested in the available timeframe.

      (2) All of the data throughout the MS (particularly data in the lung) should be presented in male and female mice. For example, the induction of ACE in the lungs of Marco-/- female mice should be absent. Similar concerns relate to the dexamethasone suppression studies. Also would be useful if the single cell data could be examined by sex--should be possible even post hoc using Xist etc.

      Given the limitations outlined in our previous response to reviewers it was not possible to repeat every experiment from the original manuscript. We were able to measure the expression of lung Ace mRNA, ACE protein, adrenal weights, adrenal expression of steroid biosynthetic enzymes, presence of myeloid cells, and levels of serum electrolytes in female animals. These are presented in figures 1G, 3B, 4A, 4E, 4F, 4I, and 4J. We have elected to not present single cell seq data according to sex as it did not indicate substantial differences between males and females in Marco or Ace expression and so does not substantively change our approach.

      (3) IF is notoriously unreliable in the lung, which has high levels of autofluorescence. This is the only method used to show ACE levels are increased in the absence of Marco. Orthogonal methods (e.g. immunoblots of flow-sorted cells, or ideally CITE-seq that includes both male and female mice) should be used.

      We used negative controls to guide our settings during acquisition of immunofluorescent images. Additionally, we also used qPCR to show an increase in Ace mRNA expression in the lung in addition to the protein level. This data was presented in the original manuscript and is further bolstered by our additional presentation of expression data for Ace mRNA and protein in female animals in this revised manuscript.

      (4) Given the central importance of ACE staining to the conclusions, validation of the antibody should be included in the supplement.

      We don’t have ACE-deficient mice so cannot do KO validation of the antibody. We did perform secondary stain controls which confirmed the signal observed is primary antibody-derived. Moreover, we specifically chose an anti-ACE antibody (Invitrogen catalogue # MA5-32741) that has undergone advanced verification with the manufacturer. We additionally tested the antibody in the brain and liver and observed no significant levels of staining.

      Author response image 1.

      (5) The link between alveolar macrophage Marco and ACE is poorly explored.

      We carried out a co-culture experiments of alveolar macrophages and endothelial cells and measure ACE/Ace expression as a consequence. This is presented in figure 5D and the discussion.

      (6) Mechanisms explaining the substantial sex difference in the primary outcome are not explored.

      This is outside the scope if this project, though we would consider exploring such experiments in future studies.

      (7) Are there physiologic consequences either in homeostasis or under stress to the increased aldosterone (or lung ACE levels) observed in Marco-/- male mice?

      We measured blood electrolytes and blood pressure in Marco-deficient and Marco-sufficient mice. The results from these experiments are presented in 4G-4M.

      Reviewer #2 (Recommendations For The Authors):

      Below is a suggestion of important control or validation experiments to be performed in order to support the authors' claims.

      (1) It is imperative to validate that the phenotype observed in MARCO-deficient mice is indeed caused by the deficiency in MARCO. To this end, littermate mice issued from the crossing between heterozygous MARCO +/- mice should be compared to each other. C57BL/6J mice can first be crossed with MARCO-deficient mice in F0, and F1 heterozygous MARCO +/- mice should be crossed together to produce F2 MARCO +/+, MARCO +/- and MARCO -/- littermate mice that can be used for experiments.

      We thank the reviewer for their comments. We recognise the concern of the reviewer but due to limited experimenter availability we are unable to undertake such a breeding programme to address this particular concern.

      (2) The use of mice in which AM, but not other cells, lack MARCO expression would demonstrate that the effect is indeed linked to AM. To this end, AM-deficient Csf2rb-deficient mice could be adoptively transferred with MARCO-deficient AM. In addition, the phenotype of MARCO-deficient mice should be restored by the adoptive transfer of wild-type, MARCO-expressing AM. Alternatively, bone marrow chimeras in which only the hematopoietic compartment is deficient in MARCO would be another option, albeit less specific for AM.

      We recognise the concern of the reviewer. We carried out a co-culture experiments of alveolar macrophages and endothelial cells and measure ACE/Ace expression as a consequence. This is presented in figure 5D and the implications explored in the discussion.

      (3) If the hypothesis of the authors is correct, then additional read-outs could be performed to reinforce their claims: levels of Angiotensin I would be lower in MARCO-deficient mice, levels of Antiotensin II would be higher in MARCO-deficient mice, Arterial blood pressure would be higher in MARCO-deficient mice, natremia would be higher in MARCO-deficient mice, while kaliemia would be lower in MARCO-deficient mice. Similar read-outs could also be performed in the models proposed in point 2).

      We measured blood electrolytes and blood pressure in Marco-deficient and Marco-sufficient mice. The results from these experiments are presented in 4G-4M.

      (4) Co-culture experiments between MARCO-sufficient or deficient alveolar macrophages and lung endothelial cells, combined with the assessment of ACE expression, would allow the authors to evaluate whether the AM-expressed MARCO can directly regulate ACE expression.

      To address this concern we carried out a co-culture experiment as described above.

    1. Author response:

      General Statements

      We are delighted that all reviewers found our manuscript to be a technical advance by providing a much sought after method to arrest budding yeast cells in metaphase of mitosis or both meiotic metaphases. The reviewers also valued our use of this system to make new discoveries in two areas. First, we provided evidence that the spindle checkpoint is intrinsically weaker in meiosis I and showed that this is due to PP1 phosphatase. Second, we determined how the composition and phosphorylation of the kinetochore changes during meiosis, providing key insights into kinetochore function and providing a rich dataset for future studies.

      The reviewers also made some extremely helpful suggestions to improve our manuscript, which we will now implement:

      (1) Improvements to the discussion throughout the manuscript. The reviewers recommended that we focus our discussion on the novel findings of the manuscript and drew out some key points of interest that deserve more attention. We fully agree with this and we will address this in a revised version.

      (2) We will add a new supplemental figure to help interpret the mass spectrometry data, to address Reviewer #3, point 4.

      (3) We are currently performing an additional control experiment to address the minor point 1 from reviewer #3. Our experiment to confirm that SynSAC relies on endogenous checkpoint proteins was missing the cell cycle profile of cells where SynSAC was not induced for comparison. We will add this control to our full revision.

      (4) In our full revision we will also include representative images of spindle morphology as requested by Reviewer #1, point 2

      Description of the planned revisions

      Reviewer #1 (Evidence, reproducibility and clarity):

      These authors have developed a method to induce MI or MII arrest. While this was previously possible in MI, the advantage of the method presented here is that it works for MII, and chemically inducible because it is based on a system that is sensitive to the addition of ABA. Depending on when the ABA is added, they achieve a MI or MII delay. The ABA promotes dimerizing fragments of Mps1 and Spc105 that can't bind their chromosomal sites. The evidence that the MI arrest is weaker than the MII arrest is convincing and consistent with published data and indicating the SAC in MI is less robust than MII or mitosis. The authors use this system to find evidence that the weak MI arrest is associated with PP1 binding to Spc105. This is a nice use of the system.

      The remainder of the paper uses the SynSAC system to isolate populations enriched for MI or MII stages and conduct proteomics. This shows a powerful use of the system but more work is needed to validate these results, particularly in normal cells.

      Overall the most significant aspect of this paper is the technical achievement, which is validated by the other experiments. They have developed a system and generated some proteomics data that maybe useful to others when analyzing kinetochore composition at each division. Overall, I have only a few minor suggestions.

      We appreciate the reviewers’ support of our study.

      (1) In wild-type - Pds1 levels are high during M1 and A1, but low in MII. Can the authors comment on this? In line 217, what is meant by "slightly attenuated? Can the authors comment on how anaphase occurs in presence of high Pds1? There is even a low but significant level in MII.

      The higher levels of Pds1 in meiosis I compared to meiosis II has been observed previously using immunofluorescence and live imaging[1–3]. Although the reasons are not completely clear, we speculate that there is insufficient time between the two divisions to re-accumulate Pds1 prior to separase re-activation.

      We agree “slightly attenuated” was confusing and we have re-worded this sentence to read “Addition ABA at the time of prophase release resulted in Pds1securin stabilisation throughout the time course, consistent with delays in both metaphase I and II”.

      We do not believe that either anaphase I or II occur in the presence of high Pds1. Western blotting represents the amount of Pds1 in the population of cells at a given time point. The time between meiosis I and II is very short even when treated with ABA. For example, in Figure 2B, spindle morphology counts show that the anaphase I peak is around 40% at its maxima (105 min) and around 40% of cells are in either metaphase I or metaphase II, and will be Pds1 positive. In contrast, due to the better efficiency of meiosis II, anaphase II hardly occurs at all in these conditions, since anaphase II spindles (and the second nuclear division) are observed at very low frequency (maximum 10%) from 165 minutes onwards. Instead, metaphase II spindles partially or fully breakdown, without undergoing anaphase extension. Taking Pds1 levels from the western blot and the spindle data together leads to the conclusion that at the end of the time-course, these cells are biochemically in metaphase II, but unable to maintain a robust spindle. Spindle collapse is also observed in other situations where meiotic exit fails, and potentially reflects an uncoupling of the cell cycle from the programme governing gamete differentiation[3–5]. We will explain this point in a revised version while referring to representative images that from evidence for this, as also requested by the reviewer below.

      (2) The figures with data characterizing the system are mostly graphs showing time course of MI and MII. There is no cytology, which is a little surprising since the stage is determined by spindle morphology. It would help to see sample sizes (ie. In the Figure legends) and also representative images. It would also be nice to see images comparing the same stage in the SynSAC cells versus normal cells. Are there any differences in the morphology of the spindles or chromosomes when in the SynSAC system?

      This is an excellent suggestion and will also help clarify the point above. We will provide images of cells at the different stages. For each timepoint, 100 cells were scored. We have already included this information in the figure legends 

      (3) A possible criticism of this system could be that the SAC signal promoting arrest is not coming from the kinetochore. Are there any possible consequences of this? In vertebrate cells, the RZZ complex streams off the kinetochore. Yeast don't have RZZ but this is an example of something that is SAC dependent and happens at the kinetochore. Can the authors discuss possible limitations such as this? Does the inhibition of the APC effect the native kinetochores? This could be good or bad. A bad possibility is that the cell is behaving as if it is in MII, but the kinetochores have made their microtubule attachments and behave as if in anaphase.

      In our view, the fact that SynSAC does not come from kinetochores is a major advantage as this allows the study of the kinetochore in an unperturbed state. It is also important to note that the canonical checkpoint components are all still present in the SynSAC strains, and perturbations in kinetochore-microtubule interactions would be expected to mount a kinetochore-driven checkpoint response as normal. Indeed, it would be interesting in future work to understand how disrupting kinetochore-microtubule attachments alters kinetochore composition (presumably checkpoint proteins will be recruited) and phosphorylation but this is beyond the scope of this work. In terms of the state at which we are arresting cells – this is a true metaphase because cohesion has not been lost but kinetochore-microtubule attachments have been established. This is evident from the enrichment of microtubule regulators but not checkpoint proteins in the kinetochore purifications from metaphase I and II. While this state is expected to occur only transiently in yeast, since the establishment of proper kinetochore-microtubule attachments triggers anaphase onset, the ability to capture this properly bioriented state will be extremely informative for future studies. We appreciate the reviewers’ insight in highlighting these interesting discussion points which we will include in a revised version.

      Reviewer #1 (Significance):

      These authors have developed a method to induce MI or MII arrest. While this was previously possible in MI, the advantage of the method presented here is it works for MII, and chemically inducible because it is based on a system that is sensitive to the addition of ABA. Depending on when the ABA is added, they achieve a MI or MII delay. The ABA promotes dimerizing fragments of Mps1 and Spc105 that can't bind their chromosomal sites. The evidence that the MI arrest is weaker than the MII arrest is convincing and consistent with published data and indicating the SAC in MI is less robust than MII or mitosis. The authors use this system to find evidence that the weak MI arrest is associated with PP1 binding to Spc105. This is a nice use of the system.

      The remainder of the paper uses the SynSAC system to isolate populations enriched for MI or MII stages and conduct proteomics. This shows a powerful use of the system but more work is needed to validate these results, particularly in normal cells.

      Overall the most significant aspect of this paper is the technical achievement, which is validated by the other experiments. They have developed a system and generated some proteomics data that maybe useful to others when analyzing kinetochore composition at each division.

      We appreciate the reviewer’s enthusiasm for our work.

      Reviewer #2 (Evidence, reproducibility and clarity):

      The manuscript submitted by Koch et al. describes a novel approach to collect budding yeast cells in metaphase I or metaphase II by synthetically activating the spinde checkpoint (SAC). The arrest is transient and reversible. This synchronization strategy will be extremely useful for studying meiosis I and meiosis II, and compare the two divisions. The authors characterized this so-named syncSACapproach and could confirm previous observations that the SAC arrest is less efficient in meiosis I than in meiosis II. They found that downregulation of the SAC response through PP1 phosphatase is stronger in meiosis I than in meiosis II. The authors then went on to purify kinetochore-associated proteins from metaphase I and II extracts for proteome and phosphoproteome analysis. Their data will be of significant interest to the cell cycle community (they compared their datasets also to kinetochores purified from cells arrested in prophase I and -with SynSAC in mitosis).

      I have only a couple of minor comments:

      (1) I would add the Suppl Figure 1A to main Figure 1A. What is really exciting here is the arrest in metaphase II, so I don't understand why the authors characterize metaphase I in the main figure, but not metaphase II. But this is only a suggestion.

      This is a good suggestion, we will do this in our full revision.

      (2) Line 197, the authors state: “...SyncSACinduced a more pronounced delay in metaphase II than in metaphase I”. However, line 229 and 240 the authors talk about a "longer delay in metaphase <i compared to metaphase II"... this seems to be a mix-up.

      Thank you for pointing this out, this is indeed a typo and we have corrected it.

      (3) The authors describe striking differences for both protein abundance and phosphorylation for key kinetochore associated proteins. I found one very interesting protein that seems to be very abundant and phosphorylated in metaphase I but not metaphase II, namely Sgo1. Do the authors think that Sgo1 is not required in metaphase II anymore? (Top hit in suppl Fig 8D).

      This is indeed an interesting observation, which we plan to investigate as part of another study in the future. Indeed, data from mouse indicates that shugoshin-dependent cohesin deprotection is already absent in meiosis II in mouse oocytes[6], though whether this is also true in yeast is not known. Furthermore, this does not rule out other functions of Sgo1 in meiosis II (for example promoting biorientation). We will include this point in the discussion.

      Reviewer #2 (Significance):

      The technique described here will be of great interest to the cell cycle community. Furthermore, the authors provide data sets on purified kinetochores of different meiotic stages and compare them to mitosis. This paper will thus be highly cited, for the technique, and also for the application of the technique.

      Reviewer #3 (Evidence, reproducibility and clarity):

      In their manuscript, Koch et al. describe a novel strategy to synchronize cells of the budding yeast Saccharomyces cerevisiae in metaphase I and metaphase II, thereby facilitating comparative analyses between these meiotic stages. This approach, termed SynSAC, adapts a method previously developed in fission yeast and human cells that enables the ectopic induction of a synthetic spindle assembly checkpoint (SAC) arrest by conditionally forcing the heterodimerization of two SAC components upon addition of the plant hormone abscisic acid (ABA). This is a valuable tool, which has the advantage that induces SAC-dependent inhibition of the anaphase promoting complex without perturbing kinetochores. Furthermore, since the same strategy and yeast strain can be also used to induce a metaphase arrest during mitosis, the methodology developed by Koch et al. enables comparative analyses between mitotic and meiotic cell divisions. To validate their strategy, the authors purified kinetochores from meiotic metaphase I and metaphase II, as well as from mitotic metaphase, and compared their protein composition and phosphorylation profiles. The results are presented clearly and in an organized manner.

      We are grateful to the reviewer for their support.

      Despite the relevance of both the methodology and the comparative analyses, several main issues should be addressed:

      (1) In contrast to the strong metaphase arrest induced by ABA addition in mitosis (Supp. Fig. 2), the SynSAC strategy only promotes a delay in metaphase I and metaphase II as cells progress through meiosis. This delay extends the duration of both meiotic stages, but does not markedly increase the percentage of metaphase I or II cells in the population at a given timepoint of the meiotic time course (Fig. 1C). Therefore, although SynSAC broadens the time window for sample collection, it does not substantially improve differential analyses between stages compared with a standard NDT80 prophase block synchronization experiment. Could a higher ABA concentration or repeated hormone addition improve the tightness of the meiotic metaphase arrest?

      For many purposes the enrichment and extended time for sample collection is sufficient, as we demonstrate here. However, as pointed out by the reviewer below, the system can be improved by use of the 4A-RASA mutations to provide a stronger arrest (see our response below). We did not experiment with higher ABA concentrations or repeated addition since the very robust arrest achieved with the 4A-RASA mutant deemed this unnecessary.

      (2) Unlike the standard SynSAC strategy, introducing mutations that prevent PP1 binding to the SynSAC construct considerably extended the duration of the meiotic metaphase arrests. In particular, mutating PP1 binding sites in both the RVxF (RASA) and the SILK (4A) motifs of the Spc105(1-455)-PYL construct caused a strong metaphase I arrest that persisted until the end of the meiotic time course (Fig. 3A). This stronger and more prolonged 4A-RASA SynSAC arrest would directly address the issue raised above. It is unclear why the authors did not emphasize more this improved system. Indeed, the 4A-RASA SynSAC approach could be presented as the optimal strategy to induce a conditional metaphase arrest in budding yeast meiosis, since it not only adapts but also improves the original methods designed for fission yeast and human cells. Along the same lines, it is surprising that the authors did not exploit the stronger arrest achieved with the 4A-RASA mutant to compare kinetochore composition at meiotic metaphase I and II.

      We agree that the 4A-RASA mutant is the best tool to use for the arrest and going forward this will be our approach. We collected the proteomics data and the data on the SynSAC mutant variants concurrently, so we did not know about the improved arrest at the time the proteomics experiment was done. Because very good arrest was already achieved with the unmutated SynSAC construct, we could not justify repeating the proteomics experiment which is a large amount of work using significant resources. However, we will highlight the potential of the 4A-RASA mutant more prominently in our full revision.

      (3) The results shown in Supp. Fig. 4C are intriguing and merit further discussion. Mitotic growth in ABA suggest that the RASA mutation silences the SynSAC effect, yet this was not observed for the 4A or the double 4A-RASA mutants. Notably, in contrast to mitosis, the SynSAC 4A-RASA mutation leads to a more pronounced metaphase I meiotic delay (Fig. 3A). It is also noteworthy that the RVAF mutation partially restores mitotic growth in ABA. This observation supports, as previously demonstrated in human cells, that Aurora B-mediated phosphorylation of S77 within the RVSF motif is important to prevent PP1 binding to Spc105 in budding yeast as well.

      We agree these are intriguing findings that highlight key differences as to the wiring of the spindle checkpoint in meiosis and mitosis and potential for future studies, however, currently we can only speculate as to the underlying cause. The effect of the RASA mutation in mitosis is unexpected and unexplained. However, the fact that the 4A-RASA mutation causes a stronger delay in meiosis I compared to mitosis can be explained by a greater prominence of PP1 phosphatase in meiosis. Indeed, our data (Figure 4A) show that the PP1 phosphatase Glc7 and its regulatory subunit Fin1 are highly enriched on kinetochores at all meiotic stages compared to mitosis.

      We agree that the improved growth of the RVAF mutant is intriguing and points to a role of Aurora B-mediated phosphorylation, though previous work has not supported such a role [7].

      We will include a discussion of these important points in a revised version.

      (4) To demonstrate the applicability of the SynSAC approach, the authors immunoprecipitated the kinetochore protein Dsn1 from cells arrested at different meiotic or mitotic stages, and compared kinetochore composition using data independent acquisition (DIA) mass spectrometry. Quantification and comparative analyses of total and kinetochore protein levels were conducted in parallel for cells expressing either FLAG-tagged or untagged Dsn1 (Supp. Fig. 7A-B). To better detect potential changes, protein abundances were next scaled to Dsn1 levels in each sample (Supp. Fig. 7C-D). However, it is not clear why the authors did not normalize protein abundance in the immunoprecipitations from tagged samples at each stage to the corresponding untagged control, instead of performing a separate analysis. This would be particularly relevant given the high sensitivity of DIA mass spectrometry, which enabled quantification of thousands of proteins. Furthermore, the authors compared protein abundances in tagged-samples from mitotic metaphase and meiotic prophase, metaphase I and metaphase II (Supp. Fig. 7E-F). If protein amounts in each case were not normalized to the untagged controls, as inferred from the text (lines 333 to 338), the observed differences could simply reflect global changes in protein expression at different stages rather than specific differences in protein association to kinetochores.

      While we agree with the reviewer that at first glance, normalising to no tag appears to be the most appropriate normalisation, in practice there is very low background signal in the no tag sample which means that any random fluctuations have a big impact on the final fold change used for normalisation. This approach therefore introduces artefacts into the data rather than improving normalisation.

      To provide reassurance that our kinetochore immunoprecipitations are specific, and that the background (no tag) signal is indeed very low, we will provide a new supplemental figure showing the volcanos comparing kinetochore purifications at each stage with their corresponding no tag control.

      It is also important to note that our experiment looks at relative changes of the same protein over time, which we expect to be relatively small in the whole cell lysate. We previously documented proteins that change in abundance in whole cell lysates throughout meiosis[8]. In this study, we found that relatively few proteins significantly change in abundance.

      Our aim in the current study was to understand how the relative composition of the kinetochore changes and for this, we believe that a direct comparison to Dsn1, a central kinetochore protein which we immunoprecipitated is the most appropriate normalisation.

      (5) Despite the large amount of potentially valuable data generated, the manuscript focuses mainly on results that reinforce previously established observations (e.g., premature SAC silencing in meiosis I by PP1, changes in kinetochore composition, etc.). The discussion would benefit from a deeper analysis of novel findings that underscore the broader significance of this study.

      We strongly agree with this point and we will re-frame the discussion to focus on the novel findings, as also raised by the other reviewers.

      Finally, minor concerns are:

      (1) Meiotic progression in SynSAC strains lacking Mad1, Mad2 or Mad3 is severely affected (Fig. 1D and Supp. Fig. 1), making it difficult to assess whether, as the authors state, the metaphase delays depend on the canonical SAC cascade. In addition, as a general note, graphs displaying meiotic time courses could be improved for clarity (e.g., thinner data lines, addition of axis gridlines and external tick marks, etc.).

      We will generate the data to include a checkpoint mutant +/- ABA for direct comparison. We will take steps to improve the clarity of presentation of the meiotic timecourse graphs, though our experience is that uncluttered graphs make it easier to compare trends.

      (2) Spore viability following SynSAC induction in meiosis was used as an indicator that this experimental approach does not disrupt kinetochore function and chromosome segregation. However, this is an indirect measure. Direct monitoring of genome distribution using GFP-tagged chromosomes would have provided more robust evidence. Notably, the SynSAC mad3Δ mutant shows a slight viability defect, which might reflect chromosome segregation defects that are more pronounced in the absence of a functional SAC.

      Spore viability is a much more sensitive way of analysing segregation defects that GFP-labelled chromosomes. This is because GFP labelling allows only a single chromosome to be followed. On the other hand, if any of the 16 chromosomes mis-segregate in a given meiosis this would result in one or more aneuploid spores in the tetrad, which are typically inviable. The fact that spore viability is not significantly different from wild type in this analysis indicates that there are no major chromosome segregation defects in these strains, and we therefore do not plan to do this experiment.

      (3) It is surprising that, although SAC activity is proposed to be weaker in metaphase I, the levels of CPC/SAC proteins seem to be higher at this stage of meiosis than in metaphase II or mitotic metaphase (Fig. 4A-B).

      We agree, this is surprising and we will point this out in the revised discussion. We speculate that the challenge in biorienting homologs which are held together by chiasmata, rather than back-to-back kinetochores results in a greater requirement for error correction in meiosis I. Interestingly, the data with the RASA mutant also point to increased PP1 activity in meiosis I, and we additionally observed increased levels of PP1 (Glc7 and Fin1) on meiotic kinetochores, consistent with the idea that cycles of error correction and silencing are elevated in meiosis I.

      (4) Although a more detailed exploration of kinetochore composition or phosphorylation changes is beyond the scope of the manuscript, some key observations could have been validated experimentally (e.g., enrichment of proteins at kinetochores, phosphorylation events that were identified as specific or enriched at a certain meiotic stage, etc.).

      We agree that this is beyond the scope of the current study but will form the start of future projects from our group, and hopefully others.

      (5) Several typographical errors should be corrected (e.g., "Knetochores" in Fig. 4 legend, "250uM ABA" in Supp. Fig. 1 legend, etc.)

      Thank you for pointing these out, they have been corrected.

      Reviewer #3 (Significance):

      Koch et al. describe a novel methodology, SynSAC, to synchronize budding yeast cells in metaphase I or metaphase II during meiosis, as well and in mitotic metaphase, thereby enabling differential analyses among these cell division stages. Their approach builds on prior strategies originally developed in fission yeast and human cells models to induce a synthetic spindle assembly checkpoint (SAC) arrest by conditionally forcing the heterodimerization of two SAC proteins upon addition of abscisic acid (ABA). The results from this manuscript are of special relevance for researchers studying meiosis and using Saccharomyces cerevisiae as a model. Moreover, the differential analysis of the composition and phosphorylation of kinetochores from meiotic metaphase I and metaphase II adds interest for the broader meiosis research community. Finally, regarding my expertise, I am a researcher specialized in the regulation of cell division.

      Description of the revisions that have already been incorporated in the transferred manuscript

      We have only corrected minor typos as detailed above.

      Description of analyses that authors prefer not to carry out

      The revisions we plan are detailed above. There are just two revisions we believe are either unnecessary or beyond the scope, both minor concerns of Reviewer #3. For clarity we have reproduced them, along with our justification below. In the latter case, the reviewer also acknowledged that further work in this direction is beyond the scope of the current study.

      (2) Spore viability following SynSAC induction in meiosis was used as an indicator that this experimental approach does not disrupt kinetochore function and chromosome segregation. However, this is an indirect measure. Direct monitoring of genome distribution using GFP-tagged chromosomes would have provided more robust evidence. Notably, the SynSAC mad3Δ mutant shows a slight viability defect, which might reflect chromosome segregation defects that are more pronounced in the absence of a functional SAC.

      Spore viability is a much more sensitive way of analysing segregation defects that GFP-labelled chromosomes. This is because GFP labelling allows only a single chromosome to be followed. On the other hand, if any of the 16 chromosomes mis-segregate in a given meiosis this would result in one or more aneuploid spores in the tetrad, which are typically inviable. The fact that spore viability is not significantly different from wild type in this analysis indicates that there are no major chromosome segregation defects in these strains, and we therefore do not plan to do this experiment.

      (4) Although a more detailed exploration of kinetochore composition or phosphorylation changes is beyond the scope of the manuscript, some key observations could have been validated experimentally (e.g., enrichment of proteins at kinetochores, phosphorylation events that were identified as specific or enriched at a certain meiotic stage, etc.).

      We agree that this is beyond the scope of the current study but will form the start of future projects from our group, and hopefully others.

      (1) Salah, S.M., and Nasmyth, K. (2000). Destruction of the securin Pds1p occurs at the onset of anaphase during both meiotic divisions in yeast. Chromosoma 109, 27–34.

      (2) Matos, J., Lipp, J.J., Bogdanova, A., Guillot, S., Okaz, E., Junqueira, M., Shevchenko, A., and Zachariae, W. (2008). Dbf4-dependent CDC7 kinase links DNA replication to the segregation of homologous chromosomes in meiosis I. Cell 135, 662–678.

      (3) Marston, A.L.A.L., Lee, B.H.B.H., and Amon, A. (2003). The Cdc14 phosphatase and the FEAR network control meiotic spindle disassembly and chromosome segregation. Developmental cell 4, 711–726. https://doi.org/10.1016/S1534-5807(03)00130-8.

      (4) Attner, M.A., and Amon, A. (2012). Control of the mitotic exit network during meiosis. Molecular Biology of the Cell 23, 3122–3132. https://doi.org/10.1091/mbc.E12-03-0235.

      (5) Pablo-Hernando, M.E., Arnaiz-Pita, Y., Nakanishi, H., Dawson, D., del Rey, F., Neiman, A.M., and de Aldana, C.R.V. (2007). Cdc15 Is Required for Spore Morphogenesis Independently of Cdc14 in Saccharomyces cerevisiae. Genetics 177, 281–293. https://doi.org/10.1534/genetics.107.076133.

      (6) El Jailani, S., Cladière, D., Nikalayevich, E., Touati, S.A., Chesnokova, V., Melmed, S., Buffin, E., and Wassmann, K. (2025). Eliminating separase inhibition reveals absence of robust cohesin protection in oocyte metaphase II. EMBO J 44, 5187–5214. https://doi.org/10.1038/s44318-025-00522-0.

      (7) Rosenberg, J.S., Cross, F.R., and Funabiki, H. (2011). KNL1/Spc105 Recruits PP1 to Silence the Spindle Assembly Checkpoint. Current Biology 21, 942–947. https://doi.org/10.1016/j.cub.2011.04.011.

      (8) Koch, L.B., Spanos, C., Kelly, V., Ly, T., and Marston, A.L. (2024). Rewiring of the phosphoproteome executes two meiotic divisions in budding yeast. EMBO J 43, 1351–1383. https://doi.org/10.1038/s44318-024-00059-8.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review)

      (1) It might be good to further discuss potential molecular mechanisms for increasing the TF off rate (what happens at the mechanistic level). 

      This is now expanded in the Discussion

      (2) To improve readability, it would be good to make consistent font sizes on all figures to make sure that the smallest font sizes are readable. 

      We have normalised figure text as much as is feasible.

      (3) upDARs and downDARs - these abbreviations are defined in the figure legend but not in the main text. 

      We have removed references to these terms from the text and included a definition in the figure legend. 

      (4) Figure 3B - the on-figure legend is a bit unclear; the text legend does not mention the meaning of "DEG". 

      We have removed this panel as it was confusing and did not demonstrate any robust conclusion. 

      (5) The values of apparent dissociation rates shown in Figure 5 are a bit different from values previously reported in literature (e.g., see Okamoto et al., 20203, PMC10505915). Perhaps the authors could comment on this. Also, it would be helpful to add the actual equation that was used for the curve fitting to determine these values to the Methods section. 

      We have included an explanation of the curve fitting equation in the Methods as suggested.

      The apparent dissociation rate observed is a sum of multiple rates of decay – true dissociation rate (k<sub>off</sub>), signal loss caused by photobleaching k<sub>pb</sub>, and signal loss caused by defocusing/tracking error (k<sub>tl</sub>).

      k<sub>off</sub><sup>app</sup> = k<sub>off</sub>+ k<sub>pb</sub> + k<sub>tl</sub>

      We are making conclusions about relative changes in k<sub>off</sub><sup>app</sup> upon CHD4 depletion, not about the absolute magnitude of true in k<sub>off</sub> or TF residence times.Our conclusions extend to true in k<sub>off</sub> on the assumption that k<sub>pb</sub> and k<sub>tl</sub> are equal across all samples imaged due to identical experimental conditions and analysis. k<sub>pb</sub> and k<sub>tl</sub> vary hugely across experimental set-ups, especially with different laser powers, so other k<sub>off</sub> or k<sub>off</sub><sup>app</sup> values reported in the literature would be expected to differ from ours. Time-lapse experiments or independent determination of k<sub>pb</sub> (and k<sub>tl</sub>) would be required to make any statements about absolute values of k<sub>off</sub>

      (6) Regarding the discussion about the functionality of low-affinity sites/low accessibility regions, the authors may wish to mention the recent debates on this (https://www.nature.com/articles/s41586-025-08916-0; https://www.biorxiv.org/content/10.1101/2025.10.12.681120v1). 

      We have now included a discussion of this point and referenced both papers.

      (7) It may be worth expanding figure legends a bit, because the definitions of some of the terms mentioned on the figures are not very easy to find in the text. 

      We have endeavoured to define all relevant terms in the figure legends. 

      Reviewer #2 (Public review): 

      (1) Figure 2 shows heat maps of RNA-seq results following a time course of CHD4 depletion (0, 1, 2 hours...). Usually, the red/blue colour scale is used to visualise differential expression (fold-difference). Here, genes are coloured in red or blue even at the 0-hour time point. This confused me initially until I discovered that instead of folddifference, a z-score is plotted. I do not quite understand what it means when a gene that is coloured blue at the 0-hour time point changes to red at a later time point. Does this always represent an upregulation? I think this figure requires a better explanation. 

      The heatmap displays z-scores, meaning expression for each gene has been centred and scaled across the entire time course. As a result, time zero is not a true baseline, it simply shows whether the gene’s expression at that moment is above or below its own mean. A transition from blue to red therefore indicates that the gene increases relative to its overall average, which typically corresponds to upregulation, but it doesn’t directly represent fold-change from the 0-hour time point. We have now included a brief explanation of this in the figure legend to make this point clear.  

      (2) Figure 5D: NANOG, SOX2 binding at the KLF4 locus. The authors state that the enhancers 68, 57, and 55 show a gain in NANOG and SOX2 enrichment "from 30 minutes of CHD4 depletion". This is not obvious to me from looking at the figure. I can see an increase in signal from "WT" (I am assuming this corresponds to the 0 hours time point) to "30m", but then the signals seem to go down again towards the 4h time point. Can this be quantified? Can the authors discuss why TF binding seems to increase only temporarily (if this is the case)? 

      We have edited the text to more accurately reflect what is going on in the screen shot. We have also replaced “WT” with “0” as this more accurately reflects the status of these cells. 

      (3) There is no real discussion of HOW CHD4/NuRD counteracts TF binding (i.e. by what molecular mechanism). I understand that the data does not really inform us on this. Still, I believe it would be worthwhile for the authors to discuss some ideas, e.g., local nucleosome sliding vs. a direct (ATP-dependent?) action on the TF itself. 

      We now include more speculation on this point in the Discussion.

      Reviewer #3 (Public review): 

      The main weakness can be summarised as relating to the fact that authors interpret all rapid changes following CHD4 degradation as being a direct effect of the loss of CHD4 activity. The possibility that rapid indirect effects arise does not appear to have been given sufficient consideration. This is especially pertinent where effects are reported at sites where CHD4 occupancy is initially low. 

      We acknowledge that we cannot definitively say any effect is a direct consequence of CHD4 depletion and have mitigated statements in the Results and Discussion. 

      Reviewing Editor Comments: 

      I am pleased to say all three experts had very complementary and complimentary comments on your paper - congratulations. Reviewer 3 does suggest toning down a few interpretations, which I suggest would help focus the manuscript on its greater strengths. I encourage a quick revision to this point, which will not go back to reviewers, before you request a version of record. I would also like to take this opportunity to thank all three reviewers for excellent feedback on this paper. 

      As advised we have mitigated the points raised by the reviewers. 

      Reviewer #2 (Recommendations for the authors): 

      p9, top: The sentence starting with "Genes increasing in expression after four hours...." is very difficult to understand and should be rephrased or broken up. 

      We agree. This has been completely re-written. 

      Reviewer #3 (Recommendations for the authors): 

      Sites of increased chromatin accessibility emerge more slowly than sites of lost chromatin accessibility. Figure 1D, a little increase in accessibility at 30min, but a more noticeable decrease at 30min. The sites of increased accessibility also have lower absolute accessibility than observed at locations where accessibility is lost. This raises the possibility that the sites of increased accessibility represent rapid but indirect changes occurring following loss of CHD4. Consistent with this, enrichment for CHD4 and MDB3 by CUT and TAG is far higher at sites of decreased accessibility. The low level of CHD4 occupancy observed at sites where accessibility increases may not be relevant to the reason these sites are affected. Such small enrichments can be observed when aligning to other genomic features. The authors interpret their findings as indicating that low occupancy of CHD4 exerts a long-lasting repressive effect at these locations. This is one possible explanation; however, an alternative is that these effects are indirect. Perhaps driven by the very large increase in TF binding that is observed following CHD4 degradation and which appears to occur at many locations regardless of whether CHD4 is present. 

      The reviewer is right to point out that we don’t know what is direct and what is indirect. All we know is that changes happen very rapidly upon CHD4 depletion. The changes in standard ATAC-seq signal appear greater at the sites showing decreased accessibility than those increasing, however the starting points are very different: a small increase from very low accessibility will likely be a higher fold change than a more visible decrease from very high accessibility (Fig. 1D). In contrast, Figure 6 shows a more visible increase in Tn5 integrations at sites increasing in accessibility at 30 minutes than the change in sites decreasing in accessibility at 30 minutes. We therefore disagree that the sites increasing in accessibility are more likely to be indirect targets. In further support of this, there is a rapid increase in MNase resistance at these sites upon MBD3 reintroduction (Fig. 6I), possibly indicating a direct impact of NuRD on these sites. 

      Substantial changes in Nanog and SOX2 binding are observed across the time course. These changes are very large, with 43k or 78k additional sites detected. How is this possible? Does the amount of these TF's present in cells change? The argument that transient occupancy of CHD4 acts to prevent TF's binding to what is likely to be many 100's of thousands of sites (if the data for Nanog and SOX2 are representative of other transcription factors such as KLF4) seems unlikely. 

      The large number of different sites identified gaining TF binding is likely to be a reflection of the number of cells being analysed: within the 10<sup>5</sup>-10<sup>6</sup> cells used for a Cut&Run experiment we detect many sites gaining TF binding. In individual cells we agree it would be unlikely for that many sites to become bound at the same time. We detect no changes in the amounts of Nanog or Sox2 in our cells across 4 hour CHD4 depletion time course. However, we maintain that low frequency interactions of CHD4 with a site can counteract low frequency TF binding and prevent it from stimulating opening of a cryptic enhancer. 

      While increased TF binding is observed at sites of gained accessibility, the changes in TF occupancy at the lost sites do not progress continuously across the time course. In addition, the changes in occupancy are small in comparison to those observed at the gained sites. The text comments on an increase in SOX2 and Nanog occupancy at 30 min, but there is either no change or a loss by 4 hours. It's difficult to know what to conclude from this. 

      At sites losing accessibility the enrichment of both Nanog and Sox2 increases at 30 minutes. We suspect this is due to the loss of CHD4’s TF-removal activity. Thereafter the two TFs show different trends: Nanog enrichment then decreases again, probably due to the decrease in accessibility at these sites. Sox2, by contrast, does not change very much, possibly due to its higher pioneering ability. It is true that the amounts of change are very small here, however Cut&Run was performed in triplicate and the summary graphs are plotted with standard error of the mean (which is often too small to see), demonstrating that the detected changes are highly significant. (We neglected to refer to the SEM  in our figure legends: this has now been corrected.) At sites where CHD4 maintains chromatin compaction, the amount of transcription factor binding goes from zero or nearly zero to some finite number, hence the fold change is very large. In contrast the changes at sites losing accessibility starts from high enrichment so fold changes are much smaller. 

      Changes in the diffusive motion of tagged TF's are measured. The data is presented as an average of measurements of individual TF's. What might be anticipated is that subpopulations of TF's would exhibit distinct behaviours. At many locations, occupancy of these TF's are presumably unchanged. At 1 hour, many new sites are occupied, and this would represent a subpopulation with high residence. A small population of TF's would be subject to distinct effects at the sites where accessibility reduces at the onehour time point. The analysis presented fails to distinguish populations of TF's exhibiting altered mobility consistent with the proportion of the TF's showing altered binding. 

      We agree that there are likely subpopulations of TFs exhibiting distinct binding behaviours, and our modality of imaging captures this, but to distinguish subpopulations within this would require a lot more data.

      However, there is no reason to believe that the TF binding at the new sites being occupied at 1 hr would have a difference in residence time to those sites already stably bound by TFs in the wildtype, i.e. that they would exhibit a different limitation to their residence time once bound compared to those sites. We do capture more stably bound trajectories per cell, but that’s not what we’re reporting on - it’s the dissociation rate of those that have already bound in a stable manner at sites where TF occupancy is detected also by ChIP.

      The analysis of transcription shown in Figure 2 indicates that high-quality data has been obtained, showing progressive changes to transcription. The linkage of the differentially expressed genes to chromatin changes shown in Figure 3 is difficult to interpret. The curves showing the distance distribution for increased or decreased DARs are quite similar for up- and down-regulated genes. The frequency density for gained sites is slightly higher, but not as much higher as would be expected, given these sites are c6fold more abundant than the sites with lost accessibility. The data presented do not provide a compelling link between the CHD4-induced chromatin changes and changes to transcription; the authors should consider revising to accommodate this. It is possible that much of the transcriptional response even at early time points is indirect. This is not unprecedented. For example, degradation of SOX2, a transcriptional activator, results in both repression and activation of similar numbers of genes https://pmc.ncbi.nlm.nih.gov/articles/PMC10577566/ 

      We agree that these figures do not provide a compelling link between the observed chromatin changes and gene expression changes. That 50K increased sites are, on average, located farther away from misregulated genes than are the 8K decreasing sites highlights that this is rarely going to be a case of direct derepression of a silenced gene, but rather distal sites could act as enhancers to spuriously activate transcription. This would certainly be a rare event, but could explain the low-level transcriptional noise seen in NuRD mutants. We have edited the wording to make this clearer.

      The model presented in Figure 7 includes distinct roles at sites that become more or less accessible following inactivation of CHD4. This is perplexing as it implies that the same enzymes perform opposing functions at some of the different sites where they are bound. 

      Our point is that it does the same thing at both kinds of sites, but the nature of the sites means that the consequences of CHD4 activity will be different. We have tried to make this clear in the text. 

      At active sites, it is clear that CHD4 is bound prior to activation of the degron and that chromatin accessibility is reduced following depletion. Changes in TF occupancy are complex, perhaps reflecting slow diffusion from less accessible chromatin and a global increase in the abundance of some pluripotency transcription factors such as SOX2 and Nanog that are competent for DNA binding. The link between sites of reduced accessibility and transcription is less clear. 

      At the inactive sites, the increase in accessibility could be driven by transcription factor binding. There is very little CHD4 present at these sites prior to activation of the degron, and TF binding may induce chromatin opening, which could be considered a rapid but indirect effect of the CHD4 degron. The link to transcription is not clear from the data presented, but it would be anticipated that in some cases it would drive activation. 

      We acknowledge these points and have indicated this possibility in the Results and the Discussion.

      No Analysis is performed to identify binding sequences enriched at the locations of decreased accessibility. This could potentially define transcription factors involved in CHD4 recruitment or that cause CHD4 to function differently in different contexts. 

      HOMER analyses failed to provide any unique insights. The sites going down are highly accessible in ES cells: they have TF binding sites that one would expect in ES cells. The increasing sites show an enrichment for G-rich sequences, which reflects the binding preference of CHD4.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This useful study presents Altair-LSFM, a solid and well-documented implementation of a light-sheet fluorescence microscope (LSFM) designed for accessibility and cost reduction. While the approach offers strengths such as the use of custom-machined baseplates and detailed assembly instructions, its overall impact is limited by the lack of live-cell imaging capabilities and the absence of a clear, quantitative comparison to existing LSFM platforms. As such, although technically competent, the broader utility and uptake of this system by the community may be limited.

      We thank the editors and reviewers for their thoughtful evaluation of our work and for recognizing the technical strengths of the Altair-LSFM platform, including the custom-machined baseplates and detailed documentation provided to promote accessibility and reproducibility. Below, we provide point-by-point responses to each referee comment. In the process, we have significantly revised the manuscript to include live-cell imaging data and a quantitative evaluation of imaging speed. We now more explicitly describe the different variants of lattice light-sheet microscopy—highlighting differences in their illumination flexibility and image acquisition modes—and clarify how Altair-LSFM compares to each. We further discuss challenges associated with the 5 mm coverslip and propose practical strategies to overcome them. Additionally, we outline cost-reduction opportunities, explain the rationale behind key equipment selections, and provide guidance for implementing environmental control. Altogether, we believe these additions have strengthened the manuscript and clarified both the capabilities and limitations of AltairLSFM.

      Public Reviews:

      Reviewer #1 (Public review): 

      Summary: 

      The article presents the details of the high-resolution light-sheet microscopy system developed by the group. In addition to presenting the technical details of the system, its resolution has been characterized and its functionality demonstrated by visualizing subcellular structures in a biological sample.

      Strengths: 

      (1) The article includes extensive supplementary material that complements the information in the main article.

      (2) However, in some sections, the information provided is somewhat superficial.

      We thank the reviewer for their thoughtful assessment and for recognizing the strengths of our manuscript, including the extensive supplementary material. Our goal was to make the supplemental content as comprehensive and useful as possible. In addition to the materials provided with the manuscript, our intention is for the online documentation (available at thedeanlab.github.io/altair) to serve as a living resource that evolves in response to user feedback. We would therefore greatly appreciate the reviewer’s guidance on which sections were perceived as superficial so that we can expand them to better support readers and builders of the system.

      Weaknesses:

      (1) Although a comparison is made with other light-sheet microscopy systems, the presented system does not represent a significant advance over existing systems. It uses high numerical aperture objectives and Gaussian beams, achieving resolution close to theoretical after deconvolution. The main advantage of the presented system is its ease of construction, thanks to the design of a perforated base plate.

      We appreciate the reviewer’s assessment and the opportunity to clarify our intent. Our primary goal was not to introduce new optical functionality beyond that of existing high-performance light-sheet systems, but rather to substantially reduce the barrier to entry for non-specialist laboratories. Many open-source implementations, such as OpenSPIM, OpenSPIN, and Benchtop mesoSPIM, similarly focused on accessibility and reproducibility rather than introducing new optical modalities, yet have had a measureable impact on the field by enabling broader community participation. Altair-LSFM follows this tradition, providing sub-cellular resolution performance comparable to advanced systems like LLSM, while emphasizing reproducibility, ease of construction through a precision-machined baseplate, and comprehensive documentation to facilitate dissemination and adoption.

      (2) Using similar objectives (Nikon 25x and Thorlabs 20x), the results obtained are similar to those of the LLSM system (using a Gaussian beam without laser modulation). However, the article does not mention the difficulties of mounting the sample in the implemented configuration.

      We appreciate the reviewer’s comment and agree that there are practical challenges associated with handling 5 mm diameter coverslips in this configuration. In the revised manuscript, we now explicitly describe these challenges and provide practical solutions. Specifically, we highlight the use of a custommachined coverslip holder designed to simplify mounting and handling, and we direct readers to an alternative configuration using the Zeiss W Plan-Apochromat 20×/1.0 objective, which eliminates the need for small coverslips altogether.

      (3) The authors present a low-cost, open-source system. Although they provide open source code for the software (navigate), the use of proprietary electronics (ASI, NI, etc.) makes the system relatively expensive. Its low cost is not justified.

      We appreciate the reviewer’s perspective and understand the concern regarding the use of proprietary control hardware such as the ASI Tiger Controller and NI data acquisition cards. Our decision to use these components was intentional: relying on a unified, professionally supported and maintained platform minimizes complexity associated with sourcing, configuring, and integrating hardware from multiple vendors, thereby reducing non-financial barriers to entry for non-specialist users.

      Importantly, these components are not the primary cost driver of Altair-LSFM (they represent roughly 18% of the total system cost). Nonetheless, for individuals where the price is prohibitive, we also outline several viable cost-reduction options in the revised manuscript (e.g., substituting manual stages, omitting the filter wheel, or using industrial CMOS cameras), while discussing the trade-offs these substitutions introduce in performance and usability. These considerations are now summarized in Supplementary Note 1, which provides a transparent rationale for our design and cost decisions.

      Finally, we note that even with these professional-grade components, Altair-LSFM remains substantially less expensive than commercial systems offering comparable optical performance, such as LLSM implementations from Zeiss or 3i.

      (4) The fibroblast images provided are of exceptional quality. However, these are fixed samples. The system lacks the necessary elements for monitoring cells in vivo, such as temperature or pH control.

      We thank the reviewer for their positive comment regarding the quality of our data. As noted, the current manuscript focuses on validating the optical performance and resolution of the system using fixed specimens to ensure reproducibility and stability.

      We fully agree on the importance of environmental control for live-cell imaging. In the revised manuscript, we now describe in detail how temperature regulation can be achieved using a custom-designed heated sample chamber, accompanied by detailed assembly instructions on our GitHub repository and summarized in Supplementary Note 2. For pH stabilization in systems lacking a 5% CO₂ atmosphere, we recommend supplementing the imaging medium with 10–25 mM HEPES buffer. Additionally, we include new live-cell imaging data demonstrating that Altair-LSFM supports in vitro time-lapse imaging of dynamic cellular processes under controlled temperature conditions.

      Reviewer #2 (Public review): 

      Summary: 

      The authors present Altair-LSFM (Light Sheet Fluorescence Microscope), a high-resolution, open-source microscope, that is relatively easy to align and construct and achieves sub-cellular resolution. The authors developed this microscope to fill a perceived need that current open-source systems are primarily designed for large specimens and lack sub-cellular resolution or are difficult to construct and align, and are not stable. While commercial alternatives exist that offer sub-cellular resolution, they are expensive. The authors' manuscript centers around comparisons to the highly successful lattice light-sheet microscope, including the choice of detection and excitation objectives. The authors thus claim that there remains a critical need for high-resolution, economical, and easy-to-implement LSFM systems. 

      We thank the reviewer for their thoughtful summary. We agree that existing open-source systems primarily emphasize imaging of large specimens, whereas commercial systems that achieve sub-cellular resolution remain costly and complex. Our aim with Altair-LSFM was to bridge this gap—providing LLSM-level performance in a substantially more accessible and reproducible format. By combining high-NA optics with a precision-machined baseplate and open-source documentation, Altair offers a practical, high-resolution solution that can be readily adopted by non-specialist laboratories.

      Strengths: 

      The authors succeed in their goals of implementing a relatively low-cost (~ USD 150K) open-source microscope that is easy to align. The ease of alignment rests on using custom-designed baseplates with dowel pins for precise positioning of optics based on computer analysis of opto-mechanical tolerances, as well as the optical path design. They simplify the excitation optics over Lattice light-sheet microscopes by using a Gaussian beam for illumination while maintaining lateral and axial resolutions of 235 and 350 nm across a 260-um field of view after deconvolution. In doing so they rest on foundational principles of optical microscopy that what matters for lateral resolution is the numerical aperture of the detection objective and proper sampling of the image field on to the detection, and the axial resolution depends on the thickness of the light-sheet when it is thinner than the depth of field of the detection objective. This concept has unfortunately not been completely clear to users of high-resolution light-sheet microscopes and is thus a valuable demonstration. The microscope is controlled by an open-source software, Navigate, developed by the authors, and it is thus foreseeable that different versions of this system could be implemented depending on experimental needs while maintaining easy alignment and low cost. They demonstrate system performance successfully by characterizing their sheet, point-spread function, and visualization of sub-cellular structures in mammalian cells, including microtubules, actin filaments, nuclei, and the Golgi apparatus.

      We thank the reviewer for their thoughtful and generous assessment of our work. We are pleased that the manuscript’s emphasis on fundamental optical principles, design rationale, and practical implementation was clearly conveyed. We agree that Altair’s modular and accessible architecture provides a strong foundation for future variants tailored to specific experimental needs. To facilitate this, we have made all Zemax simulations, CAD files, and build documentation openly available on our GitHub repository, enabling users to adapt and extend the system for diverse imaging applications.

      Weaknesses:

      There is a fixation on comparison to the first-generation lattice light-sheet microscope, which has evolved significantly since then:

      (1) The authors claim that commercial lattice light-sheet microscopes (LLSM) are "complex, expensive, and alignment intensive", I believe this sentence applies to the open-source version of LLSM, which was made available for wide dissemination. Since then, a commercial solution has been provided by 3i, which is now being used in multiple cores and labs but does require routine alignments. However, Zeiss has also released a commercial turn-key system, which, while expensive, is stable, and the complexity does not interfere with the experience of the user. Though in general, statements on ease of use and stability might be considered anecdotal and may not belong in a scientific article, unreferenced or without data.

      We thank the reviewer for this thoughtful and constructive comment. We have revised the manuscript to more clearly distinguish between the original open-source implementation of LLSM and subsequent commercial versions by 3i and ZEISS. The revised Introduction and Discussion now explicitly note that while open-source and early implementations of LLSM can require expert alignment and maintenance, commercial systems—particularly the ZEISS Lattice Lightsheet 7—are designed for automated operation and stable, turn-key use, albeit at higher cost and with limited modifiability. We have also moderated earlier language regarding usability and stability to avoid anecdotal phrasing.

      We also now provide a more objective proxy for system complexity: the number of optical elements that require precise alignment during assembly and maintenance thereafter. The original open-source LLSM setup includes approximately 29 optical components that must each be carefully positioned laterally, angularly, and coaxially along the optical path. In contrast, the first-generation Altair-LSFM system contains only nine such elements. By this metric, Altair-LSFM is considerably simpler to assemble and align, supporting our overarching goal of making high-resolution light-sheet imaging more accessible to non-specialist laboratories.

      (2) One of the major limitations of the first generation LLSM was the use of a 5 mm coverslip, which was a hinderance for many users. However, the Zeiss system elegantly solves this problem, and so does Oblique Plane Microscopy (OPM), while the Altair-LSFM retains this feature, which may dissuade widespread adoption. This limitation and how it may be overcome in future iterations is not discussed.

      We thank the reviewer for this helpful comment. We agree that the use of 5 mm diameter coverslips, while enabling high-NA imaging in the current Altair-LSFM configuration, may pose a practical limitation for some users. We now discuss this more explicitly in the revised manuscript. Specifically, we note that replacing the detection objective provides a straightforward solution to this constraint. For example, as demonstrated by Moore et al. (Lab Chip, 2021), pairing the Zeiss W Plan-Apochromat 20×/1.0 detection objective with the Thorlabs TL20X-MPL illumination objective allows imaging beyond the physical surfaces of both objectives, eliminating the need for small-format coverslips. In the revised text, we propose this modification as an accessible path toward greater compatibility with conventional sample mounting formats. We also note in the Discussion that Oblique Plane Microscopy (OPM) inherently avoids such nonstandard mounting requirements and, owing to its single-objective architecture, is fully compatible with standard environmental chambers.

      (3) Further, on the point of sample flexibility, all generations of the LLSM, and by the nature of its design, the OPM, can accommodate live-cell imaging with temperature, gas, and humidity control. It is unclear how this would be implemented with the current sample chamber. This limitation would severely limit use cases for cell biologists, for which this microscope is designed. There is no discussion on this limitation or how it may be overcome in future iterations.

      We thank the reviewer for this important observation and agree that environmental control is critical for live-cell imaging applications. It is worth noting that the original open-source LLSM design, as well as the commercial version developed by 3i, provided temperature regulation but did not include integrated control of CO2 or humidity. Despite this limitation, these systems have been widely adopted and have generated significant biological insights. We also acknowledge that both OPM and the ZEISS implementation of LLSM offer clear advantages in this respect, providing compatibility with standard commercial environmental chambers that support full regulation of temperature, CO₂, and humidity.

      In the revised manuscript, we expand our discussion of environmental control in Supplementary Note 2, where we describe the Altair-LSFM chamber design in more detail and discuss its current implementation of temperature regulation and HEPES-based pH stabilization. Additionally, the Discussion now explicitly notes that OPM avoids the challenges associated with non-standard sample mounting and is inherently compatible with conventional environmental enclosures.

      (4) The authors' comparison to LLSM is constrained to the "square" lattice, which, as they point out, is the most used optical lattice (though this also might be considered anecdotal). The LLSM original design, however, goes far beyond the square lattice, including hexagonal lattices, the ability to do structured illumination, and greater flexibility in general in terms of light-sheet tuning for different experimental needs, as well as not being limited to just sample scanning. Thus, the Alstair-LSFM cannot compare to the original LLSM in terms of versatility, even if comparisons to the resolution provided by the square lattice are fair.

      We agree that the original LLSM design offers substantially greater flexibility than what is reflected in our initial comparison, including the ability to generate multiple lattice geometries (e.g., square and hexagonal), operate in structured illumination mode, and acquire volumes using both sample- and lightsheet–scanning strategies. To address this, we now include Supplementary Note 3 that provides a detailed overview of the illumination modes and imaging flexibility afforded by the original LLSM implementation, and how these capabilities compare to both the commercial ZEISS Lattice Lightsheet 7 and our AltairLSFM system. In addition, we have revised the discussion to explicitly acknowledge that the original LLSM could operate in alternative scan strategies beyond sample scanning, providing greater context for readers and ensuring a more balanced comparison.

      (5) There is no demonstration of the system's live-imaging capabilities or temporal resolution, which is the main advantage of existing light-sheet systems.

      In the revised manuscript, we now include a demonstration of live-cell imaging to directly validate AltairLSFM’s suitability for dynamic biological applications. We also explicitly discuss the temporal resolution of the system in the main text (see Optoelectronic Design of Altair-LSFM), where we detail both software- and hardware-related limitations. Specifically, we evaluate the maximum imaging speed achievable with Altair-LSFM in conjunction with our open-source control software, navigate.

      For simplicity and reduced optoelectronic complexity, the current implementation powers the piezo through the ASI Tiger Controller, which modestly reduces its bandwidth. Nonetheless, for a 100 µm stroke typical of light-sheet imaging, we achieved sufficient performance to support volumetric imaging at most biologically relevant timescales. These results, along with additional discussion of the design trade-offs and performance considerations, are now included in the revised manuscript and expanded upon in the supplementary material.

      While the microscope is well designed and completely open source, it will require experience with optics, electronics, and microscopy to implement and align properly. Experience with custom machining or soliciting a machine shop is also necessary. Thus, in my opinion, it is unlikely to be implemented by a lab that has zero prior experience with custom optics or can hire someone who does. Altair-LSFM may not be as easily adaptable or implementable as the authors describe or perceive in any lab that is interested, even if they can afford it. The authors indicate they will offer "workshops," but this does not necessarily remove the barrier to entry or lower it, perhaps as significantly as the authors describe.

      We appreciate the reviewer’s perspective and agree that building any high-performance custom microscope—Altair-LSFM included—requires a basic understanding of (or willingness to learn) optics, electronics, and instrumentation. Such a barrier exists for all open-source microscopes, and our goal is not to eliminate this requirement entirely but to substantially reduce the technical and logistical challenges that typically accompany the construction of custom light-sheet systems.

      Importantly, no machining experience or in-house fabrication capabilities are required. Users can simply submit the provided CAD design files and specifications directly to commercial vendors for fabrication. We have made this process as straightforward as possible by supplying detailed build instructions, recommended materials, and vendor-ready files through our GitHub repository. Our dissemination strategy draws inspiration from other successful open-source projects such as mesoSPIM, which has seen widespread adoption—over 30 implementations worldwide—through a similar model of exhaustive documentation, open-source software, and community support via user meetings and workshops.

      We also recognize that documentation alone cannot fully replace hands-on experience. To further lower barriers to adoption, we are actively working with commercial vendors to streamline procurement and assembly, and Altair-LSFM is supported by a Biomedical Technology Development and Dissemination (BTDD) grant that provides resources for hosting workshops, offering real-time community support, and developing supplementary training materials.

      In the revised manuscript, we now expand the Discussion to explicitly acknowledge these implementation considerations and to outline our ongoing efforts to support a broad and diverse user base, ensuring that laboratories with varying levels of technical expertise can successfully adopt and maintain the Altair-LSFM platform.

      There is a claim that this design is easily adaptable. However, the requirement of custom-machined baseplates and in silico optimization of the optical path basically means that each new instrument is a new design, even if the Navigate software can be used. It is unclear how Altair-LSFM demonstrates a modular design that reduces times from conception to optimization compared to previous implementations.

      We thank the reviewer for this insightful comment and agree that our original language regarding adaptability may have overstated the degree to which Altair-LSFM can be modified without prior experience. It was not our intention to imply that the system can be easily redesigned by users with limited technical background. Meaningful adaptations of the optical or mechanical design do require expertise in optical layout, optomechanical design, and alignment.

      That said, for laboratories with such expertise, we aim to facilitate modifications by providing comprehensive resources—including detailed Zemax simulations, complete CAD models, and alignment documentation. These materials are intended to reduce the development burden for expert users seeking to tailor the system to specific experimental requirements, without necessitating a complete re-optimization of the optical path from first principles.

      In the revised manuscript, we clarify this point and temper our language regarding adaptability to better reflect the realistic scope of customization. Specifically, we now state in the Discussion: “For expert users who wish to tailor the instrument, we also provide all Zemax illumination-path simulations and CAD files, along with step-by-step optimization protocols, enabling modification and re-optimization of the optical system as needed.” This revision ensures that readers clearly understand that Altair-LSFM is designed for reproducibility and straightforward assembly in its default configuration, while still offering the flexibility for modification by experienced users.

      Reviewer #3 (Public review):

      Summary: 

      This manuscript introduces a high-resolution, open-source light-sheet fluorescence microscope optimized for sub-cellular imaging. The system is designed for ease of assembly and use, incorporating a custommachined baseplate and in silico optimized optical paths to ensure robust alignment and performance. The authors demonstrate lateral and axial resolutions of ~235 nm and ~350 nm after deconvolution, enabling imaging of sub-diffraction structures in mammalian cells. The important feature of the microscope is the clever and elegant adaptation of simple gaussian beams, smart beam shaping, galvo pivoting and high NA objectives to ensure a uniform thin light-sheet of around 400 nm in thickness, over a 266 micron wide Field of view, pushing the axial resolution of the system beyond the regular diffraction limited-based tradeoffs of light-sheet fluorescence microscopy. Compelling validation using fluorescent beads and multicolor cellular imaging highlights the system's performance and accessibility. Moreover, a very extensive and comprehensive manual of operation is provided in the form of supplementary materials. This provides a DIY blueprint for researchers who want to implement such a system.

      We thank the reviewer for their thoughtful and positive assessment of our work. We appreciate their recognition of Altair-LSFM’s design and performance, including its ability to achieve high-resolution, imaging throughout a 266-micron field of view. While Altair-LSFM approaches the practical limits of diffraction-limited performance, it does not exceed the fundamental diffraction limit; rather, it achieves near-theoretical resolution through careful optical optimization, beam shaping, and alignment. We are grateful for the reviewer’s acknowledgment of the accessibility and comprehensive documentation that make this system broadly implementable.

      Strengths:

      (1) Strong and accessible technical innovation: With an elegant combination of beam shaping and optical modelling, the authors provide a high-resolution light-sheet system that overcomes the classical light-sheet tradeoff limit of a thin light-sheet and a small field of view. In addition, the integration of in silico modelling with a custom-machined baseplate is very practical and allows for ease of alignment procedures. Combining these features with the solid and super-extensive guide provided in the supplementary information, this provides a protocol for replicating the microscope in any other lab.

      (2) Impeccable optical performance and ease of mounting of samples: The system takes advantage of the same sample-holding method seen already in other implementations, but reduces the optical complexity.

      At the same time, the authors claim to achieve similar lateral and axial resolution to Lattice-light-sheet microscopy (although without a direct comparison (see below in the "weaknesses" section). The optical characterization of the system is comprehensive and well-detailed. Additionally, the authors validate the system imaging sub-cellular structures in mammalian cells.

      (3) Transparency and comprehensiveness of documentation and resources: A very detailed protocol provides detailed documentation about the setup, the optical modeling, and the total cost.

      We thank the reviewer for their thoughtful and encouraging comments. We are pleased that the technical innovation, optical performance, and accessibility of Altair-LSFM were recognized. Our goal from the outset was to develop a diffraction-limited, high-resolution light-sheet system that balances optical performance with reproducibility and ease of implementation. We are also pleased that the use of precisionmachined baseplates was recognized as a practical and effective strategy for achieving performance while maintaining ease of assembly.

      Weaknesses: 

      (1) Limited quantitative comparisons: Although some qualitative comparison with previously published systems (diSPIM, lattice light-sheet) is provided throughout the manuscript, some side-by-side comparison would be of great benefit for the manuscript, even in the form of a theoretical simulation. While having a direct imaging comparison would be ideal, it's understandable that this goes beyond the interest of the paper; however, a table referencing image quality parameters (taken from the literature), such as signalto-noise ratio, light-sheet thickness, and resolutions, would really enhance the features of the setup presented. Moreover, based also on the necessity for optical simplification, an additional comment on the importance/difference of dual objective/single objective light-sheet systems could really benefit the discussion.

      In the revised manuscript, we have significantly expanded our discussion of different light-sheet systems to provide clearer quantitative and conceptual context for Altair-LSFM. These comparisons are based on values reported in the literature, as we do not have access to many of these instruments (e.g., DaXi, diSPIM, or commercial and open-source variants of LLSM), and a direct experimental comparison is beyond the scope of this work.

      We note that while quantitative parameters such as signal-to-noise ratio are important, they are highly sample-dependent and strongly influenced by imaging conditions, including fluorophore brightness, camera characteristics, and filter bandpass selection. For this reason, we limited our comparison to more general image-quality metrics—such as light-sheet thickness, resolution, and field of view—that can be reliably compared across systems.

      Finally, per the reviewer’s recommendation, we have added additional discussion clarifying the differences between dual-objective and single-objective light-sheet architectures, outlining their respective strengths, limitations, and suitability for different experimental contexts.

      (2) Limitation to a fixed sample: In the manuscript, there is no mention of incubation temperature, CO₂ regulation, Humidity control, or possible integration of commercial environmental control systems. This is a major limitation for an imaging technique that owes its popularity to fast, volumetric, live-cell imaging of biological samples.

      We fully agree that environmental control is critical for live-cell imaging applications. In the revised manuscript, we now describe the design and implementation of a temperature-regulated sample chamber in Supplementary Note 2, which maintains stable imaging conditions through the use of integrated heating elements and thermocouples. This approach enables precise temperature control while minimizing thermal gradients and optical drift. For pH stabilization, we recommend the use of 10–25 mM HEPES in place of CO₂ regulation, consistent with established practice for most light-sheet systems, including the initial variant of LLSM. Although full humidity and CO₂ control are not readily implemented in dual-objective configurations, we note that single-objective designs such as OPM are inherently compatible with commercial environmental chambers and avoid these constraints. Together, these additions clarify how environmental control can be achieved within Altair-LSFM and situate its capabilities within the broader LSFM design space.

      (3) System cost and data storage cost: While the system presented has the advantage of being opensource, it remains relatively expensive (considering the 150k without laser source and optical table, for example). The manuscript could benefit from a more direct comparison of the performance/cost ratio of existing systems, considering academic settings with budgets that most of the time would not allow for expensive architectures. Moreover, it would also be beneficial to discuss the adaptability of the system, in case a 30k objective could not be feasible. Will this system work with different optics (with the obvious limitations coming with the lower NA objective)? This could be an interesting point of discussion. Adaptability of the system in case of lower budgets or more cost-effective choices, depending on the needs.

      We agree that cost considerations are critical for adoption in academic environments. We would also like to clarify that the quoted $150k includes the optical table and laser source. In the revised manuscript, Supplementary Note 1 now includes an expanded discussion of cost–performance trade-offs and potential paths for cost reduction.

      Last, not much is said about the need for data storage. Light-sheet microscopy's bottleneck is the creation of increasingly large datasets, and it could be beneficial to discuss more about the storage needs and the quantity of data generated.

      In the revised manuscript, we now include Supplementary Note 4, which provides a high-level discussion of data storage needs, approximate costs, and practical strategies for managing large datasets generated by light-sheet microscopy. This section offers general guidance—including file-format recommendations, and cost considerations—but we note that actual costs will vary by institution and contractual agreements.

      Conclusion:

      Altair-LSFM represents a well-engineered and accessible light-sheet system that addresses a longstanding need for high-resolution, reproducible, and affordable sub-cellular light-sheet imaging. While some aspects-comparative benchmarking and validation, limitation for fixed samples-would benefit from further development, the manuscript makes a compelling case for Altair-LSFM as a valuable contribution to the open microscopy scientific community. 

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) A picture, or full CAD design of the complete instrument, should be included as a main figure.

      A complete CAD rendering of the microscope is now provided in Supplementary Figure 4.

      (2) There is no quantitative comparison of the effects of the tilting resonant galvo; only a cartoon, a figure should be included.

      The cartoon was intended purely as an educational illustration to conceptually explain the role of the tilting resonant galvo in shaping and homogenizing the light sheet. To clarify this intent, we have revised both the figure legend and corresponding text in the main manuscript. For readers seeking quantitative comparisons, we now reference the original study that provides a detailed analysis of this optical approach, as well as a review on the subject.

      (3) Description of L4 is missing in the Figure 1 caption.

      Thank you for catching this omission. We have corrected it.

      (4) The beam profiles in Figures 1c and 3a, please crop and make the image bigger so the profile can be appreciated. The PSFs in Figure 3c-e should similarly be enlarged and presented using a dynamic range/LUT such that any aberrations can be appreciated.

      In Figure 1c, our goal was to qualitatively illustrate the uniformity of the light-sheet across the full field of view, while Figure 1d provided the corresponding quantitative cross-section. To improve clarity, we have added an additional figure panel offering a higher-magnification, localized view of the light-sheet profile. For Figure 3c–e, we have enlarged the PSF images and adjusted the display range to better convey the underlying signal and allow subtle aberrations to be appreciated.

      (5) It is unclear why LLSM is being used as the gold standard, since in its current commercial form, available from Zeiss, it is a turn-key system designed for core facilities. The original LLSM is also a versatile instrument that provides much more than the square lattice for illumination, including structured illumination, hexagonal lattices, live-cell imaging, wide-field illumination, different scan modes, etc. These additional features are not even mentioned when compared to the Altair-LSFM. If a comparison is to be provided, it should be fair and balanced. Furthermore, as outlined in the public review, anecdotal statements on "most used", "difficult to align", or "unstable" should not be provided without data.

      In the revised manuscript, we have carefully removed anecdotal statements and, where appropriate, replaced them with quantitative or verifiable information. For instance, we now explicitly report that the square lattice was used in 16 of the 20 figure subpanels in the original LLSM publication, and we include a proxy for optical complexity based on the number of optical elements requiring alignment in each system.

      We also now clearly distinguish between the original LLSM design—which supports multiple illumination and scanning modes—and its subsequent commercial variants, including the ZEISS Lattice Lightsheet 7, which prioritizes stability and ease of use over configurational flexibility (see Supplementary Note 3).

      (6) The authors should recognize that implementing custom optics, no matter how well designed, is a big barrier to cross for most cell biology labs.

      We fully understand and now acknowledge in the main text that implementing custom optics can present a significant barrier, particularly for laboratories without prior experience in optical system assembly. However, similar challenges were encountered during the adoption of other open-source microscopy platforms, such as mesoSPIM and OpenSPIM, both of which have nonetheless achieved widespread implementation. Their success has largely been driven by exhaustive documentation, strong community support, and standardized design principles—approaches we have also prioritized in Altair-LSFM. We have therefore made all CAD files, alignment guides, and detailed build documentation publicly available and continue to develop instructional materials and community resources to further reduce the barrier to adoption.

      (7) Statements on "hands on workshops" though laudable, may not be appropriate to include in a scientific publication without some documentation on the influence they have had on implanting the microscope.

      We understand the concern. Our intention in mentioning hands-on workshops was to convey that the dissemination effort is supported by an NIH Biomedical Technology Development and Dissemination grant, which includes dedicated channels for outreach and community engagement. Nonetheless, we agree that such statements are not appropriate without formal documentation of their impact, and we have therefore removed this text from the revised manuscript.

      (8) It is claimed that the microscope is "reliable" in the discussion, but with no proof, long-term stability should be assessed and included.

      Our experience with Altair-LSFM has been that it remains well-aligned over time—especially in comparison to other light-sheet systems we worked on throughout the last 11 years—we acknowledge that this assessment is anecdotal. As such, we have omitted this claim from the revised manuscript.

      (9) Due to the reliance on anecdotal statements and comparisons without proof to other systems, this paper at times reads like a brochure rather than a scientific publication. The authors should consider editing their manuscript accordingly to focus on the technical and quantifiable aspects of their work.

      We agree with the reviewer’s assessment and have revised the manuscript to remove anecdotal comparisons and subjective language. Where possible, we now provide quantitative metrics or verifiable data to support our statements.

      Reviewer #3 (Recommendations for the authors):

      Other minor points that could improve the manuscript (although some of these points are explained in the huge supplementary manual): 

      (1) The authors explain thoroughly their design, and they chose a sample-scanning method. I think that a brief discussion of the advantages and disadvantages of such a method over, for example, a laserscanning system (with fixed sample) in the main text will be highly beneficial for the users.

      In the revised manuscript, we now include a brief discussion in the main text outlining the advantages and limitations of a sample-scanning approach relative to a light-sheet–scanning system. Specifically, we note that for thin, adherent specimens, sample scanning minimizes the optical path length through the sample, allowing the use of more tightly focused illumination beams that improve axial resolution. We also include a new supplementary figure illustrating how this configuration reduces the propagation length of the illumination light sheet, thereby enhancing axial resolution.

      (2) The authors justify selecting a 0.6 NA illumination objective over alternatives (e.g., Special Optics), but the manuscript would benefit from a more quantitative trade-off analysis (beam waist, working distance, sample compatibility) with other possibilities. Within the objective context, a comparison of the performances of this system with the new and upcoming single-objective light-sheet methods (and the ones based also on optical refocusing, e.g., DAXI) would be very interesting for the goodness of the manuscript.

      In the revised manuscript, we now provide a quantitative trade-off analysis of the illumination objectives in Supplementary Note 1, including comparisons of beam waist, working distance, and sample compatibility. This section also presents calculated point spread functions for both the 0.6 NA and 0.67 NA objectives, outlining the performance trade-offs that informed our design choice. In addition, Supplementary Note 3 now includes a broader comparison of Altair-LSFM with other light-sheet modalities, including diSPIM, ASLM, and OPM, to further contextualize the system’s capabilities within the evolving light-sheet microscopy landscape.

      (3) The modularity of the system is implied in the context of the manuscript, but not fully explained. The authors should specify more clearly, for example, if cameras could be easily changed, objectives could be easily swapped, light-sheet thickness could be tuned by changing cylindrical lens, how users might adapt the system for different samples (e.g., embryos, cleared tissue, live imaging), .etc, and discuss eventual constraints or compatibility issues to these implementations.

      Altair-LSFM was explicitly designed and optimized for imaging live adherent cells, where sample scanning and short light-sheet propagation lengths provide optimal axial resolution (Supplementary Note 3). While the same platform could be used for superficial imaging in embryos, systems implementing multiview illumination and detection schemes are better suited for such specimens. Similarly, cleared tissue imaging typically requires specialized solvent-compatible objectives and approaches such as ASLM that maximize the field of view. We have now added some text to the Design Principles section that explicitly state this.

      Altair-LSFM offers varying levels of modularity depending on the user’s level of expertise. For entry-level users, the illumination numerical aperture—and therefore the light-sheet thickness and propagation length—can be readily adjusted by tuning the rectangular aperture conjugate to the back pupil of the illumination objective, as described in the Design Principles section. For mid-level users, alternative configurations of Altair-LSFM, including different detection objectives, stages, filter wheels, or cameras, can be readily implemented (Supplementary Note 1). Importantly, navigate natively supports a broad range of hardware devices, and new components can be easily integrated through its modular interface. For expert users, all Zemax simulations, CAD models, and step-by-step optimization protocols are openly provided, enabling complete re-optimization of the optical design to meet specific experimental requirements.

      (4) Resolution measurements before and after deconvolution are central to the performance claim, but the deconvolution method (PetaKit5D) is only briefly mentioned in the main text, it's not referenced, and has to be clarified in more detail, coherently with the precision of the supplementary information. More specifically, PetaKit5D should be referenced in the main text, the details of the deconvolution parameters discussed in the Methods section, and the computational requirements should also be mentioned. 

      In the revised manuscript, we now provide a dedicated description of the deconvolution process in the Methods section, including the specific parameters and algorithms used. We have also explicitly referenced PetaKit5D in the main text to ensure proper attribution and clarity. Additionally, we note the computational requirements associated with this analysis in the same section for completeness.

      (5)  Image post-processing is not fully explained in the main text. Since the system is sample-scanning based, no word in the main text is spent on deskewing, which is an integral part of the post-processing to obtain a "straight" 3D stack. Since other systems implement such a post-processing algorithm (for example, single-objective architectures), it would be beneficial to have some discussion about this, and also a brief comparison to other systems in the main text in the methods section. 

      In the revised manuscript, we now explicitly describe both deskewing (shearing) and deconvolution procedures in the Alignment and Characterization section of the main text and direct readers to the Methods section. We also briefly explain why the data must be sheared to correct for the angled sample-scanning geometry for LLSM and Altair-LSFM, as well as both sample-scanning and laser-scanning-variants of OPMs.

      (6) A brief discussion on comparative costs with other systems (LLSM, dispim, etc.) could be helpful for non-imaging expert researchers who could try to implement such an optical architecture in their lab.

      Unfortunately, the exact costs of commercial systems such as LLSM or diSPIM are typically not publicly available, as they depend on institutional agreements and vendor-specific quotations. Nonetheless, we now provide approximate cost estimates in Supplementary Note 1 to help readers and prospective users gauge the expected scale of investment relative to other advanced light-sheet microscopy systems.

      (7) The "navigate" control software is provided, but a brief discussion on its advantages compared to an already open-access system, such as Micromanager, could be useful for the users.

      In the revised manuscript, we now include Supplementary Note 5 that discusses the advantages and disadvantages of different open-source microscope control platforms, including navigate and MicroManager. In brief, navigate was designed to provide turnkey support for multiple light-sheet architectures, with pre-configured acquisition routines optimized for Altair-LSFM, integrated data management with support for multiple file formats (TIFF, HDF5, N5, and Zarr), and full interoperability with OMEcompliant workflows. By contrast, while Micro-Manager offers a broader library of hardware drivers, it typically requires manual configuration and custom scripting for advanced light-sheet imaging workflows.

      (8) The cost and parts are well documented, but the time and expertise required are not crystal clear.Adding a simple time estimate (perhaps in the Supplement Section) of assembly/alignment/installation/validation and first imaging will be very beneficial for users. Also, what level of expertise is assumed (prior optics experience, for example) to be needed to install a system like this? This can help non-optics-expert users to better understand what kind of adventure they are putting themselves through.

      We thank the reviewer for this helpful suggestion. To address this, we have added Supplementary Table S5, which provides approximate time estimates for assembly, alignment, validation, and first imaging based on the user’s prior experience with optical systems. The table distinguishes between novice (no prior experience), moderate (some experience using but not assembling optical systems), and expert (experienced in building and aligning optical systems) users. This addition is intended to give prospective builders a realistic sense of the time commitment and level of expertise required to assemble and validate AltairLSFM.

      Minor things in the main text:

      (1) Line 109: The cost is considered "excluding the laser source". But then in the table of costs, you mention L4cc as a "multicolor laser source", for 25 K. Can you explain this better? Are the costs correct with or without the laser source? 

      We acknowledge that the statement in line 109 was incorrect—the quoted ~$150k system cost does include the laser source (L4cc, listed at $25k in the cost table). We have corrected this in the revised manuscript.

      (2) Line 113: You say "lateral resolution, but then you state a 3D resolution (230 nm x 230 nm x 370 nm). This needs to be fixed.

      Thank you, we have corrected this.

      (3) Line 138: Is the light-sheet uniformity proven also with a fluorescent dye? This could be beneficial for the main text, showing the performance of the instrument in a fluorescent environment.

      The light-sheet profiles shown in the manuscript were acquired using fluorescein to visualize the beam. We have revised the main text and figure legends to clearly state this.

      (4) Line 149: This is one of the most important features of the system, defying the usual tradeoff between light-sheet thickness and field of view, with a regular Gaussian beam. I would clarify more specifically how you achieve this because this really is the most powerful takeaway of the paper.

      We thank the reviewer for this key observation. The ability of Altair-LSFM to maintain a thin light sheet across a large field of view arises from diffraction effects inherent to high NA illumination. Specifically, diffraction elongates the PSF along the beam’s propagation direction, effectively extending the region over which the light sheet remains sufficiently thin for high-resolution imaging. This phenomenon, which has been the subject of active discussion within the light-sheet microscopy community, allows Altair-LSFM to partially overcome the conventional trade-off between light-sheet thickness and propagation length. We now clarify this point in the main text and provide a more detailed discussion in Supplementary Note 3, which is explicitly referenced in the discussion of the revised manuscript.

      (5) Line 171: You talk about repeatable assembly...have you tried many different baseplates? Otherwise, this is a complicated statement, since this is a proof-of-concept paper. 

      We thank the reviewer for this comment. We have not yet validated the design across multiple independently assembled baseplates and therefore agree that our previous statement regarding repeatable assembly was premature. To avoid overstating the current level of validation, we have removed this statement from the revised manuscript.

      (6) Line 187: same as above. You mention "long-term stability". For how long did you try this? This should be specified in numbers (days, weeks, months, years?) Otherwise, it is a complicated statement to make, since this is a proof-of-concept paper.

      We also agree that referencing long-term stability without quantitative backing is inappropriate, and have removed this statement from the revised manuscript.

      (7) Line 198: "rapid z-stack acquisition. How rapid? Also, what is the limitation of the galvo-scanning in terms of the imaging speed of the system? This should be noted in the methods section.

      In the revised manuscript, we now clarify these points in the Optoelectronic Design section. Specifically, we explicitly note that the resonant galvo used for shadow reduction operates at 4 kHz, ensuring that it is not rate-limiting for any imaging mode. In the same section, we also evaluate the maximum acquisition speeds achievable using navigate and report the theoretical bandwidth of the sample-scanning piezo, which together define the practical limits of volumetric acquisition speed for Altair-LSFM.

      (8) Line 234: Peta5Kit is discussed in the additional documentation, but should be referenced here, as well.

      We now reference and cite PetaKit5D.

      (9) Line 256: "values are on par with LLSM", but no values are provided. Some details should also be provided in the main text.

      In the revised manuscript, we now provide the lateral and axial resolution values originally reported for LLSM in the main text to facilitate direct comparison with Altair-LSFM. Additionally, Supplementary Note 3 now includes an expanded discussion on the nuances of resolution measurement and reporting in lightsheet microscopy.

      Figures:

      (1) Figure 1 could be implemented with Figure 3. They're both discussing the validation of the system (theoretically and with simulations), and they could be together in different panels of the same figure. The experimental light-sheet seems to be shown in a transmission mode. Showing a pattern in a fluorescent dye could also be beneficial for the paper.

      In Figure 1, our goal was to guide readers through the design process—illustrating how the detection objective’s NA sets the system’s resolution, which defines the required pixel size for Nyquist sampling and, in turn, the field of view. We then use Figure 1b–c to show how the illumination beam was designed and simulated to achieve that field of view. In contrast, Figure 3 presents the experimental validation of the illumination system. To avoid confusion, we now clarify in the text that the light sheet shown in Figure 3 was visualized in a fluorescein solution and imaged in transmission mode. While we agree that Figures 1 and 3 both serve to validate the system, we prefer to keep them as separate figures to maintain focus within each panel. We believe this organization better supports the narrative structure and allows readers to digest the theoretical and experimental validations independently.

      (2) Figure 3: Panels d and e show the same thing. Why would you expect that xz and yz profiles should be different? Is this due to the orientation of the objectives towards the sample?

      In Figure 3, we present the PSF from all three orthogonal views, as this provides the most transparent assessment of PSF quality—certain aberration modes can be obscured when only select perspectives are shown. In principle, the XZ and YZ projections should be equivalent in a well-aligned system. However, as seen in the XZ projection, a small degree of coma is present that is not evident in the YZ view. We now explicitly note this observation in the revised figure caption to clarify the difference between these panels.

      (3) Figure 4's single boxes lack a scale bar, and some of the Supplementary Figures (e.g. Figure 5) lack detailed axis labels or scale bars. Also, in the detailed documentation, some figures are referred to as Figure 5. Figure 7 or, for example, figure 6. Figure 8, and this makes the cross-references very complicated to follow

      In the revised manuscript, we have corrected these issues. All figures and supplementary figures now include appropriate scale bars, axis labels, and consistent formatting. We have also carefully reviewed and standardized all cross-references throughout the main text and supplementary documentation to ensure that figure numbering is accurate and easy to follow.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:  

      ZMAT3 is a p53 target gene that the Lal group and others have shown is important for p53mediated tumor suppression, and which plays a role in the control of RNA splicing. In this manuscript, Lal and colleagues perform quantitative proteomics of cells with ZMAT3 knockout and show that the enzyme hexokinase HKDC1 is the most upregulated protein. Mechanistically, the authors show that ZMAT3 does not appear to directly regulate the expression of HKDC1; rather, they show that the transcription factor c-JUN was strongly enriched in ZMAT3 pull-downs in IP-mass spec experiments, and they perform IP-western to demonstrate an interaction between c-JUN and ZMAT3. Importantly, the authors demonstrate, using ChIP-qPCR, that JUN is present at the HKDC1 gene (intron 1) in ZMAT3 WT cells and shows markedly enhanced binding in ZMAT3 KO cells. The data best fit a model whereby p53 transactivates ZMAT3, leading to decreased JUN binding to the HKDC1 promoter, and altered mitochondrial respiration.  

      Strengths:

      The authors use multiple orthogonal approaches to test the majority of their findings.  The authors offer a potentially new activity of ZMAT3 in tumor suppression by p53: the control of mitochondrial respiration.  

      Weaknesses:

      Some indication as to whether other c-JUN target genes are also regulated by ZMAT3 would improve the broad relevance of the authors' findings.  

      We thank the reviewer for the kind words and the thoughtful suggestion. As recommended, to identify additional c-JUN targets potentially regulated by ZMAT3, we intersected the genes upregulated upon ZMAT3 knockout (from our RNA-seq data) with the ChIP-Atlas dataset for human c-JUN and cross-referenced these with c-JUN peaks from three ENCODE cell lines. From this analysis, we selected for further analysis the top 4 candidate genes - LAMA2, VSNL1, SAMD3, and IL6R (Figure 5-figure supplement 2A-D). Like HKDC1, these genes were upregulated in ZMAT3-KO cells, and this upregulation was abolished upon siRNA-mediated JUN knockdown in ZMAT3-KO cells (Figure 5-figure supplement 2E). Moreover, by ChIP-qPCR we observed increased JUN binding to the JUN peak for these genes in ZMAT3-KO cells as compared to the ZMAT3-WT (Figure 5- figure supplement 2F). As described on page 11 of the revised manuscript, these results suggest that the ZMAT3/JUN axis negatively regulates HKDC1 expression and additional c-JUN target genes.   

      Reviewer #2 (Public review):

      Summary:

      The study elucidates the role of the recently discovered mediator of p53 tumor suppressive activity, ZMAT3. Specifically, the authors find that ZMAT3 negatively regulates HKDC1, a gene involved in the control of mitochondrial respiration and cell proliferation.  

      Strengths:

      Mechanistically, ZMAT3 suppresses HKDC1 transcription by sequestering JUN and preventing its binding to the HKDC1 promoter, resulting in reduced HKDC1 expression. Conversely, p53 mutation leads to ZMAT3 downregulation and HKDC1 overexpression, thereby promoting increased mitochondrial respiration and proliferation. This mechanism is novel; however, the authors should address several points.  

      Weaknesses:

      The authors conduct mechanistic experiments (e.g., transcript and protein quantification, luciferase assays) to demonstrate regulatory interactions between p53, ZMAT3, JUN, and HKDC1. These findings should be supported with functional assays, such as proliferation, apoptosis, or mitochondrial respiration analyses.  

      We thank the reviewer for appreciating our work and for this valuable suggestion. The reviewer rightly pointed out that supporting the regulatory interactions between p53, ZMAT3, JUN and HKDC1 with functional assays such as proliferation, apoptosis and mitochondrial respiration analyses would strengthen our mechanistic data. During the revision of our manuscript, we attempted to address this point by performing simultaneously knockdown of these proteins; however, we observed substantial toxicity under these conditions, making the functional assays technically unfeasible. This outcome was not unexpected as knockdown of JUN or HKDC1 individually results in growth defects.  We therefore focused our efforts on addressing the recommendation for authors.  

      Reviewer #3 (Public review):

      Summary:  

      In their manuscript, Kumar et al. investigate the mechanisms underlying the tumor suppressive function of the RNA binding protein ZMAT3, a previously described tumor suppressor in the p53 pathway. To this end, they use RNA-sequencing and proteomics to characterize changes in ZMAT3-deficient cells, leading them to identify the hexokinase HKDC1 as upregulated with ZMAT3 deficiency first in colorectal cancer cells, then in other cell types of both mouse and human origin. This increase in HKDC1 is associated with increased mitochondrial respiration. As ZMAT3 has been reported as an RNA-binding and DNA-binding protein, the authors investigated this via PAR-CLIP and ChIP-seq but did not observe ZMAT3 binding to HKDC1 pre-mRNA or DNA. Thus, to better understand how ZMAT3 regulates HKDC1, the authors used quantitative proteomics to identify ZMAT3interacting proteins. They identified the transcription factor JUN as a ZMAT3-interacting protein and showed that JUN promotes the increased HKDC1 RNA expression seen with ZMAT3 inactivation. They propose that ZMAT3 inhibits JUN-mediated transcriptional induction of HKDC1 as a mechanism of tumor suppression. This work uncovers novel aspects of the p53 tumor suppressor pathway.  

      Strengths:

      This novel work sheds light on one of the most well-established yet understudied p53 target genes, ZMAT3, and how it contributes to p53's tumor suppressive functions. Overall, this story establishes a p53-ZMAT3-HKDC1 tumor suppressive axis, which has been strongly substantiated using a variety of orthogonal approaches, in different cell lines and with different data sets.  

      Weaknesses:

      While the role of p53 and ZMAT3 in repressing HKDC1 is well substantiated, there is a gap in understanding how ZMAT3 acts to repress JUN-driven activation of the HKDC1 locus. How does ZMAT3 inhibit JUN binding to HKDC1? Can targeted ChIP experiments or RIP experiments be used to make a more definitive model? Can ZMAT3 mutants help to understand the mechanisms? Future work can further establish the mechanisms underlying how ZMAT3 represses JUN activity.  

      We thank the reviewer for the kind words and the invaluable suggestion. The reviewer has an excellent point regarding how ZMAT3 inhibits JUN binding to HKDC1 locus.Our new data included in the revised manuscript show that the ZMAT3-JUN interaction is lost in the presence of DNase or RNase, indicating that the interaction requires both DNA and RNA. This result suggests that ZMAT3 and JUN  form an RNA-dependent, chromatin- associated complex. Although not directly investigated in our study, this finding is consistent with emerging evidence that RBPs can function as chromatin-associated cofactors in transcription. For example, functional interplay between transcription factor YY1 and the RNA binding protein RBM25 co-regulates a broad set of genes, where RBM25 appears to engage promoters first and then recruit YY1, with RNA proposed to guide target recognition. We have discussed this possibility in the discussion section of revised manuscript (page 13). We agree that future work using ZMAT3 mutants and targeted ChIP or RIP assays will be valuable to delineate the precise mechanism by which ZMAT3 inhibits JUN binding to its target genes.   

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      ZMAT3 is a p53 target gene that the Lal group and others have shown is important for p53mediated tumor suppression, and which plays a role in the control of RNA splicing. In this manuscript, Lal and colleagues perform quantitative proteomics of cells with ZMAT3 knockout and show that the enzyme hexokinase HKDC1 is the most upregulated protein. HKDC1 is emerging as an important player in human cancer. Importantly, the authors show both acute (gene silencing) and chronic (CRISPR KO) approaches to silence ZMAT3, and they do this in several cell lines. Notably, they show that ZMAT3 silencing leads to impaired mitochondrial respiration, in a manner that is rescued by silencing of HKDC1. Mechanistically, the authors show that ZMAT3 does not appear to directly regulate the expression of HKDC1; rather, they show that the transcription factor c-JUN was strongly enriched in ZMAT3 pull-downs in IP-mass spec experiments, and they perform IP-western to demonstrate an interaction between c-JUN and ZMAT3. Importantly, the authors demonstrate, using ChIP-qPCR, that JUN is present at the HKDC1 gene (intron 1) in ZMAT3 WT cells, and shows markedly enhanced binding in ZMAT3 KO cells. The data best fit a model whereby p53 transactivates ZMAT3, leading to decreased JUN binding to the HKDC1 promoter (intron 1), and altered mitochondrial respiration. The findings are compelling, and the authors use multiple orthogonal approaches to test most findings. And the authors offer a potentially new activity of ZMAT3 in tumor suppression by p53: the control of mitochondrial respiration. As such, enthusiasm is high for this manuscript. 

      Addressing the following question would improve the manuscript. 

      It is not clear how many (other) c-JUN target genes might be impacted by ZMAT3; other important c-JUN targets in cancer include GLS1, WEE1, SREBP1, GLUT1, and CD36, so there could be a global impact on metabolism in ZMAT3 KO cells. Can the authors perform qPCR on these targets in ZMAT3 WT and KO cells and see if these target genes are differentially expressed? 

      We thank the reviewer for this thoughtful suggestion. As recommended, we examined the expression of key c-JUN target genes GLS1 (also known as GLS), WEE1, SREBP1, GLUT1, and CD36 in ZMAT3-WT and ZMAT3-KO cells. We first analyzed publicly available JUN ChIP-Seq data from three ENCODE cell lines, which revealed JUN binding peaks near or upstream of exon 1 for GLS1/GLS, SREBP1, and SLC2A1/GLUT1, but not for WEE1 or CD36 (Appendix 1, panels A-E). Based on these results, we performed RT-qPCR for GLS1/GLS, SREBP1 and SLC2A1 in ZMAT3-WT and ZMAT3-KO cells, with or without JUN knockdown. GLS mRNA was significantly reduced upon JUN knockdown in both ZMAT3-WT cells and ZMAT3-KO cells, but it was not upregulated upon loss of ZMAT3, indicating that GLS is a JUN target gene, but it is not regulated by ZMAT3. In contrast, SREBF1 or SLC2A1 expression remained unchanged upon ZMAT3 loss or JUN knockdown (Appendix 1 panels F-H). These data suggest that the ZMAT3/JUN axis does not regulate the expression of these genes.

      To identify additional c-JUN targets potentially regulated by ZMAT3, we intersected the genes upregulated upon ZMAT3 knockout (from our RNA-seq data) with the ChIP-Atlas dataset for human c-JUN and cross-referenced these with c-JUN peaks from three ENCODE cell lines. From this analysis, we selected for further analysis the top 4 candidate genes - LAMA2, VSNL1, SAMD3, and IL6R (Figure 5-figure supplement 2A-D). Like HKDC1, these genes were upregulated in ZMAT3-KO cells, and this upregulation was abolished upon siRNA-mediated JUN knockdown in ZMAT3-KO cells (Figure 5-figure supplement 2E). Moreover, by ChIP-qPCR we observed increased JUN binding to the JUN peak for these genes in ZMAT3-KO cells as compared to the ZMAT3-WT (Figure 5- figure supplement 2F). As described on page 11 of the revised manuscript, these results suggest that the ZMAT3/JUN axis negatively regulates HKDC1 expression and additional c-JUN target genes.   

      Minor concerns: 

      (1) Line 150: observed a modest. 

      (2) Line 159: Figure 2G appears to be inaccurately cited. 

      (3) Line 191: assays to measure. 

      We thank the reviewer for pointing these out. These minor concerns have been addressed in the text.  

      Reviewer #2 (Recommendations for the authors): 

      (1) Figure 1E: Can the authors clarify what the numbers on the left side of the chart represent? Do they refer to the scale?

      The numbers on the Y-axis represent the -log 10 (p- value) where higher values correspond to more significant changes. For visualization purposes, the significant changes are shown in red.  

      (2) Page 5, line 123: The sentence "As expected, ZMAT3 mRNA levels were decreased in the ZMAT3-KO cells" is redundant, as this information was already mentioned on page 4, line 103.  

      We thank the reviewer for noticing this redundancy. The repeated sentence has been removed in the revised manuscript.  

      (3) Page 5: The authors state: "Transcriptome-wide, upon loss of ZMAT3, 606 genes were significantly up-regulated (adj. p < 0.05 and 1.5-fold change) and 552 were down-regulated, with a median fold change of 1.76 and 0.55 for the up- and down-regulated genes, respectively." Later, on page 6, they write: "Comparison of the RNA-seq data from ZMAT3WT vs. ZMAT3-KO and CTRL siRNA vs. ZMAT3 siRNA-transfected HCT116 cells indicated that 1023 genes were commonly up-regulated, and 1042 were commonly down-regulated upon ZMAT3 loss (Figure S2C and D)." Why is the number of deregulated transcripts higher in the ZMAT3-WT vs. ZMAT3-KO comparison than in the CTRL siRNA vs. ZMAT3 siRNA comparison? Are the authors using less stringent criteria in the second analysis? This point should be clarified. 

      We thank the reviewer for highlighting this point. The reviewer is correct that less stringent criteria were used in the second analysis. On page 5, we applied stringent thresholds (adjusted p-value < 0.05 and 1.5-fold change) to identify high-confidence transcriptome-wide changes upon ZMAT3 loss. In contrast, for the comparison of both RNA-seq datasets (ZMAT3-WT vs. KO and siCTRL vs. siZMAT3), we included genes that were consistently up- or downregulated, without applying a fold change threshold, focusing instead on significantly altered genes (adjusted p < 0.05) in both datasets. This allowed us to capture broader and more reproducible transcriptomic changes that occur upon ZMAT3 depletion, including modest but significant changes upon transient ZMAT3 knockdown with siRNAs. We have now clarified this distinction on page 6 of the revised manuscript.

      (4) Figures 2B and 2E: The authors should provide quantification of HKDC1 protein levels normalized to a loading control. In addition, they should assess HKDC1 protein abundance upon ZMAT3 interference in SWI1222 and HCEC1CT cells, not just in HepG2 and HCT116 cells. 

      We thank the reviewer for this suggestion. We have now quantified all immunoblots presented throughout the manuscript, including those shown in Figures 2B and 2E, and all other figures containing protein analyses. Band intensities were quantified using ImageJ densitometry and normalized to GAPDH as the loading control. In addition, as suggested, we examined HKDC1 protein levels following ZMAT3 knockdown in two additional cell lines, SW1222 and HCEC-1CT. Consistent with our observations in HepG2 and HCT116 cells, ZMAT3 depletion led to increased HKDC1 protein levels in both SW1222 and HCEC-1CT cells. These new data are now included in Figure 2-figure supplement 1F and G. We have updated the Results section, figure legends, and figures to reflect these additions.

      (5) Figure 3A: It is unclear which gene was knocked out in the "KO cells." The authors should clearly specify this.

      We thank the reviewer for pointing this out. We have now updated Figure 3A.

      (6) Figure 3D: The result appears counterintuitive in comparison to Figure 3E. Why does HKDC1 knockdown reduce cell confluency more in ZMAT3 KO cells than in control (ZMAT3 wild-type) cells? The authors should explain this discrepancy more clearly.

      We thank the reviewer for this insightful comment. As shown in Figure 3D and 3E, knockdown of HKDC1 resulted in a greater decrease in proliferation in ZMAT3-KO cells than in ZMAT3-WT cells. This observation was indeed unexpected, given that HKDC1 acts downstream of ZMAT3. One possible explanation is that elevated HKDC1 expression in ZMAT3-KO cells increases their reliance on HKDC1 for sustaining proliferation, and that HKDC1 may also participate in additional pathways in ZMAT3-KO cells. Consequently, transient knockdown of HKDC1 in ZMAT3-KO cells would have a more pronounced effect on proliferation due to their increased dependency on HKDC1 activity. In contrast, ZMAT3WT cells which express lower levels of HKDC1 are less dependent on its function and therefore less sensitive to its depletion. We have now clarified this point on page 8 of the revised manuscript.  

      Reviewer #3 (Recommendations for the authors):  

      (1) Why do the authors start their analysis by knocking out the p53 response element in Zmat3? That should be clarified. In addition, since clones were picked after CRISPR KO of Zmat3, were experiments done to confirm that p53 signaling was not disrupted?

      We thank the reviewer for this thoughtful question. We began our study by targeting the p53 response element (p53RE) in the ZMAT3 locus because the basal expression of ZMAT3 is regulated by p53 (Muys, Bruna R. et al., Genes & Development, 2021). Deleting the p53RE therefore allowed us to markedly reduce ZMAT3 expression without disrupting the entire ZMAT3 locus. We have clarified this rationale on page 4 of the revised manuscript. To ensure that p53 signaling was not affected by this modification, we verified that canonical p53 targets such as p21 were equivalently induced in both ZMAT3WT and KO cells following Nutlin treatment and that p53 induction was unchanged(Figure 4F and Figure 1 – figure supplement 1A).

      (2) Throughout the text, many immunoblots are used to validate the knockouts and knockdowns used, but some clarification is needed. In Figure S1A, the Zmat3-WT sample seems to have significantly more p53 than the Zmat3 KO sample. Does Zmat3 KO compromise p53 levels in other experiments? It would be good to understand if Zmat3 affects p53 function by affecting its levels. Also, the p21 blot is overloaded.

      We thank the reviewer for this helpful observation. To determine whether ZMAT3 knockout affects p53 function by affecting its levels, we repeated the experiment three independent times. Western blots from these biological replicates, together with protein quantification, are now included in Appendix-2 and Figure 1-figure supplement 1A. These data show no significant differences in p53 or p21 induction between ZMAT3-WT and ZMAT3-KO cells following Nutlin treatment. In the revised manuscript, we have replaced the blot in Figure 1-figure supplement 1A with a more representative image from one of these replicate experiments.

      In Figure 2E, HKDC1 protein levels are not shown for the SW1222 and HCEC-1CT cell lines, 

      We thank the reviewer for this suggestion. HKDC1 protein levels in SW1222 and HCEC1-CT cells following ZMAT3 knockdown are now included as Figure 2- figure supplement 1F and 1G, together with the corresponding quantification.

      and Zmat3 does not appear as its characteristic two bands on the blot. What does this signify?

      We thank the reviewer for this observation. Endogenous ZMAT3 typically appears as two closely migrating bands on immunoblots. As shown in Figure 4D and Appendix 2A and 2B, these two bands are observed at the expected molecular weight following Nutlin treatment and are specific to ZMAT3, as they are markedly reduced in ZMAT3-KO cells. In contrast, only a single ZMAT3 band is visible in Figure 2E. This likely reflects limited resolution of the two bands in some blots rather than a biological difference.   

      (3) Why does HKDC1 knockdown only have an effect on metabolic phenotypes when ZMAT3 is gone? In Figure 3A, there does not seem to be a decrease in hexokinase activity in the siCTRL + siHKDC1 condition compared to siCTRL alone. Also, in Figure 3A, does phosphorylation activity of HKDC1 necessarily reflect glucose uptake, as stated? Additionally, in Figure 3C, there is no effect on mitochondrial respiration with siHKDC1, even though recent studies have shown a significant effect of HKDC1 on this.

      We thank the reviewer for raising these important questions. As noted, HKDC1 knockdown alone in wild-type cells (siCTRL + siHKDC1) does not significantly reduce hexokinase activity (Figure 3A). This likely reflects the low basal expression of HKDC1 in these cells. Thus, the metabolic phenotype may only become apparent when HKDC1 expression exceeds a functional threshold, as observed in ZMAT3-KO cells where HKDC1 is upregulated.

      Regarding the glucose uptake assay, HKDC1 itself is not phosphorylated; rather, it phosphorylates a non-catabolizable glucose analog, 2-deoxyglucose (2-DG) upon cellular uptake. According to the manufacturer’s protocol, intracellular 2-DG is phosphorylated by hexokinases to 2-deoxyglucose-6-phosphate (2-DG6P), which cannot be further metabolized and therefore accumulates. The accumulated 2-DG6P is quantified using a luminescence-based readout. This assay is widely used as a surrogate for glucose uptake because it reflects both glucose import and phosphorylation — the first step of glycolytic flux. As for the lack of change in mitochondrial respiration (Figure 3C), we acknowledge that some studies have reported mitochondrial roles for HKDC1 under basal conditions; however, such effects may be cell type-specific.

      (4) The emphasis on glycolysis signatures is confusing, as in the end, glycolysis does not seem to be affected by ZMAT3 status, but mitochondrial respiration is affected. Can the text be clarified to address this? It is also difficult to understand the role of oxygen consumption rate (OCR) in ZMAT3 phenotypes, as it does not fully track with proliferation. For example, ZMAT3 KD has the highest OCR, and the other conditions have similar OCRs but different proliferative rates in Figure 3D. Also, the colors used in Figure 3 to denote different genotypes change between B/C and D, which is confusing.

      We thank the reviewer for pointing out the inconsistency in the colors of the graph in Figure 2, which we have now corrected. Our data indicates that ZMAT3 regulates mitochondrial respiration without significantly affecting glycolysis. It is possible that mitochondria in ZMAT3-KO cells are oxidizing more substrates that are not produced by glycolysis. Additional work will be required to fully determine these mechanisms. We have clarified this on page 8 of the revised manuscript.      

      (5) The lack of ZMAT3 binding to RNAs in PAR-CLIP is not proof that it does not do so. A more targeted approach should be used, using individual RIP assays. The authors should also analyze the splicing of HKDC1, which could be affected by ZMAT3.

      As suggested, we performed ZMAT3 RNA IP experiments (RIP) using doxycycline-inducible HCT116-ZMAT3-FLAG cells. However, we did not observe significant enrichment of HKDC1 mRNA in the ZMAT3 IPs (Figure 5 – figure supplement 1A), consistent with previously published ZMAT3 RIP-seq data (Bersani et al, Oncotarget, 2016). These findings further support the notion that ZMAT3 does not directly bind to HKDC1 mRNA in these cells. We Accordingly, we have modified the text on page 10 of the revised manuscript.

      In addition, as suggested by the reviewer, we analyzed changes in splicing of HKDC1 pre-mRNA using rMATS in HCT116 cells by comparing our previously published RNA-seq data from siCTRL and siZMAT3-transfected HCT116 cells (Muys et al, Genes Dev, 2021). We focused on splicing events with an FDR < 0.05 and a delta PSI > |0.1| (representing at least a 10% change in splicing). The splicing analysis (data not shown) did not reveal any significant alterations in HKDC1 pre-mRNA splicing upon ZMAT3 knockdown. Corresponding text has been updated on page 10 of the revised manuscript.

      (6) The authors say that they examine JUN binding at the HKDC1 promoter several times, but they focus on intron 1 in Figure 5. They should revise the text accordingly, and they should also show JUN ChIP data traces for the whole HKDC1 locus in Figure 5C.

      We thank the reviewer for this helpful suggestion. As recommended, we have revised the text throughout the manuscript and replaced HKDC1 promoter with HKDC1 intron 1 DNA to accurately reflect our analysis, and Figure 5 now shows the JUN ChIP-seq signal across the entire HKDC1 locus.

      (7) In the ZMAT3 and JUN interaction assays, were these tested in the presence of DNAse or RNAse to determine if nucleic acids mediate the interaction?

      We thank the reviewer for this valuable suggestion. To test whether nucleic acids mediate the ZMAT3-JUN interaction, we performed ZMAT3 immunoprecipitation (IPs) in the presence or absence of DNase and RNase from doxycycline-inducible ZMAT3-FLAG expressing HCT116 cells. The ZMAT3-JUN interaction was lost upon treatment with either DNase or RNase, indicating that the interaction is mediated by nucleic acids. This data has been added in the revised manuscript (Figure 5-figure supplement 1D and on page 11).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review)

      Weaknesses:

      (1) The activity of the dominant negatives lacks appropriate controls. This is crucial given that mouse mutants for PG5, PG6, PG7, and three of the four PG4 genes show no major effects on limb induction or growth. Understanding these discrepancies is essential.

      We thank the reviewer for emphasizing the importance of appropriate controls for the dominant-negative experiments. Dominant-negative Hox constructs have been successfully and widely used in previous studies, supporting the reliability of this approach. In our experiments, electroporation of the dominant-negative constructs into the limb field produced clear and reproducible effects when compared with both unoperated embryos and embryos electroporated with a GFP control construct. The GFP construct serves as an appropriate control, as it accounts for any effects of electroporation or exogenous protein expression without altering Hox gene function. We therefore conclude that the observed phenotypes specifically reflect dominant-negative Hox activity rather than procedural artifacts.

      The absence of overt limb phenotypes in PG4–PG7 mouse mutants likely reflects both functional redundancy among Hox paralogs and the difficulty of detecting subtle limbspecific effects in bilateral, systemically affected embryos. In contrast, the chick embryo system allows unilateral gene manipulation, providing an internal control and greater sensitivity for detecting weak or localized effects that may be masked in whole-animal mouse mutants.

      (2) The authors mention redundancies in Hox activity, consistent with numerous previous reports. However, they only use single dominant-negative versions of each Hox paralog gene individually. If Hox4 and Hox5 functions are redundant, experiments should include simultaneous dominant negatives for both groups.

      We thank the reviewer for this thoughtful suggestion. We fully agree that functional redundancy among Hox paralogs is an important consideration. However, Hox gene interactions are highly context-dependent and not strictly additive. Simultaneous interference with multiple Hox groups often leads to complex or compensatory effects that are difficult to interpret mechanistically, particularly when using dominant-negative constructs that may affect overlapping transcriptional networks.

      Our current experimental design, which targets individual paralog groups, allows us to attribute observed phenotypes to specific Hox activities and to interpret the results more precisely. Moreover, as shown in previous studies, simultaneous knockdown of multiple Hox genes does not necessarily produce stronger. For these reasons, we believe that the present single–dominant-negative experiments are the most informative and sufficient for addressing the specific questions in this study.

      (3) The main conclusion that Hox4 and Hox5 provide permissive cues on which Hox6/7 induce the forelimb is not sufficiently supported by the data. An experiment expressing simultaneous dnHox4/5 and Hox6/7 is needed. If the hypothesis is correct, this should block Hox6/7's capacity to expand the limb bud or generate an extra bulge.

      We thank the reviewer for this insightful suggestion. However, because of the extensive functional redundancy and regulatory interdependence within the Hox network, simultaneous inhibition of Hox4 and Hox5 is unlikely to produce a simple or interpretable outcome. Previous studies have shown that combinatorial Hox manipulations can trigger compensatory changes in other Hox genes, often obscuring rather than clarifying specific relationships.

      In our study, the proposed permissive role of Hox4/5 is supported by the spatial and temporal patterns of Hox expression and by the phenotypic effects observed upon individual dominant-negative perturbations. These data together suggest that Hox4/5 establish a forelimb-competent domain, on which Hox6/7 subsequently act to promote limb outgrowth. We therefore believe that the current evidence sufficiently supports this model without necessitating the additional combined experiment, which may not provide clear mechanistic insight due to redundancy effects.

      (4) The identity of the extra bulge or extended limb bud is unclear. The only marker supporting its identity as a forelimb is Tbx5, while other typical limb development markers are absent. Tbx5 is also expressed in other regions besides the forelimb, and its presence does not guarantee forelimb identity. For instance, snakes express Tbx5 in the lateral mesoderm along much of their body axis.

      We thank the reviewer for this important comment. We agree that Tbx5 expression alone may be not sufficient to define forelimb identity. However, in our experiments, the induced bulge displays several additional characteristics consistent with early limb identity (in pre-AER stage). First, the Tbx5 expression we observe corresponds to the stage when the limb field is already specified, not the earlier broad mesodermal phase described in other systems. Second, the induced domain also expresses Lmx1, a marker of dorsal limb mesenchyme, further supporting its limb-specific nature. Third, our RNA sequencing analysis reveals upregulation of multiple genes associated with early limb development pathways, providing molecular evidence for limb-type identity rather than non-specific mesodermal expansion. Taken together, these results strongly indicate that the induced bulge represents a forelimb-like structure rather than a generic mesodermal thickening.

      (5) It is important to analyze the skeletons of all embryos to assess the effect of reduced limb buds upon dnHox expression and determine whether extra skeletal elements develop from the extended bud or ectopic bulge.

      We thank the reviewer for this helpful suggestion. We have analyzed the cartilage structures of the operated embryos. No skeletal elements were detected within the ectopic wing bud in the neck region. Furthermore, we did not observe any significant structural changes in the wing skeleton following loss-of-function (dnHox) experiments. These observations indicate that the ectopic bulges do not progress to form skeletal elements, consistent with their identity as early limb-like outgrowths rather than fully developed limbs.

      Reviewer #2 (Public review):

      Weaknesses

      (1) By contrast to the GOF experiments that induce ectopic limb budding, the LOF experiments, which use dominant negative forms of Hoxa4, Hoxa5, Hoxa6, and Hoxa7, are more challenging to interpret due to the absence of data on the specificity of the dominant negative constructs. Absent such controls, one cannot be certain that effects on limb development are due to disruption of the specific Hox proteins that are being targeted.

      We thank the reviewer for raising this important point regarding the specificity of the dominant-negative constructs. The dnHox constructs used in this study were generated by truncating the C-terminal region of each Hox protein, a strategy that removes the homeodomain and has been demonstrated to act as a specific dominant-negative by interfering with the corresponding Hox function without broadly affecting unrelated Hox genes. This approach has been successfully validated and used in previous work (Moreau et al., Curr. Biol. 2019), where similar constructs effectively and specifically inhibited Hox activity in the chick embryo.

      (2) A test of their central hypothesis regarding the necessity and sufficiency of the Hox genes under investigation would be to co-transfect the neck with full-length Hoxa6/a7 AND the dnHoxA4/a5. If their hypothesis is correct, then the dn constructs should block the limb-inducing ability of Hoxa6/a7 overexpression (again, validation of specificity of the DN constructs is important here)

      We thank the reviewer for this insightful suggestion. We agree that, in principle, coelectroporation of dnHox4/5 with Hox6/7 could test the hierarchical relationship between these genes. However, due to the extensive redundancy and regulatory interdependence among Hox genes, simultaneous manipulation of multiple genes often leads to compensatory effects or complex outcomes that are difficult to interpret mechanistically. As discussed in our response to Point 3 of the reviewer 1, inhibition of only one or two Hox4/5 paralogs is unlikely to completely abolish the permissive function of this group.

      Our current data — showing that Hox6/7 gain-of-function can induce ectopic limb-like outgrowths, while dnHox4/5 and dnHox6/7 lead to reduced limb formation — already provide strong evidence for both the necessity and sufficiency of these Hox activities in forelimb positioning. We therefore believe that the existing experiments adequately support our proposed model without the need for additional combinatorial manipulations.

      (3) The paper could be strengthened by providing some additional data, which should already exist in their RNA-Seq dataset, such as supplementary material that shows the actual gene expression data that are represented in the Venn diagram, heatmap, and GO analysis in Figure 3.

      We thank the reviewer for this constructive suggestion. In response, we have added a table (Table 3) listing the genes expressed in both the native limb/wing bud and the Hoxa6-induced wing bud, as identified from our RNA-Seq dataset. This table provides the underlying data for the Venn diagram, heatmap, and GO analysis presented in Figure 3. We agree that including these data improves transparency and helps readers better appreciate the molecular similarity between the induced and native limb buds.

      (4) The results of these experiments in chick embryos are rather unexpected based on previous knockout experiments in mice, and this needs to be discussed.

      We thank the reviewer for this important point. We have addressed this issue in our response to Reviewer 1, Point 1, and have expanded the relevant discussion in the manuscript. Briefly, we believe that the apparent discrepancy between chick and mouse results arises from both the high degree of functional redundancy among Hox paralogs and the limitations of detecting subtle limb-specific effects in systemic mouse mutants, where both sides of the embryo are equally affected. In contrast, the chick system allows unilateral gene manipulation, providing an internal control and greatly enhancing sensitivity to detect weak or localized effects. Thus, the chick embryo model can reveal subtle Hox-dependent limb-induction activities that are masked in conventional mouse knockout approaches.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In the manuscript submission by Zhao et al. entitled, "Cardiac neurons expressing a glucagon-like receptor mediate cardiac arrhythmia induced by high-fat diet in Drosophila" the authors assert that cardiac arrhythmias in Drosophila on a high fat diet is due in part to adipokinetic hormone (Akh) signaling activation. High fat diet induces Akh secretion from activated endocrine neurons, which activate AkhR in posterior cardiac neurons. Silencing or deletion of Akh or AkhR blocks arrhythmia in Drosophila on high fat diet. Elimination of one of two AkhR expressing cardiac neurons results in arrhythmia similar to high fat diet.

      Strengths:

      The authors propose a novel mechanism for high fat diet induced arrhythmia utilizing the Akh signaling pathway that signals to cardiac neurons.

      Comments on revisions:

      The authors have addressed my other concerns. The only outstanding issue is in regard to the following comment:

      The authors state that "HFD led to increased heartbeat and an irregular rhythm." In representative examples shown, HFD resulted in pauses, slower heart rate, and increased irregularity in rhythm but not consistently increased heart rate (Figures 1B, 3A, and 4C). Based on the cited work by Ocorr et al (https://doi.org/10.1073/pnas.0609278104), Drosophila heart rate is highly variable with periods of fast and slow rates, which the authors attributed to neuronal and hormonal inputs. Ocorr et al then describe the use of "semi-intact" flies to remove autonomic input to normalize heart rate. Were semi-intact flies used? If not, how was heart rate variability controlled? And how was heart rate "increase" quantified in high fat diet compared to normal fat diet? Lastly, how does one measure "arrhythmia" when there is so much heart rate variability in normal intact flies?

      The authors state that 8 sec time windows were selected at the discretion of the imager for analysis. I don't know how to avoid bias unless the person acquiring the imaging is blinded to the condition and the analysis is also done blind. Can you comment whether data acquisition and analysis was done in a blinded fashion? If not, this should be stated as a limitation of the study.

      Drosophila heart rate is highly variable. During the recording, we were biased to choose a time window when heartbeat was fairly stable. This is a limitation of the study, which we mentioned in the revised version. We chose to use intact over “semi-intact” flies with an intention to avoid damaging the cardiac neurons. 

      Reviewer #3 (Public review):

      Zhao et al. provide new insights into the mechanism by which a high-fat diet (HFD) induces cardiac arrhythmia employing Drosophila as a model. HFD induces cardiac arrhythmia in both mammals and Drosophila. Both glucagon and its functional equivalent in Drosophila Akh are known to induce arrhythmia. The study demonstrates that Akh mRNA levels are increased by HFD and both Akh and its receptor are necessary for high-fat diet-induced cardiac arrhythmia, elucidating a novel link. Notably, Zhao et al. identify a pair of AKH receptor-expressing neurons located at the posterior of the heart tube. Interestingly, these neurons innervate the heart muscle and form synaptic connections, implying their roles in controlling the heart muscle. The study presented by Zhao et al. is intriguing, and the rigorous characterization of the AKH receptor-expressing neurons would significantly enhance our understanding of the molecular mechanism underlying HFD-induced cardiac arrhythmia.

      Many experiments presented in the manuscript are appropriate for supporting the conclusions while additional controls and precise quantifications should help strengthen the authors' arguments. The key results obtained by loss of Akh (or AkhR) and genetic elimination of the identified AkhR-expressing cardiac neurons do not reconcile, complicating the overall interpretation.

      We thank the reviewer for the positive comments. We believe that more signaling pathways are active in the AkhR neurons and regulate rhythmic heartbeat. We are current searching for the molecules and pathways that act on the AkhR cardiac neurons to regulate the heartbeat. Thus, AkhR neuron x shall have a more profound effect. Loss of AkhR is not equivalent to AkhR neuron ablation. 

      The most exciting result is the identification of AkhR-expressing neurons located at the posterior part of the heart tube (ACNs). The authors attempted to determine the function of ACNs by expressing rpr with AkhR-GAL4, which would induce cell death in all AkhRexpressing cells, including ACNs. The experiments presented in Figure 6 are not straightforward to interpret. Moreover, the conclusion contradicts the main hypothesis that elevated Akh is the basis of HFD-induced arrhythmia. The results suggest the importance of AkhR-expressing cells for normal heartbeat. However, elimination of Akh or AkhR restores normal rhythm in HFD-fed animals, suggesting that Akh and AkhR are not important for maintaining normal rhythms. If Akh signaling in ACNs is key for HFD-induced arrhythmia, genetic elimination of ACNs should unalter rhythm and rescue the HFD-induced arrhythmia. An important caveat is that the experiments do not test the specific role of ACNs. ACNs should be just a small part of the cells expressing AkhR. Specific manipulation of ACNs will significantly improve the study. Moreover, the main hypothesis suggests that HFD may alter the activity of ACNs in a manner dependent on Akh and AkhR. Testing how HFD changes calcium, possibly by CaLexA (Figure 2) and/or GCaMP, in wild-type and AkhR mutant could be a way to connect ACNs to HFD-induced arrhythmia. Moreover, optogenetic manipulation of ACNs may allow for specific manipulation of ACNs.

      We thank the reviewer for suggesting the detailed experiments and we believe that address these points shall consolidate the results. As AkhR-Gal4 also expresses in the fat body, we set out to build a more specific driver. We planned to use split-Gal4 system (Luan et al. 2006. PMID: 17088209). The combination of pan neuronal Elav-Gal4.DBD and AkhRp65.AD shall yield AkhR neuron specific driver. We selected 2580 bp AkhR upstream DNA and cloned into pBPp65ADZpUw plasmid (Addgene plasmid: #26234). After two rounds of injection, however, we were not able to recover a transgenic line.

      We used GCaMP to record the calcium signal in the AkhR neurons. AkhR-Gal4>GCaMP has extremely high levels of fluorescence in the cardiac neurons under normal condition.

      We are screening Gal4 drivers, trying to find one line that is specific to the cardiac neurons and has a lower level of driver activity.   

      Interestingly, expressing rpr with AkhR-GAL4 was insufficient to eliminate both ACNs. It is not clear why it didn't eliminate both ACNs. Given the incomplete penetrance, appropriate quantifications should be helpful. Additionally, the impact on other AhkR-expressing cells should be assessed. Adding more copies of UAS-rpr, AkhR-GAL4, or both may eliminate all ACNs and other AkhR-expressing cells. The authors could also try UAS-hid instead of UASrpr.

      We quantified the AkhR neuron ablation and found that about 69% (n=28) showed a single ACN in AkhR-Gal4>rpr flies. It is more challenging to quantify other AkhR-expressing cells, as they are wide-spread distributed. We tried to add more copies of UAS-rpr or AkhR-Gal4, which caused developmental defects (pupa lethality). Thus, as mentioned above, we are trying to find a more specific driver for targeting the cardiac neurons.

      Recommendations for the authors:

      Reviewer #3 (Recommendations for the authors):

      The authors refer 'crop' as the functional equivalent of the human stomach. Considering the difference in their primary functions, this cannot be justified.

      In Drosophila, the crop functions analogously to the stomach in vertebrates. It is a foregut storage and preliminary processing organ that regulates food passage into the midgut. It’s more than a simple reservoir. Crop engages in enzymatic mixing, neural control, and active motility.

      Line 163 and 166, APCs are not neurons.

      Akh-producing cells (APCs) in Drosophila are neuroendocrine cells, residing in the corpora cardiaca (CC). While they produce and secrete the hormone AKH (akin to glucagon), they are not brain interneurons per se. APCs share many neuronal features (vesicular release, axon-like projections) and receive neural inputs, effectively functioning as a peripheral endocrine center.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Fungal survival and pathogenicity rely on the ability to undergo reversible morphological transitions, which are often linked to nutrient availability. In this study, the authors uncover a conserved connection between glycolytic activity and sulfur amino acid biosynthesis that drives morphogenesis in two fungal model systems. By disentangling this process from canonical cAMP signaling, the authors identify a new metabolic axis that integrates central carbon metabolism with developmental plasticity and virulence.

      Strengths:

      The study integrates different experimental approaches, including genetic, biochemical, transcriptomic, and morphological analyses, and convincingly demonstrates that perturbations in glycolysis alter sulfur metabolic pathways and thus impact pseudohyphal and hyphal differentiation. Overall, this work offers new and important insights into how metabolic fluxes are intertwined with fungal developmental programs and therefore opens new perspectives to investigate morphological transitioning in fungi.

      We thank the reviewer for finding this study to be of importance and for appreciating our multipronged approach to substantiate our finding that perturbations in glycolysis alter sulfur metabolism and thus impact pseudohyphal and hyphal differentiation in fungi.

      Weaknesses:

      A few aspects could be improved to strengthen the conclusions. Firstly, the striking transcriptomic changes observed upon 2DG treatment should be analyzed in S. cerevisiae adh1 and pfk1 deletion strains, for instance, through qPCR or western blot analyses of sulfur metabolism genes, to confirm that observed changes in 2DG conditions mirror those seen in genetic mutants. Secondly, differences between methionine and cysteine in their ability to rescue the mutant phenotype in both species are not mentioned, nor discussed in more detail. This is especially important as there seem to be differences between S. cerevisiae and C. albicans, which might point to subtle but specific metabolic adaptations.

      The authors are also encouraged to refine several figure elements for clarity and comparability (e.g., harmonized axes in bar plots), condense the discussion to emphasize the conceptual advances over a summary of the results, and shorten figure legends.

      We are grateful for this valuable and constructive feedback, and we agree with the reviewer on the necessity of performing RT-qPCR analysis of sulfur metabolism genes in ∆∆pfk1 and ∆∆adh1 strains of S. cerevisiae to validate our RNA-Seq results using 2DG. We have performed this experiment, and our results show that several genes involved in the de novo biosynthesis of sulfur-containing amino acids are downregulated in both the ∆∆pfk1 and ∆∆adh1 strains, corroborating the downregulation of sulfur metabolism genes in the 2DG treated samples. This new data is now included in the revised manuscript as Supplementary Figure 2C. 

      Furthermore, we acknowledge the reviewer’s point regarding the significance of comparing the differences in the ability of methionine and cysteine to rescue filamentation defects exhibited by the mutants, between S. cerevisiae and C. albicans. The observed differences between S. cerevisiae and C. albicans likely highlight species-specific metabolic adaptations within the sulfur assimilation pathway.  While both yeasts employ the transsulfuration pathway to interconvert these sulfur-containing amino acids, the precise regulatory points including the specific enzymes, their compartmentalization, and transcriptional control are not identical. For instance, differences in the feedback inhibition mechanisms or the expression levels of key transsulfuration enzymes between S. cerevisiae and C. albicans could explain the variations in the phenotypic rescue experiments (Chebaro et al., 2017; Lombardi et al., 2024; Rouillon et al., 2000; Shrivastava et al., 2021; Thomas and Surdin-Kerjan, 1997). Furthermore, the species-specific differences in amino acid transport systems (permeases) adds another layer of complexity. S. cerevisiae primarily uses multiple, low-affinity permeases for cysteine transport (Gap1, Bap2, Bap3, Tat1, Tat2, Agp1, Gnp1, Yct1), while relying on a limited set of high-affinity transporters (like Mup1) for methionine transport, with the added complexity that its methionine transporters can also transport cysteine (Düring-Olsen et al., 1999; Huang et al., 2017; Kosugi et al., 2001; Menant et al., 2006). In contrast, C. albicans utilizes a high-affinity transporters for the uptake of both amino acids, employing Cyn1 specifically for cysteine and Mup1 for methionine, indicating a greater reliance on dedicated transport mechanisms for these sulfur-containing molecules in the pathogenic yeast (Schrevens et al., 2018; Yadav and Bachhawat, 2011). A combination of the aforesaid factors could be the potential reason for the differences in the ability of cysteine and methionine to rescue filamentation in S. cerevisiae and C. albicans.

      Finally, we have enhanced the quantitative rigor and clarity of the data presentation in the revised manuscript by implementing Y-axis uniformity across all relevant bar graphs to facilitate a more robust and direct comparative analysis. We have also condensed the discussion to emphasize the conceptual advances and have shortened the figure legends as per the reviewer suggestions

      Reviewer #2 (Public review):

      Summary:

      This manuscript investigates the interplay between glycolysis and sulfur metabolism in regulating fungal morphogenesis and virulence. Using both Saccharomyces cerevisiae and Candida albicans, the authors demonstrate that glycolytic flux is essential for morphogenesis under nitrogen-limiting conditions, acting independently of the established cAMP-PKA pathway. Transcriptomic and genetic analyses reveal that glycolysis influences the de novo biosynthesis of sulfur-containing amino acids, specifically cysteine and methionine. Notably, supplementation with sulfur sources restores morphogenetic and virulence defects in glycolysis-deficient mutants, thereby linking core carbon metabolism with sulfur assimilation and fungal pathogenicity.

      Strengths:

      The work identifies a previously uncharacterized link between glycolysis and sulfur metabolism in fungi, bridging metabolic and morphogenetic regulation, which is an important conceptual advance and fungal pathogenicity. Demonstrating that adding cysteine supplementation rescues virulence defects in animal models connects basic metabolism to infection outcomes, which adds to biomedical importance.

      We would like to thank the reviewer for the positive comments on our work. We are pleased that they recognize the novel metabolic link between glycolysis and sulfur metabolism as a key conceptual advance in fungal morphogenesis. 

      Weaknesses:

      The proposed model that glycolytic flux modulates Met30 activity post-translationally remains speculative. While data support Met4 stabilization in met30 deletion strains, the mechanism of Met30 modulation by glycolysis is not demonstrated.

      We thank the reviewer for this valuable feedback. The activity of the SCF<sup>Met30</sup> E3 ubiquitin ligase, mediated by the F box protein Met30, is dynamically regulated through both proteolytic degradation and its dissociation from the SCF complex, to coordinate sulfur metabolism and cell cycle progression (Smothers et al., 2000; Yen et al., 2005). Our transcriptomic (RNA-seq analysis) and protein expression analysis (Fig. 3J) confirms that Met30 expression is not differentially regulated in the presence of 2DG, effectively eliminating changes in synthesis or SCF<sup>Met30</sup> proteasomal degradation as the dominant regulatory mechanism. This observation is consistent with the established paradigm wherein stress signals, such as cadmium (Cd<sup>2+</sup>) exposure, rapidly inactivates the SCF<sup>Met30</sup> E3 ubiquitin ligase via the dissociation of Met30 from the Skp1 subunit of the SCF complex (Lauinger et al., 2024; Yen et al., 2005). We therefore propose that active glycolytic flux modulates SCF<sup>Met30</sup> activity post-translationally, specifically by triggering Met30 detachment from the SCF complex. This mechanism would stabilize the primary substrate, the transcription factor Met4, thus promoting the biosynthesis of sulfur-containing amino acids. Mechanistic validation of this hypothesis, particularly the assessment of Met30 dissociation from the SCF<sup>Met30</sup> complex via immunoprecipitation (IP), is technically challenging. Since these experiments will involve isolation of cells from colonies undergoing pseudohyphal differentiation, on solid media (given that pseudohyphal differentiation does not occur in liquid media that is limiting for nitrogen (Gancedo, 2001; Gimeno et al., 1992)), current cell yields (OD<sub>600</sub>≈1 from ≈80-100 colonies) are significantly below the amount of cells that is needed to obtain the required amount of total protein concentration, for standard pull down assays (OD<Sub>600</sub>≈600-800 is required to achieve 1-2 mg/ml of total protein which is the standard requirement for pull down protocols in S. cerevisiae (Lauinger et al., 2024)).

      Given that the primary objective of our study is to establish the novel regulatory link between glycolysis and sulfur metabolism in the context of fungal morphogenesis, we would like to explore these crucial mechanistic details, in depth, in a subsequent study.

      Reviewer #3 (Public review):

      This study investigates the connection between glycolysis and the biosynthesis of sulfur-containing amino acids in controlling fungal morphogenesis, using Saccharomyces cerevisiae and C. albicans as model organisms. The authors identify a conserved metabolic axis that integrates glycolysis with cysteine/methionine biosynthetic pathways to influence morphological transitions. This work broadens the current understanding of fungal morphogenesis, which has largely focused on gene regulatory networks and cAMP-dependent signaling pathways, by emphasizing the contribution of metabolic control mechanisms. However, despite the novel conceptual framework, the study provides limited mechanistic characterization of how the sulfur metabolism and glycolysis blockade directly drive morphological outcomes. In particular, the rationale for selecting specific gene deletions, such as Met32 (and not Met4), or the Met30 deletion used to probe this pathway, is not clearly explained, making it difficult to assess whether these targets comprehensively represent the metabolic nodes proposed to be critical. Further supportive data and experimental validation would strengthen the claims on connections between glycolysis, sulfur amino acid metabolism, and virulence.

      Strengths:

      (1) The delineation of how glycolytic flux regulates fungal morphogenesis through a cAMP-independent mechanism is a significant advancement. The coupling of glycolysis with the de novo biosynthesis of sulfur-containing amino acids, a requirement for morphogenesis, introduces a novel and unexpected layer of regulation.

      (2) Demonstrating this mechanism in both S. cerevisiae and C. albicans strengthens the argument for its evolutionary conservation and biological importance.

      (3) The ability to rescue the morphogenesis defect through exogenous supplementation of sulfur-containing amino acids provides functional validation.

      (4) The findings from the murine Pfk1-deficient model underscore the clinical significance of metabolic pathways in fungal infections.

      We are grateful for this comprehensive and insightful summary of our work. We deeply appreciate the reviewer's recognition of the key conceptual breakthroughs regarding the metabolic regulation of fungal morphogenesis and the clinical relevance of our findings.

      Weaknesses:

      (1) While the link between glycolysis and sulfur amino acid biosynthesis is established via transcriptomic and proteomic analysis, the specific regulation connecting these pathways via Met30 remains to be elucidated. For example, what are the expression and protein levels of Met30 in the initial analysis from Figure 2? How specific is this effect on Met30 in anaerobic versus aerobic glycolysis, especially when the pentose phosphate pathway is involved in the growth of the cells when glycolysis is perturbed ?

      We are grateful for the insightful feedback provided by the reviewer. S. cerevisiae is a Crabtree positive organism that primarily uses anaerobic glycolysis to metabolize glucose, under glucose-replete conditions (Barford and Hall, 1979; De Deken, 1966) and our pseudohyphal differentiation assays are performed in glucose-rich conditions (Gimeno et al., 1992). Furthermore, perturbation of glycolysis is known to induce compensatory upregulation of the Pentose Phosphate Pathway (PPP) (Ralser et al., 2007) and we have also observed the upregulation of the gene that encodes for transketolase-1 (Tkl1), a key enzyme in the PPP, in our RNA-seq data. Importantly, our transcriptomic (RNA-seq analysis) and protein expression analysis (Fig. 3J) confirms that Met30 expression is not differentially regulated in the presence of 2DG, effectively eliminating changes in synthesis or SCF<sup>Met30</sup> proteasomal degradation as the dominant regulatory mechanism.  This aligns with the established paradigm wherein stress signals, such as cadmium (Cd<sup>2+</sup>) exposure, rapidly inactivates SCF<sup>Met30</sup> E3 ubiquitin ligase via Met30 dissociation from the Skp1 subunit of the complex (Lauinger et al., 2024; Yen et al., 2005). We therefore propose that active glycolytic flux modulates SCF<sup>Met30</sup> activity post-translationally, specifically by triggering Met30 detachment from the SCF complex. This mechanism would stabilize the primary substrate, the transcription factor Met4, thus promoting the biosynthesis of sulfur-containing amino acids. Further experiments are required to delineate the specific role of pentose phosphate pathway in the aforesaid proposed regulation of the Met30 activity under glycolysis perturbation and this will be explored in our subsequent study.

      (2) Including detailed metabolite profiling could have strengthened the metabolic connection and provided additional insights into intermediate flux changes, i.e., measuring levels of metabolites to check if cysteine or methionine levels are influenced intracellularly. Also, it is expected to see how Met30 deletion could affect cell growth. Data on Met30 deletion and its effect on growth are not included, especially given that a viable heterozygous Met30 strain has been established. Measuring the cysteine or methionine levels using metabolomic analysis would further strengthen the claims in every section.

      We are grateful to the reviewer for this constructive feedback. To address the potential impact of met30 deletion on cell growth, we have included new data (Suppl. Fig. 4A) demonstrating that the deletion of a single copy of met30 in diploid S. cerevisiae does not compromise overall cell growth under nitrogen-limiting conditions as the ∆met30 strain grows similar to the wild-type strain. 

      Our pseudohyphal/hyphal differentiation assays show that the defects induced by glycolytic perturbation is fully rescued by the exogenous supplementation of sulfur-containing amino acids, cysteine or methionine. Since these data conclusively demonstrate that the primary metabolic limitation caused by the perturbation of glycolysis, which leads to filamentation defects is sulfur metabolism, we posit that performing comprehensive metabolic profiling would primarily reconfirm the aforesaid results. We believe that our in vitro and in vivo sulfur add-back experiments sufficiently substantiate the novel regulatory metabolic link between glycolysis and sulfur metabolism.

      (3) In comparison with the previous bioRxiv (doi: https://doi.org/10.1101/2025.05.14.654021) of this article in May 2025 to the recent bioRxiv of this article (doi: https://doi.org/10.1101/2025.05.14.654021), there have been some changes, and Met30 deletion has been recently included, and the chemical perturbation of glycolysis has been added as new data. Although the changes incorporated in the recent version of the article improved the illustration of the hypothesis in Figure 6, which connects glycolysis to Sulfur metabolism, the gene expression and protein levels of all genes involved in the illustrated hypothesis are not consistently shown. For example, in some cases, the Met4 expression is not shown (Figure 4), and the Met30 expression is not shown during profiling (gene expression or protein levels) throughout the manuscript. Lack of consistency in profiling the same set of key genes makes understanding more complicated.

      We thank the reviewer for this feedback which helps us to clarify the scope of our transcriptomic analysis. Our decision to focus our RT-qPCR experiments on downstream targets, while excluding met4 and met30 from the RT-qPCR analysis, is based on their known regulatory mechanisms. Met4 activity is predominantly regulated by post-translational ubiquitination by the SCFMet30 complex followed by its degradation (Rouillon et al., 2000; Shrivastava et al., 2021; Smothers et al., 2000)  while Met30 activity is primarily regulated by its auto-degradation or its dissociation from the SCFMet30 complex (Lauinger et al., 2024; Smothers et al., 2000; Yen et al., 2005).  Consistent with this, our RNA-Seq results indicate that neither met4 nor met30 transcripts are differentially expressed, in response to 2DG addition. For all our RT-qPCR analysis in S. cerevisiae and C. albicans, we have consistently used the same set of sulfur metabolism genes and these include met32, met3, met5, met10 and met17. Our data on protein expression analysis of Met30 in S. cerevisiae (Fig. 3J) confirms that Met30 expression is not differentially regulated in the presence of 2DG, effectively eliminating changes in synthesis or SCFMet30 proteasomal degradation as the dominant regulatory mechanism.

      (4) The demonstrated link between glycolysis and sulfur amino acid biosynthesis, along with its implications for virulence in C. albicans, is important for understanding fungal adaptation, as mentioned in the article; however, the Met4 activation was not fully characterized, nor were the data presented when virulence was assessed in Figure 4. Why is Met4 not included in Figure 4D and I? Especially, according to Figure 6, Met4 activation is crucial and guides the differences between glycolysis-active and inactive conditions.

      We thank the reviewer for their input. As the Met4 transcription factor in C. albicans is primarily regulated post-translationally through its degradation and inactivation by the SCFMet30 E3 ubiquitin ligase complex (Shrivastava et al., 2021), we opted to monitor the transcriptional status of downstream targets of Met4 (i.e., genes directly regulated by Met4), as these are the genes that exhibit the most direct and functionally relevant transcriptional changes in response to the altered Met4 levels.

      (5) Similarly, the rationale behind selecting Met32 for characterizing sulfur metabolism is unclear. Deletion of Met32 resulted in a significant reduction in pseudohyphal differentiation; why is this attributed only to Met32? What happens if Met4 is deleted? It is not justified why Met32, rather than Met4, was chosen. Figure 6 clearly hypothesizes that Met4 activation is the key to the mechanism.

      We sincerely thank the reviewer for this insightful query regarding our selection of the met32 for our gene deletion experiments. The choice of ∆∆met32 strain was strategically motivated by its unique phenotypic properties within the de novo biosynthesis of sulfur-containing amino acids pathway. While deletions of most the genes that encode for proteins involved in the de novo biosynthesis of sulfurcontaining amino acids, result in auxotrophy for methionine or cysteine, ∆∆met32 strain does not exhibit this phenotype (Blaiseau et al., 1997). This key distinction is attributed to the functional redundancy provided by the paralogous gene, met31 (Blaiseau et al., 1997). Crucially, given that the deletion of the central transcriptional regulator, met4, results in cysteine/methionine auxotrophy, the use of the ∆∆met32 strain provides an essential, viable experimental model for investigating the role of sulfur metabolism during pseudohyphal differentiation in S. cerevisiae.

      (6) The comparative RT-qPCR in Figure 5 did not account for sulfur metabolism genes, whereas it was focused only on virulence and hyphal differentiation. Is there data to support the levels of sulfur metabolism genes?

      We thank the reviewer for this feedback. We wish to respectfully clarify that the data pertaining to expression of sulfur metabolism genes in the presence of 2DG or in the ∆∆pfk1 strain in C. albicans are already included and discussed within the manuscript. These results can be found in Figure 4, panels D and I, respectively.

      (7) To validate the proposed interlink between sulfur metabolism and virulence, it is recommended that the gene sets (illustrated in Figure 6) be consistently included across all comparative data included throughout the comparisons. Excluding sulfur metabolism genes in Figure 5 prevents the experiment from demonstrating the coordinated role of glycolysis perturbation → sulfur metabolism → virulence. The same is true for other comparisons, where the lack of data on Met30, Met4, etc., makes it hard.to connect the hypothesis. It is also recommended to check the gene expression of other genes related to the cAMP pathway and report them to confirm the cAMP-independent mechanism. For example, gap2 deletion was used to confirm the effects of cAMP supplementation, but the expression of this gene was not assessed in the RNA-seq analysis in Figure 2. It would be beneficial to show the expression of cAMP-related genes to completely confirm that they do not play a role in the claims in Figure 2.

      We thank the reviewer for this valuable feedback. The transcriptional analysis of the sulfur metabolism genes in the presence of 2DG and the ∆∆pfk1 strain is shown in Figures 4D and 4I.

      Our RNA-seq analysis (Author response image 1) confirms that there is no significant transcriptional change in the expression of cAMP-PKA pathway associated genes (Log2 fold change ≥ 1 for upregulated genes and Log2 fold change ≤ -1 for downregulated genes) in 2DG treated cells compared to the untreated control cells, reinforcing our conclusion that the glycolytic regulation of fungal morphogenesis is mediated through a cAMP-PKA pathway independent mechanism.

      Author response image 1.

      (8) Although the NAC supplementation study is included in the new version of the article compared to the previous version in BioRxiv (May 2025), the link to sulfur metabolism is not well characterized in Figure 5 and their related datasets. The main focus of the manuscript is to delineate the role of sulfur metabolism; hence, it is anticipated that Figure 5 will include sulfur-related metabolic genes and their links to pfk1 deletion, using RT-PCR measurements as shown for the virulence genes.

      We thank the reviewer for this question. The relevant data are indeed present within the current submission. We respectfully direct the reviewer's attention to Figure 4, panels D and I, where the data pertaining to expression of sulfur metabolism genes in the presence of 2DG or in the ∆∆pfk1 strain in C. albicans can be found.

      (9) The manuscript would benefit from more information added to the introduction section and literature supports for some of the findings reported earlier, including the role of (i) cAMP-PKA and MAPK pathways, (ii) what is known in the literature that reports about the treatment with 2DG (role of Snf1, HXT1, and HXT3), as well as how gpa2 is involved. Some sentences in the manuscripts are repetitive; it would be beneficial to add more relevant sections to the introduction and discussion to clarify the rationale for gene choices.

      We thank the reviewer for this valuable feedback. We have incorporated these changes in our revised manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Line 107: As morphological transitions are indeed a conserved phenomenon across fungal species, hosts & environmental niches, the authors could refer to a few more here (infection structures like appressoria; fruiting bodies, etc.).

      We thank the reviewer for this valuable feedback. We have incorporated these changes in our revised manuscript.

      Line 119/120: That's a bit misleading in my opinion. Gpr1 acts as a key sensor of external carbon, while Ras proteins control the cAMP pathway as intracellular sensory proteins. That should be stated more clearly. cAMP is the output and not the sensor.

      We appreciate the reviewer's detailed attention to this signaling network. We have revised the manuscript to precisely reflect this established signaling hierarchy for maximum clarity.

      (2) Line 180: ..differentiation

      We thank the reviewer for this valuable feedback. We have incorporated this change in our revised manuscript.

      (3) Figure 1 panels C & F. The authors should provide the same scale for all experiments. Otherwise, the interpretation can be difficult. The same applies to the different bar plots in Figure 4. Have the authors quantified pseudohyphal differentiation in the cAMP add-back assays? I agree that the chosen images look convincing, but they don't reflect quantitative analyses.

      We thank the reviewer for detailed and constructive feedback. We have changed the Y-axis and made it more uniform to improve the clarity of our data presentation in the revised manuscript.

      We have also incorporated the quantitative analysis of the cAMP add-back assays in S. cerevisiae, in Figure 2 Panel L.

      (4) Line 367/68: "cysteine or methionine was able to completely rescue". Here, the authors should phrase their wording more carefully. Figure 3C shows the complete rescue of the phenotype qualitatively, but Figure 3D clearly shows that there are differences between the supplementation of cysteine and methionine, with the latter not fully restoring the phenotype.

      We sincerely appreciate the reviewer's meticulous attention to the data interpretation. We fully agree that the initial phrasing in lines 367/368 requires adjustment, as Figure 3D establishes a quantitative difference in the efficiency of phenotypic rescue between cysteine and methionine supplementation. We have revised the text to articulate this difference.

      (5) Line 568: Here, apparently, the ability to rescue the differentiation phenotype is reversed compared to the experiment with S. cerevisiae. Cysteine only results in ~20% hyphal cells, while methionine restores to wild-type-like hyphal formation. Can the authors comment on where these differences might originate from? Is there a difference in the uptake of cysteine vs. methionine in the two species or consumption rates?

      We thank the reviewer for their detailed and constructive feedback. We believe this phenotypic difference can be due to the distinct metabolic prioritization of sulfur amino acids in C. albicans. Methionine is a known trigger for hyphal differentiation in C. albicans and serves as the immediate precursor for the universal methyl donor, S-adenosylmethionine (SAM) (Schrevens et al., 2018). (Kraidlova et al., 2016). The morphological transition to hyphae involves a complex regulatory cascade which requires high rates of methylation, and this requires a rapid and direct conversion of methionine into SAM (Kraidlova et al., 2016; Schrevens et al., 2018). Cysteine, however, must first be converted into methionine via the transsulfuration pathway to produce SAM, making it metabolically less efficient for these aforesaid processes.

      Reviewer #2 (Recommendations for the authors):

      The study's comprehensive experimental approach with integrating pharmacological inhibition, genetic manipulation, transcriptomics, and infection animal model, provides strong evidence for a conserved mechanism, though some aspects need further clarification.

      Major Comments:

      (1) While the data suggest that glycolysis affects Met30 activity post-translationally, the underlying mechanism remains speculative. The authors should perform co-immunoprecipitation or ubiquitination assays to confirm whether glycolytic perturbation alters Met30-SCF complex interactions or Met4 ubiquitination levels.

      We thank the reviewer for this valuable feedback. The activity of the SCF<sup>Met30</sup> E3 ubiquitin ligase, mediated by the F box protein Met30, is dynamically regulated through both proteolytic degradation and its dissociation from the SCF complex, to coordinate sulfur metabolism and cell cycle progression (Smothers et al., 2000; Yen et al., 2005). Our transcriptomic (RNA-seq analysis) and protein expression analysis (Fig. 3J) confirms that Met30 expression is not differentially regulated in the presence of 2DG, effectively eliminating changes in synthesis or SCF<sup>Met30</sup> proteasomal degradation as the dominant regulatory mechanism. This observation is consistent with the established paradigm wherein stress signals, such as cadmium (Cd<sup>2+</sup>) exposure, rapidly inactivates the SCF<sup>Met30</sup> E3 ubiquitin ligase via the dissociation of Met30 from the Skp1 subunit of the SCF complex (Lauinger et al., 2024; Yen et al., 2005). We therefore propose that active glycolytic flux modulates SCF<sup>Met30</sup> activity post-translationally, specifically by triggering Met30 detachment from the SCF complex. This mechanism would stabilize the primary substrate, the transcription factor Met4, thus promoting the biosynthesis of sulfur-containing amino acids. Mechanistic validation of this hypothesis, particularly the assessment of Met30 dissociation from the SCF<sup>Met30 </sup>complex via immunoprecipitation (IP), is technically challenging. Since these experiments will involve isolation of cells from colonies undergoing pseudohyphal differentiation, on solid media (given that pseudohyphal differentiation does not occur in liquid media that is limiting for nitrogen (Gancedo, 2001; Gimeno et al., 1992)), current cell yields (OD<sup>600</sup>≈1 from ≈80-100 colonies) are significantly below the amount of cells that is needed to obtain the required amount of total protein concentration, for standard pull down assays (OD600≈600-800 is required to achieve 1-2 mg/ml of total protein which is the standard requirement for pull down protocols in S. cerevisiae (Lauinger et al., 2024)).

      Given that the primary objective of our study is to establish the novel regulatory link between glycolysis and sulfur metabolism in the context of fungal morphogenesis, we would like to explore these crucial mechanistic details, in depth, in a subsequent study.

      (2) 2DG can exert pleiotropic effects unrelated to glycolytic inhibition (e.g., ER stress, autophagy induction). The authors are encouraged to perform complementary metabolic flux analyses, such as quantification of glycolytic intermediates or ATP levels, to confirm specific glycolytic inhibition.

      We appreciate the reviewer's concern regarding the potential pleiotropic effects of 2DG. While we acknowledge that 2DG may induce secondary cellular stress, we are confident that the observed phenotypes are robustly attributed to glycolytic inhibition based on our complementary genetic evidence. Specifically, the deletion strains ∆∆pfk1 and ∆∆adh1, which genetically perturb distinct steps in glycolysis, recapitulate the phenotypic results observed with 2DG treatment. Given this strong congruence between chemical inhibition and specific genetic deletions of key glycolytic enzymes, we are confident that our observed phenotypes are predominantly driven by the perturbation of the glycolytic pathway by 2DG.

      (3) The differential rescue effects (cysteine-only in inhibitor assays vs. both cysteine and methionine in genetic mutants) require further explanation. The authors should discuss potential differences in metabolic interconversion or amino acid transport that may account for this observation.

      We thank the reviewer for their valuable feedback. One explanation for the observed differential rescue effects of cysteine and methionine can be due to the distinct amino acid transport systems used by S. cerevisiae to transport these amino acids. S. cerevisiae primarily uses multiple, lowaffinity permeases (Gap1, Bap2, Bap3, Tat1, Tat2, Agp1, Gnp1, Yct1) for cysteine transport, while relying on a limited set of high-affinity transporters (like Mup1) for methionine transport, with the added complexity that its methionine transporters can also transport cysteine (Düring-Olsen et al., 1999; Huang et al., 2017; Kosugi et al., 2001; Menant et al., 2006). Hence, it is likely that cysteine uptake could be happening at a higher efficiency in S. cerevisiae compared to methionine uptake. Therefore, to achieve a comparable functional rescue by exogenous supplementation of methionine, it is necessary to use a higher concentration of methionine. When we performed our rescue experiments using higher concentrations of methionine, we did not see any rescue of pseudohyphal differentiation in the presence of 2DG and in fact we noticed that, at higher concentrations of methionine, the wild-type strain failed to undergo pseudohyphal differentiation even in the absence of 2DG. This is likely due to the fact that increasing the methionine concentration raises the overall nitrogen content of the medium, thereby making the medium less nitrogen-starved. This presents a major experimental constraint, as pseudohyphal differentiation is strictly dependent on nitrogen limitation, and the elevated nitrogen resulting from the higher methionine concentration can inhibit pseudohyphal differentiation.

      (4) NAC may influence host redox balance or immune responses. The discussion should consider whether the observed virulence rescue could partly result from host-directed effects.

      We thank the reviewer for this valuable feedback. We acknowledge the role of NAC in host directed immune response. It is important to note that, in the context of certain bacterial pathogens, NAC has been reported to augment cellular respiration, subsequently increasing Reactive Oxygen Species (ROS) generation, which contributes to pathogen clearance (Shee et al., 2022). Interestingly, in our study, NAC supplementation to the mice was given prior to the infection and maintained continuously throughout the duration of the experiment. This continuous supply of NAC likely contributes to the rescue of virulence defects exhibited by the ∆∆pfk1 strain (Fig. 5I and J). Essentially, NAC likely allows the mutant to fully activate its essential virulence strategies (including morphological switching), to cause a successful infection in the host. As per the reviewer suggestion, this has been included in the discussion section of the manuscript.

      Reviewer #3 (Recommendations for the authors):

      Most of the comments related to improving the manuscript have been provided in the public review. Here are some specifics for the authors to consider:

      (1) It is important to clarify the rationale for choosing specific gene deletions over other key genes (e.g., Met32 and Met30) and explain why Met4 was not included, given its proposed central role in Figure 6.

      We sincerely thank the reviewer for this insightful query regarding our selection of the met32 for our gene deletion experiments. The choice of ∆∆met32 strain was strategically motivated by its unique phenotypic properties within the de novo biosynthesis of sulfur-containing amino acids pathway. While deletions of most the genes that encode for proteins involved in the de novo biosynthesis of sulfurcontaining amino acids, result in auxotrophy for methionine or cysteine, ∆∆met32 strain does not exhibit this phenotype (Blaiseau et al., 1997). This key distinction is attributed to the functional redundancy provided by the paralogous gene, met31 (Blaiseau et al., 1997). Crucially, given that the deletion of the central transcriptional regulator, met4, results in cysteine/methionine auxotrophy, the use of the ∆∆met32 strain provides an essential, viable experimental model for investigating the role of sulfur metabolism during pseudohyphal differentiation in S. cerevisiae.

      (2) Comparison of consistent gene and protein expression data (Met30, Met4, Met32) across all relevant figures and analyses would strengthen the mechanistic connection in a better way. Some data that might help connect the sections is not included; please see the public review for more details.

      We thank the reviewer for this valuable input, which helps us to clarify the scope of our transcriptomic analysis. Our decision to focus our RT-qPCR experiments on downstream targets, while excluding Met4 and Met30 from the RT-qPCR analysis, is based on their known regulatory mechanisms. Met4 activity is predominantly regulated by post-translational ubiquitination by the SCFMet30 complex followed by its degradation (Rouillon et al., 2000; Shrivastava et al., 2021; Smothers et al., 2000)  while Met30 activity is primarily regulated by its auto-degradation or its dissociation from the SCFMet30 complex (Lauinger et al., 2024; Smothers et al., 2000; Yen et al., 2005).  Consistent with this, our RNA-Seq results indicate that neither met4 nor met30 transcripts are differentially expressed, in response to 2DG addition. For all our RT-qPCR analysis in S. cerevisiae and C. albicans, we have consistently used the same set of sulfur metabolism genes and these include met32, met3, met5, met10 and met17. Our data on protein expression analysis of Met30 in S, cerevisiae (Fig. 3J) confirms that Met30 expression is not differentially regulated in the presence of 2DG, effectively eliminating changes in synthesis or SCFMet30 proteasomal degradation as the dominant regulatory mechanism.

      (3) Suggested to include metabolomic profiling (cysteine, methionine, and intermediate metabolites) to substantiate the proposed metabolic flux between glycolysis and sulfur metabolism.

      We thank the reviewer for this valuable input. Our pseudohyphal/hyphal differentiation assays show that the defects induced by glycolytic perturbation is fully rescued by the exogenous supplementation of sulfur-containing amino acids, cysteine or methionine. Since these data conclusively demonstrate that the primary metabolic limitation caused by the perturbation of glycolysis, which leads to filamentation defects, is sulfur metabolism, we posit that performing comprehensive metabolic profiling would primarily reconfirm the aforesaid results. We believe that our in vitro and in vivo sulfur add-back experiments sufficiently substantiate the novel regulatory metabolic link between glycolysis and sulfur-metabolism.

      (4) Data on the effects of Met30 deletion on cell growth are currently not included, and relevant controls should be included to ensure observed phenotypes are not due to general growth defects.

      We are grateful to the reviewer for this constructive feedback. To address the potential impact of met30 deletion on cell growth, we have included new data (Suppl. Fig. 4A) demonstrating that the deletion of a single copy of met30 in diploid S. cerevisiae does not compromise overall growth under nitrogen-limiting conditions as the ∆met30 strain grows similar to the wild-type strain.

      (5) Expanding RT-qPCR and data from transcriptomic analyses to include sulfur metabolism genes and key cAMP pathway genes to confirm the proposed cAMP-independent mechanism during virulence characterization is necessary.

      We thank the reviewer for this valuable feedback. The transcriptional analysis of the sulfur metabolism genes in the presence of 2DG and the ∆∆pfk1 strain is shown in Figures 4D and 4I. 

      In order to confirm that glycolysis is critical for fungal morphogenesis in a cAMP-PKA pathway independent manner under nitrogen-limiting conditions in C. albicans, we performed cAMP add-back assays. Interestingly, corroborating our S. cerevisiae data, the exogenous addition of cAMP failed to rescue hyphal differentiation defect caused by the perturbation of glycolysis through 2DG addition or by the deletion of the pfk1 gene, under nitrogen-limiting condition in C. albicans. This data is now included in Suppl. Fig. 5B.

      (6) Enhancing the introduction and discussion by providing a clearer rationale for gene selection and more detailed references to established pathways (cAMP-PKA, MAPK, Snf1/HXT regulation, gpa2 involvement) is needed to reinstate the hypothesis.

      We thank the reviewer for this valuable feedback. We have incorporated these changes in our revised manuscript.

      (7) Reducing redundancy in the text and improving figure consistency, particularly by ensuring that the gene sets depicted in Figure 6 are represented across all datasets, would strengthen the interconnections among sections.

      We thank the reviewer for this valuable feedback.  We have incorporated these changes in our revised manuscript.

      References

      Barford JP, Hall RJ. 1979. An examination of the crabtree effect in Saccharomyces cerevisiae: The role of respiratory adaptation. J Gen Microbiol. https://doi.org/10.1099/00221287-114-2-267

      Blaiseau, P. L., & Thomas, D. (1998). Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. The EMBO journal, 17(21), 6327–6336. https://doi.org/10.1093/emboj/17.21.6327

      Chebaro, Y., Lorenz, M., Fa, A., Zheng, R., & Gustin, M. (2017). Adaptation of Candida albicans to Reactive Sulfur Species. Genetics, 206(1), 151–162. https://doi.org/10.1534/genetics.116.199679

      De Deken R. H. (1966). The Crabtree effect: a regulatory system in yeast. Journal of general microbiology, 44(2), 149–156. https://doi.org/10.1099/00221287-44-2-149

      Düring-Olsen, L., Regenberg, B., Gjermansen, C., Kielland-Brandt, M. C., & Hansen, J. (1999). Cysteine uptake by Saccharomyces cerevisiae is accomplished by multiple permeases. Current genetics, 35(6), 609–617. https://doi.org/10.1007/s002940050459

      Gancedo J. M. (2001). Control of pseudohyphae formation in Saccharomyces cerevisiae. FEMS microbiology reviews, 25(1), 107–123. https://doi.org/10.1111/j.1574-6976.2001.tb00573.x

      Gimeno, C. J., Ljungdahl, P. O., Styles, C. A., & Fink, G. R. (1992). Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell, 68(6), 1077–1090. https://doi.org/10.1016/0092-8674(92)90079-r

      Huang, C. W., Walker, M. E., Fedrizzi, B., Gardner, R. C., & Jiranek, V. (2017). Yeast genes involved in regulating cysteine uptake affect production of hydrogen sulfide from cysteine during fermentation. FEMS yeast research, 17(5), 10.1093/femsyr/fox046. https://doi.org/10.1093/femsyr/fox046

      Kosugi, A., Koizumi, Y., Yanagida, F., & Udaka, S. (2001). MUP1, high affinity methionine permease, is involved in cysteine uptake by Saccharomyces cerevisiae. Bioscience, biotechnology, and biochemistry, 65(3), 728–731. https://doi.org/10.1271/bbb.65.728

      Kraidlova, L., Schrevens, S., Tournu, H., Van Zeebroeck, G., Sychrova, H., & Van Dijck, P. (2016). Characterization of the Candida albicans Amino Acid Permease Family: Gap2 Is the Only General Amino Acid Permease and Gap4 Is an S-Adenosylmethionine (SAM) Transporter Required for SAM-Induced Morphogenesis. mSphere, 1(6), e00284-16. https://doi.org/10.1128/mSphere.00284-16

      Lauinger, L., Andronicos, A., Flick, K., Yu, C., Durairaj, G., Huang, L., & Kaiser, P. (2024). Cadmium binding by the F-box domain induces p97-mediated SCF complex disassembly to activate stress response programs. Nature communications, 15(1), 3894. https://doi.org/10.1038/s41467-024-48184-6

      Lombardi, L., Salzberg, L. I., Cinnéide, E. Ó., O'Brien, C., Morio, F., Turner, S. A., Byrne, K. P., & Butler, G. (2024). Alternative sulphur metabolism in the fungal pathogen Candida parapsilosis. Nature communications, 15(1), 9190. https://doi.org/10.1038/s41467-024-53442-8

      Menant, A., Barbey, R., & Thomas, D. (2006). Substrate-mediated remodeling of methionine transport by multiple ubiquitin-dependent mechanisms in yeast cells. The EMBO journal, 25(19), 4436–4447. https://doi.org/10.1038/sj.emboj.7601330

      Ralser, M., Wamelink, M. M., Kowald, A., Gerisch, B., Heeren, G., Struys, E. A., Klipp, E., Jakobs, C., Breitenbach, M., Lehrach, H., & Krobitsch, S. (2007). Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. Journal of biology, 6(4), 10. https://doi.org/10.1186/jbiol61

      Rouillon, A., Barbey, R., Patton, E. E., Tyers, M., & Thomas, D. (2000). Feedback-regulated degradation of the transcriptional activator Met4 is triggered by the SCF(Met30 )complex. The EMBO journal, 19(2), 282–294. https://doi.org/10.1093/emboj/19.2.282

      Schrevens, S., Van Zeebroeck, G., Riedelberger, M., Tournu, H., Kuchler, K., & Van Dijck, P. (2018). Methionine is required for cAMP-PKA-mediated morphogenesis and virulence of Candida albicans. Molecular microbiology, 108(3), 258–275. https://doi.org/10.1111/mmi.13933

      Shee, S., Singh, S., Tripathi, A., Thakur, C., Kumar T, A., Das, M., Yadav, V., Kohli, S., Rajmani, R. S., Chandra, N., Chakrapani, H., Drlica, K., & Singh, A. (2022). Moxifloxacin-Mediated Killing of Mycobacterium tuberculosis Involves Respiratory Downshift, Reductive Stress, and Accumulation of Reactive Oxygen Species. Antimicrobial agents and chemotherapy, 66(9), e0059222. https://doi.org/10.1128/aac.00592-22

      Shrivastava, M., Feng, J., Coles, M., Clark, B., Islam, A., Dumeaux, V., & Whiteway, M. (2021). Modulation of the complex regulatory network for methionine biosynthesis in fungi. Genetics, 217(2), iyaa049. https://doi.org/10.1093/genetics/iyaa049

      Smothers, D. B., Kozubowski, L., Dixon, C., Goebl, M. G., & Mathias, N. (2000). The abundance of Met30p limits SCF(Met30p) complex activity and is regulated by methionine availability. Molecular and cellular biology, 20(21), 7845–7852. https://doi.org/10.1128/MCB.20.21.7845-7852.2000

      Thomas, D., & Surdin-Kerjan, Y. (1997). Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiology and molecular biology reviews : MMBR, 61(4), 503–532. https://doi.org/10.1128/mmbr.61.4.503532.1997

      Yadav, A. K., & Bachhawat, A. K. (2011). CgCYN1, a plasma membrane cystine-specific transporter of Candida glabrata with orthologues prevalent among pathogenic yeast and fungi. The Journal of biological chemistry, 286(22), 19714–19723. https://doi.org/10.1074/jbc.M111.240648

      Yen, J. L., Su, N. Y., & Kaiser, P. (2005). The yeast ubiquitin ligase SCFMet30 regulates heavy metal response. Molecular biology of the cell, 16(4), 1872–1882. https://doi.org/10.1091/mbc.e04-12-1130

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Joint Public Review:

      In this work, the authors present DeepTX, a computational tool for studying transcriptional bursting using single-cell RNA sequencing (scRNA-seq) data and deep learning. The method aims to infer transcriptional burst dynamics-including key model parameters and the associated steady-state distributions-directly from noisy single-cell data. The authors apply DeepTX to datasets from DNA damage experiments, revealing distinct regulatory patterns: IdU treatment in mouse stem cells increases burst size, promoting differentiation, while 5FU alters burst frequency in human cancer cells, driving apoptosis or survival depending on dose. These findings underscore the role of burst regulation in mediating cell fate responses to DNA damage.

      The main strength of this study lies in its methodological contribution. DeepTX integrates a non-Markovian mechanistic model with deep learning to approximate steady-state mRNA distributions as mixtures of negative binomial distributions, enabling genome-scale parameter inference with reduced computational cost. The authors provide a clear discussion of the framework's assumptions, including reliance on steady-state data and the inherent unidentifiability of parameter sets, and they outline how the model could be extended to other regulatory processes.

      The revised manuscript addresses many of the original concerns, particularly regarding sample size requirements, distributional assumptions, and the biological interpretation of inferred parameters. However, the framework remains limited by the constraints of snapshot data and cannot yet resolve dynamic heterogeneity or causality. The manuscript would also benefit from a broader contextualisation of DeepTX within the landscape of existing tools linking mechanistic modelling and single-cell transcriptomics. Finally, the interpretation of pathway enrichment analyses still warrants clarification.

      Overall, this work represents a valuable contribution to the integration of mechanistic models with highdimensional single-cell data. It will be of interest to researchers in systems biology, bioinformatics, and computational modelling.

      Recommendations for the authors:

      We thank the authors for their thorough revision and for addressing many of the points raised during the initial review. The revised manuscript presents an improved and clearer account of the methodology and its implications. However, several aspects would benefit from further clarification and refinement to strengthen the presentation and avoid overstatement.

      (1) Contextualization within the existing literature

      The manuscript would benefit from placing DeepTX more clearly in the context of other computational tools developed to connect mechanistic modelling and single-cell RNA sequencing data. This is an active area of research with notable recent contributions, including Sukys and Grima (bioRxiv, 2024), Garrido-Rodriguez et al. (PLOS Comp Biol, 2021), and Maizels (2024). Positioning DeepTX in relation to these and other relevant efforts would help readers appreciate its specific advances and contributions.

      We sincerely thank you for this valuable suggestion. We agree that situating DeepTX within the broader landscape of computational approaches linking mechanistic modeling and single-cell RNA sequencing data will clarify its contributions and advances. In this revised version, we have explicitly discussed the comparison and relation of DeepTX in the context of this active area using an individual paragraph in the Discussion section.

      Specifically, we mentioned that the DeepTX research paradigm contributes to a growing line of area aiming to link mechanistic models of gene regulation with scRNA-seq data. Maizels provided a comprehensive review of computational strategies for incorporating dynamic mechanisms into single-cell transcriptomics (Maizels RJ, 2024). In this context, RNA velocity is one of the most important examples as it infers short-term transcriptional trends based on splicing kinetics and deterministic ODEs model. However, such approaches are limited by their deterministic assumptions and cannot fully capture the stochastic nature of gene regulation. DeepTX can be viewed as an extension of this framework to stochastic modelling, explicitly addressing transcriptional bursting kinetics under DNA damage. Similarly, DeepCycle, developed by Sukys and Grima (Sukys A & Grima R, 2025), investigates transcriptional burst kinetics during the cell cycle, employing a stochastic age-dependent model and a neural network to infer burst parameters while correcting for measurement noise. By contrast, MIGNON integrates genomic variation data and static transcriptomic measurements into a mechanistic pathway model (HiPathia) to infer pathway-level activity changes, rather than gene-level stochastic transcriptional dynamics (Garrido-Rodriguez M et al., 2021). In this sense, DeepTX and MIGNON are complementary, with DeepTX resolving burst kinetics at the single-gene level and MIGNON emphasizing pathway responses to genomic perturbations, which could inspire future extensions of DeepTX that incorporate sequence-level information.

      (2) Interpretation of GO analysis

      The interpretation of the GO enrichment results in Figure 4D should be revised. While the text currently associates the enriched terms with signal transduction and cell cycle G2/M phase transition, the most significant terms relate to mitotic cell cycle checkpoint signaling. This distinction should be made clear in the main text, and the conclusions drawn from the GO analysis should be aligned more closely with the statistical results.

      We sincerely appreciate you for the insightful comment. We have carefully re-examined the GO enrichment results shown in Figure 4D and agree that the most significantly enriched terms correspond to mitotic cell cycle checkpoint signaling and signal transduction in response to DNA damage, rather than general G2/M phase transition processes. Accordingly, we have revised the main text to highlight the biological significance of mitotic cell cycle checkpoint signaling.

      Specifically, we now emphasize two key points: DNA damage and mitotic checkpoint activation are closely interconnected. (1) The mitotic checkpoint serves as a crucial safeguard to ensure accurate chromosome segregation and maintain genomic stability under DNA damage conditions. Activation of the mitotic checkpoint can influence cell fate decisions and differentiation potential (Kim EM & Burke DJ, 2008; Lawrence KS et al., 2015). (2) Sustained activation of the spindle assembly checkpoint (SAC) has been reported to induce mitotic slippage and polyploidization, which in turn may enhance the differentiation potential of embryonic stem cells  (Mantel C et al., 2007). These revisions ensure that our interpretation is consistent with the statistical enrichment results and better reflect the underlying biological processes implicated by the data.

      (3) Justification for training on simulated data

      The decision to train the model on simulated data should be clearly justified. While the advantage of having access to ground-truth parameters is understood, the manuscript would benefit from a discussion of the limitations of this approach, particularly in terms of generalizability to real datasets. Moreover, it is worth noting that many annotated scRNA-seq datasets are publicly available and could, in principle, be used to complement the training strategy.

      We thank you for this insightful comment. We chose to train DeepTXsolver on simulated data because no experimental dataset currently provides genome-wide transcriptional burst kinetics with known ground truth, which is essential for supervised learning. Simulation enables us to (i) generate large, fully annotated datasets spanning the biologically relevant parameter space, (ii) expose the solver to diverse bursting regimes (e.g., low/high burst frequency, small/large burst size, unimodal/bimodal distributions), and (iii) quantitatively benchmark model accuracy, parameter identifiability, and robustness prior to deployment on real scRNA-seq data.

      We acknowledge, however, that simulation-based training has inherent limitations in terms of generalizability. Real biological systems may deviate from the idealized bursting model, exhibit more complex noise structures, or display parameter distributions that differ from those in simulations. Moreover, the lack of ground-truth parameters in experimental scRNA-seq datasets prevents an absolute evaluation of inference accuracy. In the future work, publicly available annotated scRNA-seq datasets could be used to complement this simulation-based training strategy and enhance generalizability. We have revised the manuscript to explicitly discuss both the rationale for using simulated data and the potential limitations of this approach.

      (4) Benchmarking against external methods

      The performance of DeepTX is primarily compared to a prior method from the same group. To strengthen the methodological claims, it would be preferable to include benchmarking against additional established tools from the broader literature. This would offer a more objective evaluation of the performance gains attributed to DeepTX.

      We thank you for this constructive suggestion. We fully agree that benchmarking DeepTX against additional established tools from the broader literatures would provide a more comprehensive and objective evaluation of DeepTX . In the revised manuscript, we have included comparative analyses with other widely used methods, including nnRNA (From Shahrezaei group (Tang W et al., 2023)), txABC (from our group (Luo S et al., 2023)), txBurst (from Sandberg group (Larsson AJM et al., 2019)), txInfer (from Junhao group (Gu J et al., 2025)) (Supplementary Figure S4). The comparative results indicate that our method demonstrates superior performance in both efficiency and accuracy.

      (5) Interpretation of Figures 4-6

      The revised figures are clear and informative; however, the associated interpretations in the main text remain too strong relative to the type of analysis performed. For instance, in Figure 4, it is suggested that changes in burst size are linked to DNA damage-induced signalling cascades that affect cell cycle progression and fate decisions. While this is a plausible hypothesis, GO and GSEA analyses are correlative by nature and not sufficient to support such a mechanistic claim on their own. These analyses should be presented as exploratory, and the strength of the conclusions drawn should be tempered accordingly. Similar caution should be applied to the interpretations of Figures 5 and 6.

      We thank you for this important comment. In the revised manuscript, we have carefully moderated the interpretation of the GO and GSEA results in Figures 4, 5, and 6. Specifically, we now present these analyses as exploratory and emphasize their correlative nature, avoiding causal claims that go beyond the scope of the data. The text has been rephrased to highlight the observed associations rather than implying direct causal relationships.

      For Figure 4, we emphasize that while it is tempting to hypothesize that enhanced burst size may contribute to DNA damage-related checkpoint activation and thereby influence cell cycle progression and differentiation, our current results only indicate an association between burst size enhancement and pathways involved in DNA damage response and checkpoint signaling.

      For Figure 5, we emphasize that although our GO analysis cannot establish causality, the results are consistent with an association between 5-FU-induced changes in burst kinetics and pathways related to oxidative stress and apoptosis. Based on this, we propose a model outlining a potential process through which DNA damage may ultimately lead to cellular apoptosis.

      For Figure 6, we emphasize that these enrichment results suggest that high-dose 5FU treatment may be associated with processes such as telomerase activation and mitochondrial function maintenance, both of which have been implicated in cell survival and apoptosis evasion in previous experimental studies. For example, prior work indicates that hTERT translocation can activate telomerase pathways to support telomere maintenance and reduce oxidative stress, which is thought to contribute to apoptosis resistance. While our enrichment analysis cannot establish causality, the observed transcriptional bursting changes are consistent with these reported survival-associated mechanisms.

      (6) Discussion section framing

      The initial paragraphs of the discussion section make broad biological claims about the role of transcriptional bursting in cellular decision-making. While transcriptional bursting is undoubtedly relevant, the manuscript would benefit from a more cautious framing. It would be more appropriate to foreground the methodological contributions of DeepTX, and to present the biological insights as hypotheses or observations that may guide future experimental investigation, rather than as established conclusions.

      We thank you for this insightful comment. We have revised the discussion to clarify and appropriately temper our claims regarding transcriptional bursting. First, we now explicitly recognize that transcriptional bursting is one of multiple contributors to cellular variability, rather than the sole or dominant factor driving cellular decision-making. Second, we have restructured the opening of the discussion to prioritize the methodological contributions of DeepTX, highlighting its strength as a framework for inferring genomewide burst kinetics from scRNA-seq data. Finally, the biological insights derived from our analysis are now presented as correlative observations and potential hypotheses, which may inform and guide future experimental investigations, rather than as definitive mechanistic conclusions.

      Small Comments

      (1) Presentation of discrete distributions: In several figures (e.g., Figure 2B and Supplementary Figures S4, S6, and S8), the comparisons between empirical mRNA distributions and DeepTX-inferred distributions are visually represented using connecting lines, which may give the impression that continuous distributions are being compared to discrete ones. Given the focus on transcriptional bursting, a process inherently tied to discrete stochastic events, this representation could be misleading. The figure captions and visual style should be revised to clarify that all distributions are discrete and to avoid potential confusion. In general, it is recommended to avoid connecting points in discrete distributions with lines, as this can suggest interpolation or comparison with continuous distributions. This applies to Figures 2A and 2B in particular.

      We thank you for this valuable suggestion. To prevent any potential misinterpretation of discrete distributions as continuous ones, we have revised the visual representation of the empirical and DeepTXinferred mRNA distributions in Figures 2B, and Supplementary Figures S4, S6, and S8. Specifically, we have replaced the line plots with step plots, which more accurately capture the discrete nature of transcriptional bursting. Additionally, we have updated the figure captions to clearly state that all distributions are discrete.

      (2) Transcription is always a multi-step process. While the manuscript aims to model additional complexity introduced by DNA damage, the current phrasing (e.g., on page 5) could be read as implying that transcription becomes multi-step only under damage conditions. This should be clarified.

      We thank you for this helpful observation. We agree that transcription is inherently a multi-step process under all conditions. To avoid any possible misunderstanding, we have revised the text to clarify this point.

      Specifically, we now explain that many previous studies have employed simplified two-state models to approximate transcriptional dynamics, however, the gene expression process is inherently a multi-step process, which particularly cannot be neglected under conditions of DNA damage. DNA damage can result in slowing or even stopping the RNA pol II movement and cause many macromolecules to be recruited for damage repair. This process will affect the spatially localized behavior of the promoter, causing the dwell time of promoter inactivation and activation that cannot be approximated by a simple two state. Our work adopts a multi-step model because it is more appropriate for capturing the additional complexity introduced by DNA damage.

      (3) The first sentence of the discussion section overstates the importance of transcriptional bursting. While it is a key source of variability, it is not the only nor always the dominant one. Furthermore, its role in DNA damage response remains an emerging hypothesis rather than a general principle. The claims in this section should be moderated accordingly.

      We thank you for this valuable feedback. In the revised discussion, we have moderated the statements in the opening paragraph to better reflect the current understanding. Specifically, we now acknowledge that transcriptional bursting represents one of multiple sources of variability and is not always the dominant contributor. In addition, we have reframed the role of transcriptional bursting in DNA damage response as an emerging hypothesis, rather than a general principle. To further address this concern, we replaced conclusion-like statements with more cautious, hypothesis-oriented phrasing, presenting our observations as potential directions for future experimental validation.

      References

      Maizels, R.J. 2024. A dynamical perspective: moving towards mechanism in single-cell transcriptomics. Philos Trans R Soc Lond B Biol Sci 379: 20230049. DOI: https://dx.doi.org/10.1098/rstb.2023.0049, PMID: 38432314

      Sukys, A., Grima, R. 2025. Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data. Nucleic Acids Research 53. DOI: https://dx.doi.org/10.1093/nar/gkaf295, PMID: 40240003

      Garrido-Rodriguez, M., Lopez-Lopez, D., Ortuno, F.M., Peña-Chilet, M., Muñoz, E., Calzado, M.A., Dopazo, J. 2021. A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. PLoS Computational Biology 17: e1008748. DOI: https://dx.doi.org/10.1371/journal.pcbi.1008748, PMID: 33571195

      Kim, E.M., Burke, D.J. 2008. DNA damage activates the SAC in an ATM/ATR-dependent manner, independently of the kinetochore. PLoS Genet 4: e1000015. DOI: https://dx.doi.org/10.1371/journal.pgen.1000015, PMID: 18454191

      Lawrence, K.S., Chau, T., Engebrecht, J. 2015. DNA damage response and spindle assembly checkpoint function throughout the cell cycle to ensure genomic integrity. PLoS Genet 11: e1005150.DOI: https://dx.doi.org/10.1371/journal.pgen.1005150, PMID: 25898113

      Mantel, C., Guo, Y., Lee, M.R., Kim, M.K., Han, M.K., Shibayama, H., Fukuda, S., Yoder, M.C., Pelus, L.M., Kim, K.S., Broxmeyer, H.E. 2007. Checkpoint-apoptosis uncoupling in human and mouse embryonic stem cells: a source of karyotpic instability. Blood 109: 4518-4527. DOI: https://dx.doi.org/10.1182/blood-2006-10-054247, PMID: 17289813

      Tang, W., Jørgensen, A.C.S., Marguerat, S., Thomas, P., Shahrezaei, V. 2023. Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics. Bioinformatics 39. DOI: https://dx.doi.org/10.1093/bioinformatics/btad395, PMID: 37354494

      Luo, S., Zhang, Z., Wang, Z., Yang, X., Chen, X., Zhou, T., Zhang, J. 2023. Inferring transcriptional bursting kinetics from single-cell snapshot data using a generalized telegraph model. Royal Society Open Science 10: 221057. DOI: https://dx.doi.org/10.1098/rsos.221057, PMID: 37035293

      Larsson, A.J.M., Johnsson, P., Hagemann-Jensen, M., Hartmanis, L., Faridani, O.R., Reinius, B., Segerstolpe, A., Rivera, C.M., Ren, B., Sandberg, R. 2019. Genomic encoding of transcriptional burst kinetics. Nature 565: 251-254. DOI: https://dx.doi.org/10.1038/s41586-018-0836-1, PMID: 30602787

      Gu, J., Laszik, N., Miles, C.E., Allard, J., Downing, T.L., Read, E.L. 2025. Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data. Bioinformatics. DOI: https://dx.doi.org/10.1093/bioinformatics/btaf581, PMID: 41131798.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This study presents valuable findings that advance our understanding of mural cell dynamics and vascular pathology in a zebrafish model of cerebral small vessel disease. The authors provide compelling evidence that partial loss of foxf2 function leads to progressive, cell-intrinsic defects in pericytes and associated endothelial abnormalities across the lifespan, leveraging powerful in vivo imaging and genetic tools. The strength of evidence could be further improved by additional mechanistic insight and quantitative or lineage-tracing analyses to clarify how pericyte number and identity are affected in the mutant model.

      Thank you to the reviewers for insightful comments and for the time spent reviewing the manuscript. We have strengthened the data through responding to the comments.

      Public Reviews:

      Reviewer #1 (Public review):

      The paper by Graff et al. investigates the function of foxf2 in zebrafish to understand the progression of cerebral small vessel disease. The authors use a partial loss of foxf2 (zebrafish possess two foxf2 genes, foxf2a and foxf2b, and the authors mainly analyze homozygous mutants in foxf2a) to investigate the role of foxf2 signaling in regulating pericyte biology. They find that the number of pericytes is reduced in foxf2a mutants and that the remaining pericytes display alterations in their morphologies. The authors further find that mutant animals can develop to adulthood, but that in adult animals, both endothelial and pericyte morphologies are affected. They also show that mutant pericytes can partially repopulate the brain after genetic ablation.

      (1) Weaknesses: The results are mainly descriptive, and it is not clear how they will advance the field at their current state, given that a publication on mice has already examined the loss of foxf2 phenotype on pericyte biology (Reyahi, 2015, Dev. Cell).

      The Reyahi paper was the earliest report of foxf2 mutant brain pericytes and remains illuminating. The work was very well technically executed. Our manuscript expands and at times, contradicts, their findings. We realized that we did not fully discuss this in our discussion, and this has now been updated. The biggest difference between the two studies is in the direction of change in pericytes after foxf2 knockout, a major finding in both papers. This is where it is important to understand the differences in methods. Reyahi et al., used a conditional knockout under Wnt1:Cre which will ablate pericytes derived from neural crest, but not those derived from mesoderm, nor will it affect foxf2 expression in endothelial cells. Our model is a full constitutive knockout of the gene in all brain pericytes and endothelial cells. For GOF, Reyahi used a transgenic model with a human FOXF2 BAC integrated into the mouse germline.

      Both studies are important. We do not know enough about human phenotypes in patients with strokeassociated human FOXF2 SNVs to know the direction of change in pericyte numbers. We showed that the SNVs reduce FOXF2 gene expression in vitro (Ryu, 2022). Here we demonstrate dosage sensitivity in fish (showing phenotypes when 1 of 4 foxf2a + foxf2b alleles are lost, Figure 1F), supporting that slight reductions of FOXF2 in humans could lead to severe brain vessel phenotypes. For this reason, our work is complementary to the previously published work and suggests that future studies should focus on understanding the role of dosage, cell autonomy, and human pericyte phenotypes with respect to FOXF2. While some experiments are parallel in mouse and fish, we go further to look at cell death and regeneration, and to understand the consequences on the whole brain vasculature.

      (2) Reyahi et al. showed that loss of foxf2 in mice leads to a marked downregulation of pdgfrb expression in perivascular cells. In contrast to expectation, perivascular cell numbers were higher in mutant animals, but these cells did not differentiate properly. The authors use a transgenic driver line expressing gal4 under the control of the pdgfrb promoter and observe a reduction in pericyte (pdgfrb-expressing) cells in foxf2a mutants. In light of the mouse data, this result might be due to a similar downregulation of pdgfrb expression in fish, which would lead to a downregulation of gal4 expression and hence reduced labelling of pericytes. The authors show a reduction of pdgfrb expression also in zebrafish in foxf2b mutants (Chauhan et al., The Lancet Neurology 2016).

      Reyahi detected more pericytes in the Wnt1:Cre mouse, while we detected fewer in the foxf2a (and foxf2a;foxf2b) mutants. This may be because of different methods. For instance, because the mouse knockout is not a constitutive Foxf2 knockout, the observed increase in pericytes may be because mesodermal-derived pericytes proliferate more highly when the neural crest-derived pericytes are absent. Or does endothelial foxf2 activate pericyte proliferation when foxf2 is lost in some pericytes? It is also possible that mouse foxf2 has a different role from its fish ortholog. Despite these differences, there are common conclusions from both models. For instance, both mouse and fish show foxf2 controls capillary pericyte numbers, albeit in different directions. Both show hemorrhage and loss of vascular stability as a result. Both papers identify the developmental window as critical for setting up the correct numbers of pericytes.  

      As the reviewer suggested, it was important to test whether pdgfrb is downregulated in fish as it is in mice. To do this, we measured expression of pdgfrb in foxf2 mutants using hybridization chain reaction (HCR) of pdgfrb in foxf2 mutants. The results show no change in pdgfrb mRNA in foxf2a mutants at two independent experiments (Fig S3). Independently, we integrated pdgfrb transgene intensity (using a single allele of the transgene so there are no dose effects) in foxf2a mutants vs. wildtype. We found no difference (Fig S3) suggesting that pdgfrb is a reliable reporter for counting pericytes in the foxf2a knockout. The reviewer is correct that we previously showed downregulation of pdgfrb in foxf2b mutants at 4 dpf using colorimetric ISH. foxf2a and foxf2b are unlinked, independent genes (~400 M years apart in evolution) and may have different regulation.

      (3) It would be important to clarify whether, also in zebrafish, foxf2a/foxf2b mutants have reduced or augmented numbers of perivascular cells and how this compares to the data in the mouse.  

      We discuss methodological differences between Reyahi and our work in point (1) above. The reduction in pericytes in foxf2a;foxf2b mutants has been previously published (Ryu, 2022, Supplemental Figure 1) and shown again here in Supplemental Figure 2). Numbers are reduced in double mutants up to 10 dpf, suggesting no recovery. Further, in response to reviewer comments, we have quantified pericytes in the whole fish brain (Figure 3E-G) and show reduced pericytes in the adult, reduced vessel network length, and importantly that the pericyte density is reduced. In aggregate, our data shows pericyte reduction at 5 developmental stages from embryo through adult. The reason for different results from the mouse is unknown and may reflect a technical difference (constitutive vs Wnt1:Cre) or a species difference.  

      (4) The authors should perform additional characterization of perivascular cells using marker gene expression (for a list of markers, see e.g., Shih et al. Development 2021) and/or genetic lineage tracing.

      This is a good point. We have added HCR analysis of additional markers. Results show co-expression of foxf2a, foxf2b, nduf4la2 and pdgfrb in brain pericytes (Fig 2, Fig S3).

      (5) The authors motivate using foxf2a mutants as a model of reduced foxf2 dosage, "similar to human heterozygous loss of FOXF2". However, it is not clear how the different foxf2 genes in zebrafish interact with each other transcriptionally. Is there upregulation of foxf2b in foxf2a mutants and vice versa? This is important to consider, as Reyahi et al. showed that foxf2 gene dosage in mice appears to be important, with an increase in foxf2 gene dosage (through transgene expression) leading to a reduction in perivascular cell numbers.

      We agree that dosage is a very important concept and show phenotypes in foxf2a heterozygotes (Fig 1F). To test the potential compensation from foxf2b, we have added qPCR for foxf2b in foxf2a mutants as well as HCR of foxf2b in foxf2a mutants (Fig S3C,D). There is no change in foxf2b expression in foxf2a mutants. We discuss dosage in our discussion.

      (6) Figures 3 and 4 lack data quantification. The authors describe the existence of vascular defects in adult fish, but no quantifiable parameters or quantifications are provided. This needs to be added.

      This query was technically challenging to address, but very worthwhile. We have not seen published methods for quantifying brain pericytes along with the vascular network (certainly not in zebrafish adults), so we developed new methods of analyzing whole brain vascular parameters of cleared adult brains (Figure S6) using a combination of segmentation methods for pericytes, endothelium and smooth muscle. We have added another author (David Elliott) as he was instrumental in designing methods. We find a significant decrease in vessel network length in foxf2a mutants at 3 month and 6 months (Figures 3F and 4G). Similarly, we show a lower number of brain pericytes in foxf2a mutants (Figure 3E). Finally, we added whole brain analysis of smooth muscle coverage (Figure 4) and show no change in vSMC number or coverage of vessels at 5 and 10 dpf or adult, respectively, pointing to pericytes being the cells most affected. Thank you, this query pushed us in a very productive direction. These methods will be extremely useful in the future!

      (7) The analysis of pericyte phenotypes and morphologies is not clear. On page 6, the authors state: "In the wildtype brain, adult pericytes have a clear oblong cell body with long, slender primary processes that extend from the cytoplasm with secondary processes that wrap around the circumference of the blood vessel." Further down on the same page, the authors note: "In wildtype adult brains, we identified three subtypes of pericytes, ensheathing, mesh and thin-strand, previously characterized in murine models." In conclusion, not all pericytes have long, slender primary processes, but there are at least three different sub-types? Did the authors analyze how they might be distributed along different branch orders of the vasculature, as they are in the mouse?

      We have reworded the text on page 5/6 to be clearer that embryonic pericytes are thin strand only. Additional pericyte subtypes develop later are seen in the mature vasculature of the adult. We could not find a way to accurately analyze pericyte subtypes in the adult brain. The imaging analysis to count pericytes used soma as machine learning algorithms have been developed to count nuclei but not analyze processes.

      (8) Which type of pericyte is affected in foxf2a mutant animals? Can the authors identify the branch order of the vasculature for both wildtype and mutant animals and compare which subtype of pericyte might be most affected? Are all subtypes of pericytes similarly affected in mutant animals? There also seems to be a reduction in smooth muscle cell coverage.

      Please see the response to (7) about pericyte subtypes. In response to the reviewer’s query, we have now analyzed vSMCs in the embryonic and adult brain. In the embryonic brain we see no statistical differences in vSMC number at 5 and 10 dpf (Figure 4). In the adult, vSMC length (total length of vSMCs in a brain) and vSMC coverage (proportion of brain vessels with vSMCs) are not significantly different. This data is important because it suggests that foxf2a has a more important role in pericytes than in vSMCs.

      (9) Regarding pericyte regeneration data (Figure 7): Are the values in Figure 7D not significantly different from each other (no significance given)?

      Any graphs missing bars have no significance and were left off for clarity. We have stated this in the statistical methods.  

      (10) In the discussion, the authors state that "pericyte processes have not been studied in zebrafish".

      Ando et al. (Development 2016) studied pericyte processes in early zebrafish embryos, and Leonard et al. (Development 2022) studied zebrafish pericytes and their processes in the developing fin. We apologize, this was not meant to say that pericyte processes had not been studied before, we have reworded this to make clear the intent of the sentence. We were trying to emphasize that we are the first to quantify processes at different stages, especially  in foxf2 mutants. Processes change morphology over development, especially after 5 dpf, something that our data captures. Our images are of stages that have not been previously characterized. We added a reference to Mae et al., who found similar process length changes in a mouse knockout of a different gene, and to Leonard who previously showed overlap of processes in a different context in fish.

      Reviewer #2 (Public review):

      Summary:

      This study investigates the developmental and lifelong consequences of reduced foxf2 dosage in zebrafish, a gene associated with human stroke risk and cerebral small vessel disease (CSVD). The authors show that a ~50% reduction in foxf2 function through homozygous loss of foxf2a leads to a significant decrease in brain pericyte number, along with striking abnormalities in pericyte morphologyincluding enlarged soma and extended processes-during larval stages. These defects are not corrected over time but instead persist and worsen with age, ultimately affecting the surrounding endothelium. The study also makes an important contribution by characterizing pericyte behavior in wild-type zebrafish using a clever pericyte-specific Brainbow approach, revealing novel interactions such as pericyte process overlap not previously reported in mammals.

      Strengths:

      This work provides mechanistic insight into how subtle, developmental changes in mural cell biology and coverage of the vasculature can drive long-term vascular pathology. The authors make strong use of zebrafish imaging tools, including longitudinal analysis in transgenic lines to follow pericyte number and morphology over larval development, and then applied tissue clearing and whole brain imaging at 3 and 11 months to further dissect the longitudinal effects of foxf2a loss. The ability to track individual pericytes in vivo reveals cell-intrinsic defects and process degeneration with high spatiotemporal resolution. Their use of a pericyte-specific Zebrabow line also allows, for the first time, detailed visualization of pericytepericyte interactions in the developing brain, highlighting structural features and behaviors that challenge existing models based on mouse studies. Together, these findings make the zebrafish a valuable model for studying the cellular dynamics of CSVD.

      Weaknesses:

      (11) While the findings are compelling, several aspects could be strengthened. First, quantifying pericyte coverage across distinct brain regions (forebrain, midbrain, hindbrain) would clarify whether foxf2a loss differentially impacts specific pericyte lineages, given known regional differences in developmental origin, with forebrain pericytes being neural crest-derived and hindbrain pericytes being mesoderm-derived.

      In recently published work from our lab, we published that both neural crest and mesodermal cells contribute to pericytes in both the mid and hindbrain, and could not confirm earlier work suggesting more rigid compartmental origins (Ahuja, 2024). In the Ahuja, 2024 paper we noted that lineage experiments are often limited by n’s which is why this may not have been discovered before. This makes us skeptical that counting different regions will allow us to interpret data about neural crest and mesoderm. Further, Ahuja 2024 shows that pericyte intermediate progenitors from both mesoderm and neural crest are indistinguishable at 30 hpf through single cell sequencing and have converged on a common phenotype.  

      (12) Second, measuring foxf2b expression in foxf2a mutants would better support the interpretation that total FOXF2 dosage is reduced in a graded fashion in heterozygote and homozygote foxf2a mutants.

      We have done both qPCR for foxf2b in foxf2a mutants and HCR (quantitative ISH). This is now reported in Fig S3. 

      (13) Finally, quantifying vascular density in adult mutants would help determine whether observed endothelial changes are a downstream consequence of prolonged pericyte loss. Correlating these vascular changes with local pericyte depletion would also help clarify causality.

      We have added this data to Figure 3 and 4. Please also see response (6).

      Reviewer #3 (Public review):

      Summary:

      The goal of the work by Graff et al. is to model CSVD in the zebrafish using foxf2a mutants. The mutants show loss of cerebral pericyte coverage that persists through adulthood, but it seems foxf2a does not regulate the regenerative capacity of these cells. The findings are interesting and build on previous work from the group. Limitations of the work include little mechanistic insight into how foxf2a alters pericyte recruitment/differentiation/survival/proliferation in this context, and the overlap of these studies with previous work in fox2a/b double mutants. However, the data analysis is clean and compelling, and the findings will contribute to the field.

      (14) Please make Figures 5C and 5E red-green colorblind friendly.

      Thank you. We have changed the colors to light blue and yellow to be colorblind friendly.

      Reviewer #3 (Recommendations for the authors):

      (15) I'm not sure this reviewer totally agrees with the assessment that foxf2a loss of function, while foxf2b remains normal, is the same as FOXF2 heterozygous loss of function in humans. The discussion of the gene dosage needs to be better framed, and the authors should carry out qPCR to show that foxf2b levels are not altered in the foxf2a mutant background.

      We have added data on foxf2b expression in foxf2a mutants to Fig S3. We have updated the results.

      (16) Figure 4/SF7- is the aneurysm phenotype derived from the ECs or pericytes? Cell-type-specific rescues would be interesting to determine if phenotypes are rescued, especially the developmental phenotypes (it is appreciated that carrying out rescue experiments until adulthood is complex). When is the earliest time point that aneurysm-like structures are seen?

      This is a fascinating question, especially as we show that endothelial cells (vessel network length) are affected in the adult mutants. The foxf2a mutants that we work with here are constitutive knockouts. While a strategy to rescue foxf2a in specific lineages is being developed in the laboratory this will require a multi-generation breeding effort to get drivers, transgenes and mutants on the same background, and these fish are not currently available. Thank you for this comment- it is something we want to follow up on.

      (17) Figure 5 - This is very nice analysis.

      Thank you! We think it is informative too.

      (18) Figure 6 - needs to contain control images

      We have added wildtype images to figure 6A.

      (19) Figure 7- vessel images should be shown to demonstrate the specificity of NTR treatment to the pericytes.

      We have added the vessel images to Figure 7. We apologize for the omission.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      One possible remaining conceptual concern that might require future work is determining whether STN primarily mediates higher-level cognitive avoidance or if its activation primarily modulates motor tone.

      Our results using viral and electrolytic lesions (Fig. 11) and optogenetic inhibition of STN neurons (Fig. 10) show that signaled active avoidance is virtually abolished, and this effect is reproduced when we selectively inhibit STN fibers in the midbrain (Fig. 12). Inhibition of STN projections in either the substantia nigra pars reticulata (SNr) or the midbrain reticular tegmentum (mRt) eliminates cued avoidance responses while leaving escape responses intact. Importantly, mice continue to escape during US presentation after lesions or during photoinhibition, demonstrating that basic motor capabilities and the ability to generate rapid defensive actions are preserved.

      These findings argue against the idea that STN’s role in avoidance reflects a nonspecific suppression or facilitation of motor tone, even if the STN also contributes to general movement control. Instead, they show that STN output is required for generating “cognitively” guided cued actions that depend on interpreting sensory information and applying learned contingencies to decide when to act. Thus, while STN activity can modulate movement parameters, the loss-of-function results point to a more selective role in supporting cued, goal-directed avoidance behavior rather than a general adjustment of motor tone.

      Reviewer #2 (Public review):

      All previous weaknesses have been addressed. The authors should explain how inhibition of the STN impairing active avoidance is consistent with the STN encoding cautious action. If 'caution' is related to avoid latency, why does STN lesion or inhibition increase avoid latency, and therefore increase caution? Wouldn't the opposite be more consistent with the statement that the STN 'encodes cautious action'?

      The reviewer’s interpretation treats any increase in avoidance latency as evidence of “more caution,” but this holds only when animals are performing the avoidance behavior normally. In our intact animals, avoidance rates remain high across AA1 → AA2 → AA3, and the active avoidance trials (CS1) used to measure latency are identical across tasks (e.g., in AA2 the only change is that intertrial crossings are punished). Under these conditions, changes in latency genuinely reflect adjustments in caution, because the behavior itself is intact, actions remain tightly coupled to the cue, and the trials are identical.

      This logic does not apply when STN function is disrupted. STN inhibition or lesions reduce avoidance to near chance levels; the few crossings that do occur are poorly aligned to the CS and many likely reflect random movement rather than a cued avoidance response. Once performance collapses, latency can no longer be assumed to reflect the same cognitive process. Thus, interpreting longer latencies during STN inactivation as “more caution” would be erroneous, and we never make that claim.

      A simple analogy may help clarify this distinction. Consider a pedestrian deciding when to cross the street after a green light. If the road is deserted (like AA1), the person may step off the curb quickly. If the road is busy with many cars that could cause harm (like AA2), they may wait longer to ensure that all cars have stopped. This extra hesitation reflects caution, not an inability to cross. However, if the pedestrian is impaired (e.g., cannot clearly see the light, struggles to coordinate movements, or cannot reliably make decisions), a delayed crossing would not indicate greater caution—it would reflect a breakdown in the ability to perform the behavior itself. The same principle applies to our data: we interpret latency as “caution” only when animals are performing the active avoidance behavior normally, success rates remain high, and the trial rules are identical. Under STN inhibition or lesion, when active avoidance collapses, the latency of the few crossings that still occur can no longer be interpreted as reflecting caution. We have added these points to the Discussion.

      Reviewer #3 (Public review):

      Original Weaknesses:

      I found the experimental design and presentation convoluted and some of the results over-interpreted.

      We appreciate the reviewer’s comment, but the concern as stated is too general for us to address in a concrete way. The revised manuscript has been substantially reorganized, with simplified terminology, streamlined figures, and removal of an entire set of experiments to avoid over-interpretation. We are confident that the experimental design and results are now presented clearly and without extrapolation beyond the data. If there are specific points the reviewer finds convoluted or over-interpreted, we would be happy to address them directly.

      As presented, I don't understand this idea that delayed movement is necessarily indicative of cautious movements. Is the distribution of responses multi-modal in a way that might support this idea; or do the authors simply take a normal distribution and assert that the slower responses represent 'caution'? Even if responses are multi-modal and clearly distinguished by 'type', why should readers think this that delayed responses imply cautious responding instead of say: habituation or sensitization to cue/shock, variability in attention, motivation, or stress; or merely uncertainty which seems plausible given what I understand of the task design where the same mice are repeatedly tested in changing conditions. This relates to a major claim (i.e., in the title).

      We appreciate the reviewer’s question and address each component directly.

      (1) What we mean by “caution” and how it is operationalized

      In our study, caution is defined operationally as a systematic increase in avoidance latency when the behavioral demand becomes higher, while the trial structure and required response remain unchanged. Specifically, CS1 trials are identical in AA1, AA2, and AA3. Thus, when mice take longer to initiate the same action under more demanding contexts, the added time reflects additional evaluation before acting—consistent with longestablished interpretations of latency shifts in cognitive psychology (see papers by Donders, Sternberg, Posner) and interpretations of deliberation time in speed-accuracy tradeoff literature.

      (2) Why this interpretation does not rely on multi-modal response distributions We do not claim that “cautious” responses form a separate mode in the latency distribution. The distributions are unimodal, and caution is inferred from conditiondependent shifts in these distributions across identical trials, not from the existence of multiple peaks (see Zhou et al, 2022). Latency shifts across conditions with identical trial structure are widely used as behavioral indices of deliberation or caution.

      (3) Why alternative explanations (habituation/sensitization, motivation, attention, stress, uncertainty) do not account for these latency changes

      Importantly, nothing changes in CS1 trials between AA1 and AA2 with respect to the cue, shock, or required response. Therefore:

      - Habituation/sensitization to the cue or shock cannot explain the latency shift (the stimuli and trial type are unchanged). We have previously examined cue-evoked orienting responses and their habituation in detail (Zhou et al., 2023), and those measurements are dissociable from the latency effects described here.

      - Motivation or attention are unlikely to change selectively for identical CS1 trials when the task manipulation only adds a contingency to intertrial crossings.

      - Uncertainty also does not increase for CS1 trials, they remain fully predictable and unchanged between conditions.

      - Stress is too broad a construct to be meaningful unless clearly operationalized; moreover, any stress differences that arise from task structure would covary with caution rather than replace the interpretation.

      (4) Clarifying “types” of responses

      The reviewer’s question about “response types” appears to conflate behavioral latencies with the neuronal response “types” defined in the manuscript. The term “type” in this paper refers to neuronal activation derived from movement-based clustering, not to distinct behavioral categories of avoidance, which we term modes.

      In sum, we interpret increased CS1 latency as “caution” only when performance remains intact and trial structure is identical between conditions; under those criteria, latency reliably reflects additional cognitive evaluation before acting, rather than nonspecific changes in sensory processing, motivation, etc.

      Related to the last, I'm struggling to understand the rationale for dividing cells into 'types' based their physiological responses in some experiments.

      There is longstanding precedent in systems neuroscience for classifying neurons by their physiological response patterns, because neurons that respond similarly often play similar functional roles. For example, place cells, grid cells, direction cells, in vivo, and regular spiking, burst firing, and tonic firing in vitro are all defined by characteristic activity patterns in response to stimuli rather than anatomy or genetics alone. In the same spirit, our classifications simply reflect clusters of neurons that exhibit similar ΔF/F dynamics around behaviorally relevant events, such as movement sensitivity or avoidance modes. This is a standard analytic approach used in many studies. Thus, our rationale is not arbitrary: the “classes” and “types” arise from data-driven clustering of physiological responses, consistent with widespread practice, and they help reveal functional distinctions within the STN that would otherwise remain obscured.

      In several figures the number of subjects used was not described. This is necessary. Also necessary is some assessment of the variability across subjects.

      All the results described include the number of animals. To eliminate uncertainty, we now also include this information in figure legends.

      The only measure of error shown in many figures relates trial-to-trial or event variability, which is minimal because in many cases it appears that hundreds of trials may have been averaged per animal, but this doesn't provide a strong view of biological variability (i.e., are results consistent across animals?).

      The concern appears to stem from a misunderstanding of what the mixed-effects models quantify. The figure panels often show session-averaged traces for clarity, all statistical inferences in the paper are made at the level of animals, not trials. Mixed-effects modeling is explicitly designed for hierarchical datasets such as ours, where many trials are nested within sessions, which are themselves nested within animals.

      In our models, animal is the clustering (random) factor, and sessions are nested within animals, so variability across animals is directly estimated and used to compute the population-level effects. This approach is not only appropriate but is the most stringent and widely recommended method for analyzing behavioral and neural data with repeated measures. In other words, the significance tests and confidence intervals already fully incorporate biological variability across animals.

      Thus, although hundreds of trials per animal may be illustrated for visualization, the inferences reflect between-animal consistency, not within-animal trial repetition. The fact that the mixed-effects results are robust across animals supports the biological reliability of the findings.

      It is not clear if or how spread of expression outside of target STN was evaluated, and if or how or how many mice were excluded due to spread or fiber placements. Inadequate histological validation is presented and neighboring regions that would be difficult to completely avoid, such as paraSTN may be contributing to some of the effects.

      The STN is a compact structure with clear anatomical boundaries, and our injections were rigorously validated to ensure targeting specificity. As detailed in the Methods, every mouse underwent histological verification, and injections were quantified using the Brain Atlas Analyzer app (available on OriginLab), which we developed to align serial sections to the Allen Brain Atlas. This approach provides precise, slice-by-slice confirmation of viral spread. We have performed thousands of AAV injections and probe implants in our lab, incorporating over the years highly reliable stereotaxic procedures with multiple depth and angle checks and tools. For this study specifically, fewer than 10% of mice were excluded due to off-target expression or fiber/lesion placement. None of the included cases showed spread into adjacent structures.

      Regarding paraSTN: anatomically, paraSTN is a very small extension contiguous with STN. Our study did not attempt to dissociate subregions within STN, and the viral expression patterns we report fall within the accepted boundaries of STN. Importantly, none of our photometry probes or miniscope lenses sampled paraSTN, so contributions from that region are extremely unlikely to account for any of our neural activity results.

      Finally, our paper employs five independent loss-of-function approaches—optogenetic inhibition of STN neurons, selective inhibition of STN projections to the midbrain (in two sites: SNr and mRt), and STN lesions (electrolytic and viral). All methods converge on the same conclusion, providing strong evidence that the effects we report arise from manipulation of STN itself rather than from neighboring regions.

      Raw example traces are not provided.

      We do not think raw traces are useful here. All figures contain average traces to reflect the average activity of the estimated populations, which are already clustered per classes and types.

      The timeline of the spontaneous movement and avoidance sessions were not clear, nor the number of events or sessions per animal and how this was set. It is not clear if there was pre-training or habituation, if many or variable sessions were combined per animal, or what the time gaps between sessions was, or if or how any of these parameters might influence interpretation of the results.

      As noted, we have enhanced the description of the sessions, including the number of animals and sessions, which are daily and always equal per animals in each group of experiments. The sessions are part of the random effects in the model. In addition, we now include schematics to facilitate understanding of the procedures.  

      Comments on revised version:

      The authors removed the optogenetic stimulation experiments, but then also added a lot of new analyses. Overall the scope of their conclusions are essentially unchanged. Part of the eLife model is to leave it to the authors discretion how they choose to present their work. But my overall view of it is unchanged. There are elements that I found clear, well executed, and compelling. But other elements that I found difficult to understand and where I could not follow or concur with their conclusions.

      We respectfully disagree with the assertion that the scope of our conclusions remains unchanged. The revised manuscript differs in several fundamental ways:

      (1) Removal of all optogenetic excitation experiments

      These experiments were a substantial portion of the original manuscript, and their removal eliminated an entire set of claims regarding the causal control of cautious responding by STN excitation. The revised manuscript no longer makes these claims.

      (2) Addition of analyses that directly address the reviewers’ central concerns The new analyses using mixed-effects modeling, window-specific covariates, and movement/baseline controls were added precisely because reviewers requested clearer dissociation of sensory, motor, and task-related contributions. These additions changed not only the presentation but the interpretation of the neural signals. We now conclude that STN encodes movement, caution, and aversive signals in separable ways—not that it exclusively or causally regulates caution.

      (3) Clear narrowing of conclusions

      Our current conclusions are more circumscribed and data-driven than in the original submission. For example, we removed all claims that STN activation “controls caution,” relying instead on loss-of-function data showing that STN is necessary for performing cued avoidance—not for generating cautious latency shifts. This is a substantial conceptual refinement resulting directly from the review process.

      (4) Reorganization to improve clarity

      Nearly every section has been restructured, including terminology (mode/type/class), figure organization, and explanations of behavioral windows. These revisions were implemented to ensure that readers can follow the logic of the analyses.

      We appreciate the reviewer’s recognition that several elements were clear and compelling. For the remaining points they found difficult to understand, we have addressed each one in detail in the response and revised the manuscript accordingly. If there are still aspects that remain unclear, we would welcome explicit identification of those points so that we can clarify them further.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) Show individual data points on bar plots

      - partially addressed. Individual data points are still not shown.

      Wherever feasible, we display individual data points (e.g., Figures 1 and 2) to convey variability directly. However, in cases where figures depict hundreds of paired (repeatedmeasures) data points, showing all points without connecting them would not be appropriate, while linking them would make the figures visually cluttered and uninterpretable. All plots and traces include measures of variability (SEM), and the raw data will be shared on Dryad. When error bars are not visible, they are smaller than the trace thickness or bar line—for example, in Figure 5B, the black circles and orange triangles include error bars, but they are smaller than the symbol size.

      Also, to minimize visual clutter, only a subset of relevant comparisons is highlighted with asterisks, whereas all relevant statistical results, comparisons, and mouse/session numbers are fully reported in the Results section, with statistical analyses accounting for the clustering of data within subjects and sessions.

      (2) The active avoidance experiments are confusing when they are introduced in the results section. More explanation of what paradigms were used and what each CS means at the time these are introduced would add clarity. For example AA1, AA2 etc are explained only with references to other papers, but a brief description of each protocol and a schematic figure would really help.

      - partially addressed. A schematic figure showing the timeline would still be helpful.

      As suggested, we have added an additional panel to Fig. 5A with a schematic describing

      AA1-3 tasks. In addition, the avoidance protocols are described briefly but clearly in the Results section (second paragraph of “STN neurons activate during goal-directed avoidance contingencies”) and in greater detail in the Methods section. As stated, these tasks were conducted sequentially, and mice underwent the same number of sessions per procedure, which are indicated. All relevant procedural information has been included in these sections. Mice underwent daily sessions and learnt these tasks within 1-2 sessions, progressing sequentially across tasks with an equal number of sessions per task (7 per task), and the resulting data were combined and clustered by mouse/session in the statistical models.

      (3) How do the Class 1, 2, 3 avoids relate to Class 1 , 2, 3 neural types established in Figure 3? It seems like they are not related, and if that is the case they should be named something different from each other to avoid confusion.

      -not sufficiently addressed. The new naming system of neural 'classes' and 'types' helps with understanding that these are completely different ways of separating subpopulations within the STN. However, it is still unclear why the authors re-type the neurons based on their relation to avoids, when they classify the neurons based on their relationship to speed earlier. And it is unclear whether these neural classes and neural types have anything to do with each other. Are the neural Types related to the neural classes in any way? and what is the overlap between neural types vs classes? Which separation method is more useful for functionally defining STN populations?

      The remaining confusion stems from treating several independent analyses as if they were different versions of the same classification. In reality, each analysis asks a distinct question, and the resulting groupings are not expected to overlap or correspond. We clarify this explicitly below.

      - Movement onset neuron classes (Class A, B, C; Fig. 3):

      These classes categorize neurons based on how their ΔF/F changes around spontaneous movement onset. This analysis identifies which neurons encode the initiation and direction of movement. For instance, Class B neurons (15.9%) were inhibited as movement slowed before onset but did not show sharp activation at onset, whereas Class C neurons (27.6%) displayed a pronounced activation time-locked to movement initiation. Directional analyses revealed that Class C neurons discharged strongly during contraversive turns, while Class B neurons showed a weaker ipsiversive bias. Because neurons were defined per session and many of these recordings did not include avoidance-task sessions, these movement-onset classes were not used in the avoidance analyses.

      - Movement-sensitivity neuron classes (Class 1, 2, 3, 4; Fig. 7):

      These classes categorize neurons based on the cross-correlation between ΔF/F and head speed, capturing how each neuron’s activity scales with movement features across the entire recording session. This analysis identifies neurons that are strongly speed-modulated, weakly speed-modulated, or largely insensitive to movement. These movement-sensitivity classes were then carried forward into the avoidance analyses to ask how neurons with different kinematic relationships participate during task performance; for example, whether neurons that are insensitive to movement nonetheless show strong activation during avoidance actions.

      - Avoidance modes (Mode 1, 2, 3; Fig. 8)

      Here we classify actions, not neurons. K-means clustering is applied to the movementspeed time series during CS1 active avoidance trials only, which allows us to identify distinct action modes or variants—fast-onset versus delayed avoidance responses. This action-based classification ensures that we compare neural activity across identical movements, eliminating a major confound in studies that do not explicitly separate action variants. First, we examine how population activity differs across these avoidance modes, reflecting neural encoding of the distinct actions themselves. Second, within each mode, we then classify neurons into “types,” which simply describes how different neurons activate during that specific avoidance action (as noted next).

      - Neuron activation types within each mode (Type a, b, c; Fig.9)

      This analysis extends the mode-based approach by classifying neuronal activation patterns only within each specific avoidance mode. For each mode, we apply k-means clustering to the ΔF/F time series to identify three activation types—e.g., neurons showing little or no response, neurons showing moderate activation, and neurons showing strong or sharply timed activation. Because all trials within a mode have identical movement profiles, these activation types capture the variability of neural responses to the same avoidance behavior. Importantly, these activation “types” (a, b,

      c) are not global neuron categories. They do not correspond to, nor are they intended to map onto, the movement-based neuron classes defined earlier. Instead, they describe how neurons differ in their activation during a particular behavioral mode—that is, within a specific set of behaviorally matched trials. Because modes are defined at the trial level, the neurons contributing to each mode can differ: some neurons have trials belonging to one mode, others to two or all three. Thus, Type a/b/c groupings are not fixed properties of neurons. To prevent confusion, we refer to them explicitly as neuronal activation types, emphasizing that they characterize mode-specific response patterns rather than global cell identities.

      In conclusion, the categorizations serve entirely different analytical purposes and should not be interpreted as competing classifications. The mode-specific “types” do not reclassify or replace the movement-sensitivity classes; they capture how neurons differ within a single, well-defined avoidance action, while the movement classes reflect how neurons relate to movements in general. Each classification relates to different set of questions and overlap between them is not expected.

      To make this as clear as possible we added the following paragraph to the Results:  

      “To avoid confusion between analyses, it is important to note that the movement-sensitivity classes defined here (Class 1–4; Fig. 7) are conceptually distinct from both the movementonset classes (Class A–C; Fig. 3) and the neuronal activation “types” introduced later in the avoidance-mode analysis. The Class 1–4 grouping reflects how neurons relate to movement across the entire session, based on their cross-correlation with speed. The onset classes A–C capture neural activity specifically around spontaneous movement initiation during general exploration. In contrast, the later activation “types” are derived within each avoidance mode and describe how neurons differ in their activation patterns during identical CS1 avoidance responses. These classifications answer different questions about STN function and are not intended to correspond to one another.”

      (4) Similarly having 3 different cell types (a,b,c) in the active avoidance seems unrelated to the original classification of cell types (1,2,3), and these are different for each class of avoid. This is very confusing and it is unclear how any of these types relate to each other. Presumable the same mouse has all three classes of avoids, so there are recording from each cell during each type of avoid. So the authors could compare one cell during each avoid and determine whether it relates to movement or sound or something else. It is interesting that types a,b,c have the exact same proportions in each class of avoid, and really makes it important to investigate if these are the exact same cells or not. Also, these mice could be recorded during open field so the original neural classification (class 1, 2,3) could be applied to these same cells and then the authors can see whether each cell type defined in the open field has different response to the different avoid types. As it stands, the paper simply finds that during movement and during avoidance behaviors different cells in the STN do different things. - Similarly, the authors somewhat addressed the neural types issue, but figure 9 still has 9 different neural types and it is unclear whether the same cells that are type 'a' in mode 1 avoids are also type 'a' in mode 2 avoids, or do some switch to type b? Is there consistency between cell types across avoid modes? The authors show that type 'c' neurons are differentially elevated in mode 3 vs 2, but also describes neurons as type '2c' and statistically compare them to type '1c' neurons. Are these the same neurons? or are type 2c neurons different cells vs type 1c neurons? This is still unclear and requires clarification to be interpretable.

      We believe the remaining confusion arises from treating the different classification schemes as if they were alternative labels applied to the same neurons, when in fact they serve entirely separate analytical purposes and may not include the same neurons (see previous point). Because these classifications answer different questions, they are not expected to overlap, nor is overlap required for the interpretations we draw. It is therefore not appropriate to compare a neuron’s “type” in one avoidance mode to its movement class, or to ask whether types a/b/c across different modes are “the same cells,” since modes are defined by trial-level movement clustering rather than by neuron identity. Importantly, Types a/b/c are not intended as a new global classification of neurons; they simply summarize the variability of neuronal responses within each behaviorally matched mode. We agree that future studies could expand our findings, but that is beyond the already wide scope of the present paper. Our current analyses demonstrate a key conceptual point: when movement is held constant (via modes), STN neurons still show heterogeneous, outcome- and caution-related patterns, indicating encoding that cannot be reduced to movement alone.

      Relatedly, was the association with speed used to define each neural "class" done in the active avoidance context or in a separate (e.g. open field) experiment? This is not clear in the text.

      The cross-correlation classes were derived from the entire recording session, which included open-field and avoidance tasks recordings. The tasks include long intertrial periods with spontaneous movements. We found no difference in classes when we include only a portion of the session, such as the open field or if we exclude the avoidance interval where actions occur.

      Finally, in figure 7, why is there a separate avoid trace for each neural class? With the GRIN lens, the authors are presumably getting a sample of all cell types during each avoid, so why do the avoids differ depending on the cell type recorded?

      The entire STN population is not recorded within a single session; each session contributes only a subset of neurons to the dataset. Consequently, each neural class is composed of neurons drawn from partially non-overlapping sets of sessions, each with its own movement traces. For this reason, we plot avoidance traces separately for each neural class to maintain strict within-session correspondence between neural activity and the behavior collected in the same sessions. This prevents mixing behavioral data across sessions that did not contribute neurons to that class and ensures that all neural– behavioral comparisons remain appropriately matched. We have clarified this rationale in the revised manuscript. We note that averaging movement across classes—as is often done—would obscure these distinctions and would not preserve the necessary correspondence between neural activity and behavior. This is also clarified in Results.

      (5) The use of the same colors to mean two different things in figure 9 is confusing. AA1 vs AA2 shouldn't be the same colors as light-naïve vs light signaling CS.

      -addressed, but the authors still sometimes use the same colors to mean different things in adjacent figures (e.g. the red, blue, black colors in figure 1 and figure 2 mean totally different things) and use different colors within the same figure to represent the same thing (Figure 9AB vs Figure 9CD). This is suboptimal.

      Following the reviewer’s suggestion, in Figure 2, we changed the colors, so readers do not assume they are related to Fig. 1.

      In Figure 9, we changed the colors in C,D to match the colors in A,B.

      (6) The exact timeline of the optogenetics experiments should be presented as a schematic for understandability. It is not clear which conditions each mouse experienced in which order. This is critical to the interpretation of figure 9 and the reduction of passive avoids during STN stimulation. Did these mice have the CS1+STN stimulation pairing or the STN+US pairing prior to this experiment? If they did, the stimulation of the STN could be strongly associated with either punishment or with the CS1 that predicts punishment. If that is the case, stimulating the STN during CS2 could be like presenting CS1+CS2 at the same time and could be confusing. The authors should make it clear whether the mice were naïve during this passive avoid experiment or whether they had experienced STN stimulation paired with anything prior to this experiment.

      -addressed

      (7) Similarly, the duration of the STN stimulation should be made clear on the plots that show behavior over time (e.g. Figure 9E).

      -addressed

      (8) There is just so much data and so many conditions for each experiment here. The paper is dense and difficult to read. It would really benefit readability if the authors put only the key experiments and key figure panels in the main text and moved much of the repetative figure panels to supplemental figures. The addition of schematic drawings for behavioral experiment timing and for the different AA1, AA2, AA3 conditions would also really improve clarity.

      -partially addressed. The paper is still dense and difficult to read. No experimental schematics were added.

      As suggested, we now added the schematic to Fig. 5A.  

      New Comments:

      (9) Description of the animals used and institutional approval are missing from the methods.

      The information on animal strains and institutional approval is already included in the manuscript. The first paragraph of the Methods section states:

      “… All procedures were reviewed and approved by the institutional animal care and use committee and conducted in adult (>8 weeks) male and female mice. …”

      Additionally, the next subsection, “Strains and Adeno-Associated Viruses (AAVs),” fully specifies all mouse lines used. We therefore believe that the required descriptions of animals and institutional approval are already present and meet standard reporting.

    1. Author response:

      We thank the reviewers for their constructive and helpful feedback on our manuscript. We are delighted that they found the study to be "comprehensive and convincing" and a "tour de force" in its combination of electrophysiological recordings with large-scale digital twin screening. We appreciate that the reviewers highlighted the strengths of our multi-species approach and the "cross-species and cross-area consistency" of the results, noting that the work showcases how in silico experiments can generate concrete, experimentally validatable hypotheses.

      The reviewers also raised several important points that we plan to address in the final version of the manuscript to improve clarity and interpretation. These center on:

      Model performance in V4: Reviewer #1 raised questions regarding the comparative drop in model performance in V4 and the implications for the validity of the results (including the use of "high confidence" neurons and a request for clarification on the number of animals in the V4 dataset).

      Species differences: Both reviewers noted the value of the macaque-mouse comparison but requested a more explicit delineation of the differences between these species given their distinct ethological niches.

      The nature of inhibitory dimensions: The reviewers asked for further details on how to identify these inhibitory dimensions and the specific relationship between excitation and inhibition. We believe unraveling these mechanisms represents an exciting direction for future work, and we will explicitly mention this in the Discussion section of the final manuscript, alongside a clearer contextualization with prior literature.

      Technical clarifications: Reviewer #2 requested clarifications on specific technical details, such as the skewness thresholds used for sparsity analysis.

      In the final version of the manuscript, we will address these points by adding necessary clarifications to the text—including confirming the animal cohort details—explicitly contrasting the mouse and macaque data to highlight coding differences, and expanding our discussion. We will also ensure all technical inquiries, such as those regarding skewness and reference citations, are fully resolved.

      We believe addressing these points will significantly strengthen the manuscript.

    1. Author response:

      Public Reviews:.

      Reviewer #1 (Public review):

      Wang, Zhou et al. investigated coordination between the prefrontal cortex (PFC) and the hippocampus (Hp), during reward delivery, by analyzing beta oscillations. Beta oscillations are associated with various cognitive functions, but their role in coordinating brain networks during learning is still not thoroughly understood. The authors focused on the changes in power, peak frequencies, and coherence of beta oscillations in two regions when rats learn a spatial task over days. Inconsistent with the authors' hypothesis, beta oscillations in those two regions during reward delivery were not coupled in spectral or temporal aspects. They were, however, able to show reverse changes in beta oscillations in PFC and Hp as the animal's performance got better. The authors were also able to show a small subset of cell populations in PFC that are modulated by both beta oscillations in PFC and sharp wave ripples in Hp. A similarly modulated cell population was not observed in Hp. These results are valuable in pointing out distinct periods during a spatial task when two regions modulate their activity independently from each other.

      The authors included a detailed analysis of the data to support their conclusions. However, some clarifications would help their presentation, as well as help readers to have a clear understanding.

      (1) The crucial time point of the analysis is the goal entry. However, it needs a better explanation in the methods or in figures of what a goal entry in their behavioral task means.

      We appreciate Reviewer 1 pointing out this shortcoming and will clarify the description in the revised manuscript. Each goal is located at the end of the arm, and is equipped with a reward delivery unit. The unit has an infrared sensor. The rat breaks the infrared beam when it enters the goal.

      (2) Regarding Figure 2, the authors have mentioned in the methods that PFC tetrodes have targeted both hemispheres. It might be trivial, but a supplementary graph or a paragraph about differences or similarities between contralateral and ipsilateral tetrodes to Hp might help readers.

      We will provide the requested analysis in the full revision. We saw both hemispheres had similar properties.

      (3) The authors have looked at changes in burst properties over days of training. For the coincidence of beta bursts between PFC and Hp, is there a change in the coincidence of bursts depending on the day or performance of the animal?

      We will provide the requested analysis in the full revision.

      (4) Regarding the changes in performance through days as well as variance of the beta burst frequency variance (Figures 3C and 4C); was there a change in the number of the beta bursts as animals learn the task, which might affect variance indirectly?

      The analysis we can do here is to control for differences in the number of bursts for each category (days/performance quintile) by resampling the data to match the burst count between categories.

      (5) In the behavioral task, within a session, animals needed to alternate between two wells, but the central arm (1) was in the same location. Did the authors alternate the location of well number 1 between days to different arms? It is possible that having well number 1 in the same location through days might have an effect on beta bursts, as they would get more rewards in well number 1?

      The central arm remained the same across days since we needed the animals to learn the alternation task. In our experience, the animal needs a few days to learn the alternation rule when we switch the central arm location. For this experiment, we were interested in the initial learning process, and we kept the central constant. Switching the central arm location is a great suggestion for a follow up experiment where we can understand the effects of reward contingency change has on beta bursts.

      (6) The animals did not increase their performance in the F maze as much as they increased it in the Y maze. It would be more helpful to see a comparison between mazes in Figure 5 in terms of beta burst timing. It seems like in Y maze, unrewarded trials have earlier beta bursts in Y maze compared to F maze. Also, is there a difference in beta burst frequencies of rewarded and unrewarded trials?

      We will add this analysis in the revised manuscript.

      (7) For individual cell analysis, the authors recorded from Hp and the behavioral task involved spatial learning. It would be helpful to readers if authors mention about place field properties of the cells they have recorded from. It is known that reward cells firing near reward locations have a higher rate to participate in a sharp wave ripple. Factoring in the place field propertiesd of the cells into the analysis might give a clearer picture of the lack of modulation of HP cells by beta and sharp wave ripples.

      This is a great suggestion, and we will address this in the full revision.

      Reviewer #2 (Public review):

      We thank Reviewer 2 for their helpful comments and will address these in full in the revision. These are great suggestions to provide greater detail on the spectral and behavioral data at the goal.

      (1) When presenting the power spectra for the representative example (Figure 1), it would be appropriate to display a broader frequency band-including delta, theta, and gamma (up to ~100 Hz), rather than only the beta band.

      We will show more examples of power spectra with a wider frequency range. We did examine the wider spectra and noticed power in the beta frequency band was more prominent than others.

      What was the rat's locomotor state (e.g., running speed) after entering the reward location, during which the LFPs were recorded?

      We will add the time aligned speed profile to the spectra and raw data examples. Because goal entry is defined as the time the animals break the infrared beam at the goal (response to Reviewer 1), the rat would have come to a stop.

      If the rats stopped at the goal but still consumed the reward (i.e., exhibited very low running speed), theta rhythms might still occasionally occur, and sharp-wave ripples (SWRs) could be observed during rest.

      We typically find low theta power in the hippocampus after the animal reaches the goal location and as it consumes reward. Reviewer 2 is correct about occasional theta power at the goal. We have observed this but mostly before the animal leaves the goal location. We did find SWRs during goal periods. One example is shown in Fig. 7A.

      Do beta bursts also occur during navigation prior to goal entry?

      We did not find consistent beta bursts in PFC or CA1 on approach to goal entry. We can provide the analyses in our full revision. In our initial exploratory analysis, we found beta bursts was most prominent after goal entry, which led us to focus on post-goal entry beta for this manuscript. However, beta oscillations in the hippocampus during locomotion or exploration has been reported (Ahmed & Mehta, 2012; Berke et al., 2008; França et al., 2014; França et al., 2021; Iwasaki et al., 2021; Lansink et al., 2016; Rangel et al., 2015).

      It would be beneficial to display these rhythmic activities continuously across both the navigation and goal entry phases. Additionally, given that the hippocampal theta rhythm is typically around 7-8 Hz, while a peak at approximately 15-16 Hz is visible in the power spectra in Figure 1C, the authors should clarify whether the 22 Hz beta activity represents a genuine oscillation rather than a harmonic of the theta rhythm.

      To ensure we fully address this concern, we can provide further spectral analysis in our revised manuscript to show theta power in CA1 is reduced after goal entry. We were initially concerned about the possibility that the 22Hz power in CA1 may be a harmonic rather than a standalone oscillation band. If these are harmonics of theta, we should expect to find coincident theta at the time of bursts in the beta frequency. In Fig. 1B, Fig. 2A, we show examples of the raw LFP traces from CA1. Here, the detected bursts are not accompanied by visible theta frequency activity. For PFC, we do not always see persistent theta frequency oscillations like CA1. In PFC, we found beta bursts were frequent and visually identifiable when examining the LFP. We provided examples of the PFC LFP (Fig. 1B, Fig. 1-1, and Fig. 2A). In these cases, we see clear beta frequency oscillations lasting several cycles and these are not accompanied by any oscillations in the theta frequency in the LFP trace.

      (2) The authors claim that beta activity is independent between CA1 and PFC, based on the low coherence between these regions. However, it is challenging to discern beta-specific coherence in CA1; instead, coherence appears elevated across a broader frequency band (Figure 2 and Figure 2-1D). An alternative explanation could be that the uncoupled beta between CA1 and PFC results from low local beta coherence within CA1 itself.

      This is a legitimate concern, and we used three methods to characterize coherence and coordination between the two regions. First, we calculated coherence for tetrode pairs for times when the animal was at goals (Fig. 2B), which provides a general estimation of coherence across frequencies but lack any temporal resolution. Second, we calculated burst aligned coherence (Fig. 2-1), which provides temporal resolution relative to the burst, but the multi-taper method is constrained by the time-frequency resolution trade off. Third, we quantified the timing between the burst peaks (Fig. 2D), which will describe timing differences but the peaks for the bursts may not be symmetric. Thus, each method has its own caveats, but we drew our conclusion from the combination of results from these three analyses, which pointed to similar conclusions.

      Reviewer 2 is correct in pointing out the uniformly high coherence within CA1 across the frequency range we examined. When we inspected the raw LFP across multiple tetrodes in CA1, they were similar to each other (Fig. 2A). This likely reflects the uniformity in the LFP across recording sites in CA1, which is what we saw with coherence values across the frequency range (Fig. 2B). We found CA1 coherence between tetrode pairs within CA1 across the range, were statistically higher, compared to tetrode pairs in PFC (Fig. 2B and C), thus our results are unlikely to be explained by low beta coherence within CA1 itself. The burst aligned coherence using a multi-taper method also supports this. The coherence values within CA1 at the time of CA1 bursts is ~0.8-0.9.

      (3) In Figure 2-1E-F, visual inspection of the box plots reveals minimal differences between PFC-Ind and PFC-Coin/CA1-Coin conditions, despite reported statistical significance. It may be necessary to verify whether the significance arises from a large sample size.

      We will include the sample sizes for each of the boxplots, these should be the same as the power comparison in Fig. 2-1 A-C. The LFP within a one second window centered around the bursts are usually very similar, and the multi-taper method will return high coherence values. The p-values from statistical comparisons between the boxes are corrected using the Benjamini-Hochberg method.

      (4) In Figure 3 and Figure 4, although differences in power and frequency appear to change significantly across days, these changes are not easily discernible by visual inspection. It is worth considering whether these variations are related to increased task familiarity over days, potentially accompanied by higher running speeds.

      We agree with Reviewer 2 that familiarity increases across days, and the animal is likely running faster. The analysis for Fig. 3 and 4 includes only data from periods when the animal was at the goal and was not moving. We used linear mixed effects models to quantify the relationship between power, frequency and day or behavioral quintile.

      (5) The stronger spiking modulation by local beta oscillations shown in Figure 6 could also be interpreted in the context of uncoupled beta between CA1 and PFC. In this analysis, only spikes occurring during beta bursts should be included, rather than all spikes within a trial. The authors should verify the dataset used and consider including a representative example illustrating beta modulation of single-unit spiking.

      We agree with Reviewer 2 that the stronger modulation to local beta is another piece of evidence indicating uncoupled beta between the two regions. We appreciate this suggestion and will add examples illustrating beta modulation for single units. We want to clarify the spikes were only from periods when the animal is at the goal location on each trial and does not include the running period between goals.

      (6) As observed in Figure 7D, CA1 beta bursts continue to occur even after 2.5 seconds following goal entry, when SWRs begin to emerge. Do these oscillations alternate over time, or do they coexist with some form of cross-frequency coupling?

      This is a very interesting and helpful suggestion. Although we found SWRs generally appear later than beta bursts, it is possible the two are related on a finer timescale pointing to coordination. Our cross-correlation analysis between PFC and CA1 beta bursts only showed the relationship on the timescale of seconds. We will show a higher time-resolution version of this analysis in the revision.

      Reviewer #3 (Public review):

      Summary:

      This paper explored the role of beta rhythms in the context of spatial learning and mPFC-hippocampal dynamics. The authors characterized mPFC and hippocampal beta oscillations, examining how their coordination and their spectral profiles related to learning and prefrontal neuronal firing. Rats performed two tasks, a Y-maze and an F-maze, with the F-maze task being more cognitively demanding. Across learning, prefrontal beta oscillation power increased while beta frequency decreased. In contrast, hippocampal beta power and beta frequency decreased. This was particularly the case for the well-performed and well-learned Y-maze paradigm. The authors identified the timing of beta oscillations, revealing an interesting shift in beta burst timing relative to reward entry as learning progressed. They also discovered an interesting population of prefrontal neurons that were tuned to both prefrontal beta and hippocampal sharp-wave ripple events, revealing a spectrum of SWR-excited and SWR-inhibited neurons that were differentially phase locked to prefrontal beta rhythms.

      In sum, the authors set out to examine how beta rhythms and their coordination were related to learning and goal occupancy. The authors identified a set of learning and goal-related correlates at the level of LFP and spike-LFP interactions, but did not report on spike-behavioral correlates.

      Strengths:

      Pairing dual recordings of medial prefrontal cortex (mPFC) and CA1 with learning of spatial memory tasks is a strength of this paper. The authors also discovered an interesting population of prefrontal neurons modulated by both beta and CA1 sharp-wave ripple (SWR) events, showing a relationship between SWR-excited and SWR-inhibited neurons and beta oscillation phase.

      Weaknesses:

      Moreover, there is little detail provided about sample sizes and how data sampling is being performed (e.g., rats, sessions, or trials), raising generalizability concerns.

      We appreciate Reviewer 3’s thoughtful suggestions for making our claims convincing. We will include information about sample sizes and address each detailed recommendation in the revised manuscript.

      The authors report on a task where rats were performing sub-optimally (F-maze), weakening claims.

      Our experiment was designed to allow us to examine within the same animal, a well-performed task (Y) and a less well-performed task (F). This contrast allows us to determine differences in neural correlates. We can further dissect the relevant differences to take advantage of this experiment design.

      Likewise, it is questionable as to whether mPFC and hippocampus are dually required to perform a no-delay Y-maze task at day 5, where rats are performing near 100%.

      We agree with Reviewer 3 that the mPFC and hippocampus may not be required when the animal reaches stable performance on day 5 (Deceuninck & Kloosterman, 2024). The data we collected spans the full range of early learning (day 1) to proficiency (day 5). We wanted to understand the dynamics of beta across these learning stages.

      Recent studies suggest mPFC and hippocampus are likely to be needed, in some capacity, for learning continuous spatial alternation tasks on a range of maze geometries. Lesions, inactivation or waking activity perturbation of hippocampus or hippocampus and mPFC on the W maze alternation task slowed learning (Jadhav et al., 2012; Kim & Frank, 2009; Maharjan et al., 2018). More recently, optogenetic silencing of mPFC after sharp wave ripples on the Y maze alternation affected performance when the center arm was switched (den Bakker et al., 2023). The Y and F mazes in our study both share the continuous alternation rule, where the animal needed to avoid visiting a previously visited location on the outbound choice relative to the center, and always return to the center location.

      Further, the performance characteristics on the outbound and inbound components of our Y task is similar to the W task. We have analyzed the “inbound” and “outbound” performance of the animals on the Y maze alternation task, and they are similar to the W maze alternation task. The “inbound” or reference location component is learned quickly whereas the ”outbound”, alternation component is learned slowly. We can add this analysis to the revised manuscript.

      There would be little reason to suspect strong oscillatory coupling when task performance is poor and/or independent of mPFC-HPC communication (Jones and Wilson, 2005) potentially weakening conclusions about independent beta rhythms.

      Although many studies have examined the oscillatory coupling properties at the theta frequency between mPFC-HPC (Hyman et al., 2005; Jones & Wilson, 2005; Siapas et al., 2005), our understanding of beta frequency coordination between the two regions is less established, especially at goal locations. Beta frequency coordination at goal locations may or may not follow similar properties to theta frequency coupling. In this manuscript we are reporting the properties of goal-location beta frequency activity in mPFC-HPC networks. We are not aware of prior work describing these properties at this stage of a spatial navigation task, especially their coordination in time.

      References

      Ahmed, O. J., & Mehta, M. R. (2012). Running speed alters the frequency of hippocampal gamma oscillations. J Neurosci, 32(21), 7373-7383. https://doi.org/10.1523/JNEUROSCI.5110-11.2012

      Berke, J. D., Hetrick, V., Breck, J., & Greene, R. W. (2008). Transient 23-30 Hz oscillations in mouse hippocampus during exploration of novel environments. Hippocampus, 18(5), 519-529. https://doi.org/10.1002/hipo.20435

      Deceuninck, L., & Kloosterman, F. (2024). Disruption of awake sharp-wave ripples does not affect memorization of locations in repeated-acquisition spatial memory tasks. Elife, 13. https://doi.org/10.7554/eLife.84004

      den Bakker, H., Van Dijck, M., Sun, J. J., & Kloosterman, F. (2023). Sharp-wave-ripple-associated activity in the medial prefrontal cortex supports spatial rule switching. Cell Rep, 42(8), 112959. https://doi.org/10.1016/j.celrep.2023.112959

      França, A. S., do Nascimento, G. C., Lopes-dos-Santos, V., Muratori, L., Ribeiro, S., Lobão-Soares, B., & Tort, A. B. (2014). Beta2 oscillations (23-30 Hz) in the mouse hippocampus during novel object recognition. Eur J Neurosci, 40(11), 3693-3703. https://doi.org/10.1111/ejn.12739

      França, A. S. C., Borgesius, N. Z., Souza, B. C., & Cohen, M. X. (2021). Beta2 Oscillations in Hippocampal-Cortical Circuits During Novelty Detection. Front Syst Neurosci, 15, 617388. https://doi.org/10.3389/fnsys.2021.617388

      Hyman, J. M., Zilli, E. A., Paley, A. M., & Hasselmo, M. E. (2005). Medial prefrontal cortex cells show dynamic modulation with the hippocampal theta rhythm dependent on behavior. Hippocampus, 15(6), 739-749. https://doi.org/10.1002/hipo.20106

      Iwasaki, S., Sasaki, T., & Ikegaya, Y. (2021). Hippocampal beta oscillations predict mouse object-location associative memory performance. Hippocampus, 31(5), 503-511. https://doi.org/10.1002/hipo.23311

      Jadhav, S. P., Kemere, C., German, P. W., & Frank, L. M. (2012). Awake hippocampal sharp-wave ripples support spatial memory. Science (New York, N.Y.), 336(6087), 1454-1458. https://doi.org/10.1126/science.1217230

      Jones, M. W., & Wilson, M. A. (2005). Theta Rhythms Coordinate Hippocampal–Prefrontal Interactions in a Spatial Memory Task. PLoS Biology, 3(12). https://doi.org/10.1371/journal.pbio.0030402

      Kim, S. M., & Frank, L. M. (2009). Hippocampal Lesions Impair Rapid Learning of a Continuous Spatial Alternation Task. PLoS ONE, 4(5). https://doi.org/10.1371/journal.pone.0005494

      Lansink, C. S., Meijer, G. T., Lankelma, J. V., Vinck, M. A., Jackson, J. C., & Pennartz, C. M. (2016). Reward Expectancy Strengthens CA1 Theta and Beta Band Synchronization and Hippocampal-Ventral Striatal Coupling. J Neurosci, 36(41), 10598-10610. https://doi.org/10.1523/JNEUROSCI.0682-16.2016

      Maharjan, D. M., Dai, Y. Y., Glantz, E. H., & Jadhav, S. P. (2018). Disruption of dorsal hippocampal - prefrontal interactions using chemogenetic inactivation impairs spatial learning. Neurobiol Learn Mem, 155, 351-360. https://doi.org/10.1016/j.nlm.2018.08.023

      Rangel, L. M., Chiba, A. A., & Quinn, L. K. (2015). Theta and beta oscillatory dynamics in the dentate gyrus reveal a shift in network processing state during cue encounters. Front Syst Neurosci, 9, 96. https://doi.org/10.3389/fnsys.2015.00096

      Siapas, A. G., Lubenov, E. V., & Wilson, M. A. (2005). Prefrontal Phase Locking to Hippocampal Theta Oscillations. Neuron, 46(1), 141-151. https://doi.org/10.1016/j.neuron.2005.02.028.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors set out to understand how animals respond to visible light in an animal without eyes. To do so, they used the C. elegans model, which lacks eyes, but nonetheless exhibits robust responses to visible light at several wavelengths. Here, the authors report a promoter that is activated by visible light and independent of known pathways of light responses.

      Strengths:

      The authors convincingly demonstrate that visible light activates the expression of the cyp-14A5 promoter-driven gene expression in a variety of contexts and report the finding that this pathway is activated via the ZIP-2 transcriptionally regulated signaling pathway.

      Weaknesses:

      Because the ZIP-2 pathway has been reported to be activated predominantly by changes in the bacterial food source of C. elegans -- or exposure of animals to pathogens -- it remains unclear if visible light activates a pathway in C. elegans (animals) or if visible light potentially is sensed by the bacteria on the plate, which also lack eyes. Specifically, it is possible that the plates are seeded with excess E. coli, that E. coli is altered by light in some way, and in this context, alters its behavior in such a way that activates a known bacterially responsive pathway in the animals. This weakness would not affect the ability to use this novel discovery as a tool, which would still be useful to the field, but it does leave some questions about the applicability to the original question of how animals sense light in the absence of eyes.

      Thank you for the insightful questions and suggestions. We have now performed a key experiment requested. Interesting new data (Fig. S1I) show that light induction of cyp-14A5p::GFP requires live bacteria that maintain a non-starved physiological state. Neither plates without food nor plates with heat-killed OP50 support robust induction. We now include this interesting new result in the paper and revised discussion on the bacteria-modulated mechanism but note that this bacterial requirement does not alter the central conclusions of the study. Rather, it reveals an intriguing mechanistic layer, namely, that bacterial metabolic activity likely influences the animal’s sensitivity to environmental light. We are pursuing this host–microbe interaction in a separate study. In the present work, we focus on the intrinsic regulation and functional significance of cyp-14A5 under standard laboratory conditions with live OP50. Accordingly, we have revised the Results and Discussion to reflect the appropriate scope.

      Reviewer #2 (Public review):

      Summary:

      Ji, Ma, and colleagues report the discovery of a mechanism in C. elegans that mediates transcriptional responses to low-intensity light stimuli. They find that light-induced transcription requires a pair of bZIP transcription factors and induces expression of a cytochrome P450 effector. This unexpected light-sensing mechanism is required for physiologically relevant gene expression that controls behavioral plasticity. The authors further show that this mechanism can be co-opted to create light-inducible transgenes.

      Strengths:

      The authors rigorously demonstrate that ambient light stimuli regulate gene expression via a mechanism that requires the bZIP factors ZIP-2 and CEBP-2. Transcriptional responses to light stimuli are measured using transgenes and using measurements of endogenous transcripts. The study shows proper genetic controls for these effects. The study shows that this light-response does not require known photoreceptors, is tuned to specific wavelengths, and is highly unlikely to be an artifact of temperature-sensing. The study further shows that the function of ZIP-2 and CEBP-2 in light-sensing can be distinguished from their previously reported role in mediating transcriptional responses to pathogenic bacteria. The study includes experiments that demonstrate that regulatory motifs from a known light-response gene can be used to confer light-regulated gene expression, demonstrating sufficiency and suggesting an application of these discoveries in engineering inducible transgenes. Finally, the study shows that ambient light and the transcription factors that transduce it into gene expression changes are required to stabilize a learned olfactory behavior, suggesting a physiological function for this mechanism.

      Weaknesses:

      The study implies but does not show that the effects of ambient light on stabilizing a learned olfactory behavior are through the described pathway. To show this clearly, the authors should determine whether ambient light has any effect on mutants lacking CYP-14A5, ZIP-2, or CEBP-2. Other minor edits to the text and figures are suggested.

      We appreciate the reviewer’s comment. Our study indeed implies that ambient light stabilizes learned olfactory behavior through effects on the described pathway. Importantly, the existing data already address this point. Mutants lacking CYP-14A5, ZIP-2, or CEBP-2 display impaired olfactory memory even when exposed to ambient light, indicating that these genes are required for the behavioral effect of light. Consistent with this, ambient light robustly induces cyp-14A5p::GFP in wild-type animals but fails to do so in zip-2 and cebp-2 mutants, demonstrating that light-dependent transcriptional activation is blocked upstream in these pathway mutants. Together, these results support the conclusion that ambient light acts through the ZIP-2 → CEBP-2 → CYP-14A5 pathway to stabilize memory. Minor textual and figure revisions have been made where helpful to clarify this point.

      Reviewer #3 (Public review):

      Ji et al. report a novel and interesting light-induced transcriptional response pathway in the eyeless roundworm Caenorhabditis elegans that involves a cytochrome P450 family protein (CYP-14A5) and functions independently from previously established photosensory mechanisms. Although the exact mechanisms underlying photoactivation of this pathway remain unclear, light-dependent induction of CYP-14A5 requires bZIP transcription factors ZIP-2 and CEBP-2 that have been previously implicated in worm responses to pathogens. The authors then suggest that light-induced CYP-14A5 activity in the C. elegans hypoderm can unexpectedly and cell-non-autonomously contribute to retention of an olfactory memory. Finally, the authors demonstrate the potential for this pathway to enable robust light-induced control of gene expression and behavior, albeit with some restrictions. Overall, the evidence supporting the claims of the authors is convincing, and the authors' work suggests numerous interesting lines of future inquiry.

      (1) The authors determine that light, but not several other stressors tested (temperature, hypoxia, and food deprivation), can induce transcription of cyp-15A5. The authors use these experiments to suggest the potential specificity of the induction of CYP-14A5 by light. Given the established relationship between light and oxidative stress and the authors' later identification of ZIP-2, testing the effect of an oxidative stressor or pathogen exposure on transcription of cyp-14A5 would further strengthen the validity of this statement and potentially shed some insight into the underlying mechanisms.

      We appreciate the reviewer’s thoughtful suggestion. We would like to clarify that the “specificity” we refer to is the strong and preferential induction of cyp-14A5 by light among pathogen or detoxification-related genes, rather than an assertion that cyp-14A5 is exclusively light-responsive. This does not preclude the possibility that cyp-14A5 can also be activated under other conditions. Indeed, prior work from the Troemel laboratory has identified cyp-14A5 as one of many pathogen-inducible genes, consistent with its role in stress physiology. Our data show that classical pathogen-responsive genes (e.g., irg-1) are not induced by light, whereas cyp-14A5 is strongly induced, highlighting the selective engagement of this cytochrome P450 by light under the conditions tested. We have revised the text to clarify this point.

      (2) The authors suggest that short-wavelength light more robustly increases transcription of cyp-14A5 compared to equally intense longer wavelengths (Figure 2F and 2G). Here, however, the authors report intensities in lux of wavelengths tested. Measurements of and reporting the specific spectra of the incident lights and their corresponding irradiances (ideally, in some form of mW/mm2 - see Ward et al., 2008, Edwards et al., 2008, Bhatla and Horvitz, 2015, De Magalhaes Filho et al., 2018, Ghosh et al., 2021, among others, for examples) is critical for appropriate comparisons across wavelengths and facilitates cross-checking with previous studies of C. elegans light responses. On a related and more minor note, the authors place an ultraviolet shield in front of a visible light LED to test potential effects of ultraviolet light on transcription of cyp-14A5. A measurement of the spectrum of the visible light LED would help confirm if such an experiment was required. Regardless, the principal conclusions the authors made from these experiments will likely remain unchanged.

      Thank you. We have revised the text to clarify this point. “Using controlled light versus dark conditions, we confirmed the finding from an integrated cyp-14A5p::GFP reporter and observed its robust widespread GFP expression in many tissues induced by moderate-intensity (500-3000 Lux, 16-48 hr duration) LED light exposure (Fig. 1A). The photometric Lux range is approximately 0.1–0.60 mW/cm<sup>2</sup> in radiometric (total radiant power) metric given the spectrum of the LED light source.”

      (3) The authors report an interesting observation that animals exposed to ambient light (~600 lux) exhibit significantly increased memory retention compared to those maintained in darkness (Figure 4). Furthermore, light deprivation within the first 2-4 hours after learning appears to eliminate the effect of light on memory retention. These processes depend on CYP-14A5, loss of which can be rescued by re-expression of cyp-14A5 in mutant animals using a hypoderm-specific- and non-light-inducible- promoter. Taken together, the authors argue convincingly that hypodermal expression of cyp-14A5 can contribute to the retention of the olfactory memory. More broadly, these experiments suggest that cell-non-autonomous signaling can enhance retention of olfactory memory. How retention of the olfactory memory is enhanced by light generally remains unclear. In addition, the authors' experiments in Figure 1B demonstrate - at least by use of the transcriptional reporter - that light-dependent induction of cyp-14A5 transcription at 500 - 1000 lux is minimal and especially so at short duration exposures. Additional experiments, including verification of light-dependent changes in CYP-14A5 levels in the olfactory memory behavioral setup, would help further interpret these otherwise interesting results.

      We thank the reviewer for these thoughtful comments. We agree that understanding how light enhances memory retention at a mechanistic level is an important direction for future work. Regarding the light intensities used in Figure 1B, we would like to clarify that 500–1000 lux does produce a measurable and statistically significant induction of cyp-14A5p::GFP, although the magnitude is lower than that observed at higher intensities. We interpret this modest induction as physiologically relevant: intermediate light levels appear sufficient to engage the CYP-14A5–dependent program required for memory stabilization, whereas stronger light intensities are detrimental to learning and reduce behavioral performance. Thus, the behavioral paradigm uses a light regime that activates the pathway without introducing stress-associated confounders.

      (4) The experiments in Figure 4 nicely validate the usage of the cyp-14A5 promoter as a potential tool for light-dependent induction of gene expression. Despite the limitations of this tool, including those presented by the authors, it could prove useful for the community.

      Thank you and we agree. In addition, we have included in the revised manuscript the single-copy integration strains based on UAS-GAL4 that produced similar results as transgenic strains and will be even more flexible and useful for the community.

      Recommendations for the authors:

      Reviewing Editor Comments:

      While appreciating the quality and presentation of this important study, we had two major concerns that the authors need to address.

      (1) Bacteria-versus-worm origin:

      To rule out a bacterially derived stimulus, we suggest testing whether cyp-14A5p::GFP is inducible without bacteria (or killed bacteria). Checking whether the canonical immune reporters irg-5p::GFP and gst-4p::GFP are also light-inducible will further clarify this point.

      We have now performed the key experiment requested by the reviewers. Interesting new data (Fig. S1I) show that light induction of cyp-14A5p::GFP requires live bacteria that maintain a non-starved physiological state. Neither plates without food nor plates with heat-killed OP50 support robust induction. Importantly, this requirement does not alter any of the central conclusions of the study. Rather, it reveals an intriguing mechanistic layer, namely, that bacterial metabolic activity influences the animal’s sensitivity to environmental light. We are pursuing this host–microbe interaction in a separate study. In the present work, we focus on the regulation and functional significance of cyp-14A5 under standard laboratory conditions with live OP50.

      We included the data (Fig. 2D) to show that the canonical immune reporter irg-1p::GFP is not induced by the light condition that robustly induced cyp-14A5p::GFP, and gst-4p::GFP is only very mildly induced (Fig. S1J).

      (2) Pathway-behaviour link:

      The behavioural relevance of the newly described pathway is intriguing, but it needs direct support. Ideally, this would require comparing memory in WT, zip-2-/-, cebp-2-/-, and cyp-14A5-/- under both dark and light conditions. But at the very least, it would require testing if constitutive CYP-14A5 rescue in the dark bypasses the requirement of light.

      We respectfully submit that additional experiments are not required to support the behavioral conclusions. Our model posits that cyp-14A5 is required but not sufficient for memory stabilization, one component within a broader set of light-induced genes. Thus, constitutive hypodermal expression of cyp-14A5 would not be expected to bypass the requirement for ambient light. The existing data are fully consistent with this framework and conclusions of the paper.

      Reviewer #1 (Recommendations for the authors):

      Overall, I think this paper is interesting to the field of C. elegans researchers at a minimum, as a light-inducible gene expression system might have a variety of uses throughout the diverse research paradigms that use this model system. With that said, I have a couple of suggestions that I think would substantially impact the ability to interpret these findings, which might be useful for broader implications of the study.

      (1) Most importantly, the supplemental table of RNA-seq data should likely be updated and discussed further beyond the cyp-14A5 findings. First, the authors report 7,902 genes are differentially expressed in response to light and then break these into upregulated and downregulated genes. But there are only 1,785 upregulated genes and 3,632 downregulated genes. This adds up to 5417 genes, but doesn't match the 7,902 genes reported to change, and I could not find in the text if some other filters were applied that might explain this not adding up.

      Thank you for this helpful comment. We agree that the exact numbers depend on statistical thresholds and are therefore somewhat arbitrary. To avoid implying unwarranted precision, we have revised the text to state that “thousands of genes are differentially regulated by light.”

      (2) Among the upregulated genes in response to light are irg-5, irg-4, irg-6, irg-8, and gst-4. Indeed, all of these well-studied genes (or most) show even more induction by light than cyp-14A5. It is my opinion that this result needs further criticism as there are existing GFP reporters for gst-4 and irg-5 that are similarly well studied to irg-1, which is in the paper (and is not upregulated). In my opinion, the authors should test if they see activation of the irg-4 and gst-4 GFP reporters by light as well. This would not only validate their RNA-seq but might provide more important evidence for the field, as these other reporters are not considered light-inducible previously. If they are, several major studies might be impacted by this.

      Thank you for the comments. We have irg-1p::GFP and gst-4p::GFP in the lab but did not find other reporters for the genes mentioned from CGC. Neither of the two reporters showed light induction (Figs. 2D and S1J) as strongly as cyp-14A5p::GFP. It is possible that irg-1 and gst-4 RNA levels are up-regulated but not reflected in our transgenic reporters that used their promoters to drive GFP expression. Stronger light induction of cyp-14A5p::GFP is unlikely caused by the multi-copy nature of the transgene since newly generated single-copy integration strains based on the UAS-GAL4 system produced similar robust results for light induction (Fig. S1I and see Method).

      (3) Along the same lines, if at least 4 (and likely more) well characterized immune response genes are activated by light and these genes are known to mostly respond to differences in C. elegans bacterial food source/diet, then it stands to reason that maybe in this experimental context the light is not acting on "animals" at all, but rather triggering changes in E. coli (i.e. changing E. coli metabolism or pathogenicity like properties). If true, then perhaps the light affects bacteria in such a way that it activates a previously known bacterial pathogen response mechanism. This should be easy to test by seeing if this reporter is still activated by light in the presence of diverse bacterial diets, which are available from the CGC (CeMBio collection, for example). This is likely very important to the conclusions of the manuscript as it relates to animals sensing light, but might not be as important to the use of this system as a tool.

      Thank you for the insightful questions and suggestions. Interesting new data (Fig. S1I) show that light induction of cyp-14A5p::GFP requires live bacteria that maintain a non-starved physiological state. Neither plates without food nor plates with heat-killed OP50 support robust induction. Importantly, this requirement does not alter any of the central conclusions of the study. Rather, it reveals an intriguing mechanistic layer, namely, that bacterial metabolic activity influences the animal’s sensitivity to environmental light. We are pursuing this host–microbe interaction in a separate study. In the present work, we focus on the regulation and functional significance of cyp-14A5 under standard laboratory conditions with live OP50. We have revised the Results and Discussion to reflect the appropriate scope of our study and implications of the new findings.

      (4) Lastly, it seems unlikely that nearly half the C. elegans genome is transcriptionally regulated by light (or nearly half of the detected genes in the RNA-seq results). It seems likely that this list of 7,902 genes contains false positives. I would suggest upping some sort of filter, like moving to padj < 0.01 instead of 0.05, or adding a 4-fold change filter (2-fold and 0.01 still results in near 5000+ genes changing, which might explain the difference in up and down genes just being due to different padj filters. Along these lines, it is worth noting that the padj is generated using DESeq2 it appears and one of the first assumptions of DESeq2 is that the median expressed genes do not change, and there is a normalization. However, if MOST genes do change in expression, then one of the fundamental assumptions of DESeq2 is not valid, and thus would mean it might not be an appropriate analysis tool - perhaps there is some other normalization that could be done before running DESeq2 due to some other noise present in the RNA-seq runs?

      Thank you for this helpful comment. We agree that the exact numbers depend on statistical thresholds and are therefore somewhat arbitrary. To avoid implying unwarranted precision, we have revised the text to state that “thousands of genes are differentially regulated by light.”

      (5) Minor point - I would delete the reference to ER in line 92. While most CYPs do localize to the ER, the images shown are not clearly ER and probably do not have enough resolution to make claims about subcellular localization. To me, it would be easier to just delete this claim as it is not required for the main claims of the manuscript.

      Reference deleted.

      Reviewer #2 (Recommendations for the authors):

      I have one request for clarification that likely requires additional data. Figure 3 shows that ambient light stabilizes learned changes to chemotaxis and further shows that CYP-14A5 has a similar function. The implication is that light promotes CYP-14A5 expression, which somehow promotes memory consolidation. The authors should test whether memory consolidation in cyp-15A5, zip-2, or cebp-2 mutants is no longer affected by ambient light.

      It is also possible to test whether forced expression of CYP14A5 can bypass the effect of 'no light' conditions on memory consolidation.

      Thank you for the comments. We respectfully submit that additional experiments are not required to support the behavioral conclusions. Our model posits that cyp-14A5 is required but not sufficient for memory stabilization, one component within a broader set of light-induced genes. Thus, constitutive hypodermal expression of cyp-14A5 would not be expected to bypass the requirement for ambient light. The existing data are fully consistent with this framework and conclusions of the paper.

      I have several minor suggestions relating to the text and figures.

      (1) In the introduction, the authors assert that little is known about non-visual light sensing and then list many examples of molecular mechanisms of non-visual light-sensing. They should emphasize that non-visual light sensing is important and accomplished by diverse molecular mechanisms.

      Agree and revised accordingly.

      (2) Check spacing between gene names (line 109).

      Corrected.

      (3) There should be a new paragraph break when the uORF experiments are described (line 146).

      Corrected.

      (4) 'Phenoptosis' is an esoteric word. Please define it (line 206).

      Corrected.

      (5) 'p' in the transgene name cyp-14A5p::nlp-22 is in italics, unlike the rest of the manuscript.

      Corrected.

      (6) 'Acknowledgment' should be 'Acknowledgments' (line 384).

      Corrected.

      (7) The color map in panel 1B should have units.

      It was arbitrary unit (now added) to highlight relative not absolute differences.

      (8) In panel 1E, it is confusing to have 'DARK' denoted by reddish bars and 'LIGHT' denoted by bluish bars. Perhaps 'DARK' is black/dark grey and 'LIGHT' is white?

      Corrected.

      (9) In panel 1D, it takes a minute to find the purple diamond. Please mark up the volcano plot to make it easier.

      Corrected.

      Reviewer #3 (Recommendations for the authors):

      The authors generally present convincing experiments detailing interesting results in a well-written manuscript.

      One quick note: the same Bhatla and Horvitz (2015) papers appear to be cited twice [line 52].

      Corrected.

    1. Author response:

      The following is the authors’ response to the latest reviews:

      "One remaining question is the interpretation of matching variants with very low stable posterior probabilities (~0), which the authors have analyzed in detail but without fully conclusive findings. I agree with the authors that this event is relatively rare and the current sample size is limited but this might be something to keep in mind for future studies."

      Fine-mapping stabilityon matching variants with very low stable posterior probability

      We thank Reviewer 2 for encouraging us to think more about how low stable posterior probability matching variants can be interpreted. We describe a few plausible interpretations, even though – as Reviewer 2 and we have both acknowledged – our present experiments do not point to a clear and conclusive account.

      One explanation is that the locus captured by the variant might not be well-resolved, in the sense that many correlated variants exist around the locus. Thus, the variant itself is unlikely causal, but the set of variants in high LD with it may contain the true causal variant, or it's possible that the causal variant itself was not sequenced but lies in that locus. A comparison of LD patterns across ancestries at the locus would be helpful here.

      Another explanation rests on the following observation. For a variant to be matching between top and stable PICS and to also have very small stable PP, it has to have the largest PP after residualization on the ALL slice but also have positive PP with gene expression on many other slices. In other words, failing to control for potential confounders shrinks the PP. If one assumes that the matching variant is truly causal, then our observation points to an example of negative confounding (aka suppressor effect). This can occur when the confounders (PCs) are correlated with allele dosage at the causal variant in a different direction than their correlation with gene expression, so that the crude association between unresidualized gene expression and causal variant allele dosage is biased toward 0.

      Although our present study does not allow us to systematically confirm either interpretation – since we found that matching variants were depleted in causal variants in our simulations, violating the second argument, but we also found functional enrichment in analyses of GEUVADIS data though only 17 matching variants with low stable PP were reported – we believe a larger-scale study using larger cohort sizes (at least 1000 individuals per ancestry) and many more simulations (to increase yield of such cases) would be insightful.

      ———

      The following is the authors’ response to the original reviews:

      Reviewer #1:

      Major comments:

      (1) It would be interesting to see how much fine-mapping stability can improve the fine-mapping results in cross-population. One can simulate data using true genotype data and quantify the amount the fine-mapping methods improve utilizing the stability idea.

      We agree, and have performed simulation studies where we assume that causal variants are shared across populations. Specifically, by mirroring the simulation approach described in Wang et al. (2020), we generated 2,400 synthetic gene expression phenotypes across 22 autosomes, using GEUVADIS gene expression metadata (i.e., gene transcription start site) to ensure largely cis expression phenotypes were simulated. We additionally generated 1,440 synthetic gene expression phenotypes that incorporate environmental heterogeneity, to motivate our pursuit of fine-mapping stability in the first place (see Response to Reviewer 2, Comment 6). These are described in Results section “Simulation study”:

      We evaluated the performance of the PICS algorithm, specifically comparing the approach incorporating stability guidance against the residualization approach that is more commonly used — similar to our application to the real GEUVADIS data. We additionally investigated two ways of “combining” the residualization and stability guidance approaches: (1) running stability-guided PICS on residualized phenotypes; (2) prioritizing matching variants returned by both approaches. See Response to Reviewer 2, Comment 5.

      (2) I would be very interested to see how other fine-mapping methods (FINEMAP, SuSiE, and CAVIAR) perform via the stability idea.

      Thank you for this valuable comment. We ran SuSiE on the same set of simulated datasets. Specifically, we ran a version that uses residualized phenotypes (supposedly removing the effects of population structure), and also a version that incorporates stability. The second version is similar to how we incorporate stability in PICS. We investigated the performance of Stable SuSiE in a similar manner to our investigation of PICS. First we compared the performance relative to SuSiE that was run on residualized phenotypes. Motivated by our finding in PICS that prioritizing matching variants improves causal variant recovery, we did the same analysis for SuSiE. This analysis is described in Results section “Stability guidance improves causal variant recovery in SuSiE.”

      We reported overall matching frequencies and causal variant recovery rates of top and stable variants for SuSiE in Figures 2C&D.

      Frequencies with which Stable and Top SuSiE variants match, stratified by the simulation parameters, are summarized in Supplementary File 2C (reproduced for convenience in Response to Reviewer 2, Comment 3). Causal variant recovery rates split by the number of causal variants simulated, and stratified by both signal-to-noise ratio and the number of credible sets included, are reported in Figure 2—figure supplements 16-18. We reproduce Figure 2—figure supplement 18 (three causal variants scenario) below for convenience. Analogous recovery rates for matching versus non-matching top or stable variants are reported in Figure 2—figure supplements 19, 21 and 23.

      (3) I am a little bit concerned about the PICS's assumption about one causal variant. The authors mentioned this assumption as one of their method limitations. However, given the utility of existing fine-mapping methods (FINEMAP and SuSiE), it is worth exploring this domain.

      Thank you for raising this fair concern. We explored this domain, by considering simulations that include two and three causal variants (see Response to Reviewer 2, Comment 3). We looked at how well PICS recovers causal variants, and found that each potential set largely does not contain more than one causal variant (Figure 2—figure supplements 20 and 22). This can be explained by the fact that PICS potential sets are constructed from variants with a minimum linkage disequilibrium to a focal variant. On the other hand, in SuSiE, we observed multiple causal variants appearing in lower credible sets when applying stability guidance (Figure 2—figure supplements 21 and 23). A more extensive study involving more fine-mapping methods and metrics specific to violation of the one causal variant assumption could be pursued in future work.

      Reviewer #2:

      Aw et al. presents a new stability-guided fine-mapping method by extending the previously proposed PICS method. They applied their stability-based method to fine-map cis-eQTLs in the GEUVADIS dataset and compared it against what they call residualization-based method. They evaluated the performance of the proposed method using publicly available functional annotations and claimed the variants identified by their proposed stability-based method are more enriched for these functional annotations.

      While the reviewer acknowledges the contribution of the present work, there are a couple of major concerns as described below.

      Major:

      (1) It is critical to evaluate the proposed method in simulation settings, where we know which variants are truly causal. While I acknowledge their empirical approach using the functional annotations, a more unbiased, comprehensive evaluation in simulations would be necessary to assess its performance against the existing methods.

      Thank you for this point. We agree. We have performed a simulation study where we assume that causal variants are shared across populations (see response to Reviewer 1, Comment 1). Specifically, by mirroring the simulation approach described in Wang et al. (2020), we generated 2,400 synthetic gene expression phenotypes across 22 autosomes, using GEUVADIS gene expression metadata (i.e., gene transcription start site) to ensure cis expression phenotypes were simulated.

      (2) Also, simulations would be required to assess how the method is sensitive to different parameters, e.g., LD threshold, resampling number, or number of potential sets.

      Thank you for raising this point. The underlying PICS algorithm was not proposed by us, so we followed the default parameters set (LD threshold, r<sup>2</sup> \= 0.5; see Taylor et al., 2021 Bioinformatics) to focus on how stability considerations will impact the existing fine-mapping algorithm. We attempted to derive the asymptotic joint distribution of the p-values, but it was too difficult. Hence, we used 500 permutations because such a large number would allow large-sample asymptotics to kick in. However, following your critical suggestion we varied the number of potential sets in our analyses of simulated data. We briefly mention this in the Results.

      “In the Supplement, we also describe findings from investigations into the impact of including more potential sets on matching frequency and causal variant recovery…”

      A detailed write-up is provided in Supplementary File 1 Section S2 (p.2):

      “The number of credible or potential sets is a parameter in many fine-mapping algorithms. Focusing on stability-guided approaches, we consider how including more potential sets for stable fine-mapping algorithms affects both causal variant recovery and matching frequency in simulations…

      Causal variant recovery. We investigate both Stable PICS and Stable SuSiE. Focusing first on simulations with one causal variant, we observe a modest gain in causal variant recovery for both Stable PICS and Stable SuSiE, most noticeably when the number of sets was increased from 1 to 2 under the lowest signal-to-noise ratio setting…”

      We observed that increasing the number of potential sets helps with recovering causal variants for Stable PICS (Figure 2—figure supplements 13-15). This observation also accounts for the comparable power that Stable PICS has with SuSiE in simulations with low signal-to-noise ratio (SNR), when we increase the number of credible sets or potential sets (Figure 2—figure supplements 10-12).

      (3) Given the previous studies have identified multiple putative causal variants in both GWAS and eQTL, I think it's better to model multiple causal variants in any modern fine-mapping methods. At least, a simulation to assess its impact would be appreciated.

      We agree. In our simulations we considered up to three causal variants in cis, and evaluated how well the top three Potential Sets recovered all causal variants (Figure 2—figure supplements 13-15; Figure 2—figure supplement 15). We also reported the frequency of variant matches between Top and Stable PICS stratified by the number of causal variants simulated in Supplementary File 2B and 2C. Note Supplementary File 2C is for results from SuSiE fine-mapping; see Response to Reviewer 1, Comment 2.

      Supplementary File 2B. Frequencies with which Stable and Top PICS have matching variants for the same potential set. For each SNR/ “No. Causal Variants” scenario, the number of matching variants is reported in parentheses.

      Supplementary File 2C. Frequencies with which Stable and Top SuSiE have matching variants for the same credible set. For each SNR/ “No. Causal Variants” scenario, the number of matching variants is reported in parentheses.

      (4) Relatedly, I wonder what fraction of non-matching variants are due to the lack of multiple causal variant modeling.

      PICS handles multiple causal variants by including more potential sets to return, owing to the important caveat that causal variants in high LD cannot be statistically distinguished. For example, if one believes there are three causal variants that are not too tightly linked, one could make PICS return three potential sets rather than just one. To answer the question using our simulation study, we subsetted our results to just scenarios where the top and stable variants do not match. This mimics the exact scenario of having modeled multiple causal variants but still not yielding matching variants, so we can investigate whether these non-matching variants are in fact enriched in the true causal variants.

      Because we expect causal variants to appear in some potential set, we specifically considered whether these non-matching causal variants might match along different potential sets across the different methods. In other words, we compared the stable variant with the top variant from another potential set for the other approach (e.g., Stable PICS Potential Set 1 variant vs Top PICS Potential Set 2 variant). First, we computed the frequency with which such pairs of variants match. A high frequency would demonstrate that, even if the corresponding potential sets do not have a variant match, there could still be a match between non-corresponding potential sets across the two approaches, which shows that multiple causal variant modeling boosts identification of matching variants between both approaches — regardless of whether the matching variant is in fact causal.

      Low frequencies were observed. For example, when restricting to simulations where Top and Stable PICS Potential Set 1 variants did not match, about 2-3% of variants matched between the Potential Set 1 variant in Stable PICS and Potential Sets 2 and 3 variants in Top PICS; or between the Potential Set 1 variant in Top PICS and Potential Sets 2 and 3 variants in Stable PICS (Supplementary File 2D). When looking at non-matching Potential Set 2 or Potential Set 3 variants, we do see an increase in matching frequencies (between 10-20%) between Potential Set 2 variants and other potential set variants between the different approaches. However, these percentages are still small compared to the matching frequencies we observed between corresponding potential sets (e.g., for simulations with one causal variant this was 70-90% between Top and Stable PICS Potential Set 1, and for simulations with two and three causal variants this was 55-78% and 57-79% respectively).

      We next checked whether these “off-diagonal” matching variants corresponded to the true causal variants simulated. Here we find that the causal variant recovery rate is mostly less than the corresponding rate for diagonally matching variants, which together with the low matching frequency suggests that the enrichment of causal variants of “off-diagonal” matching variants is much weaker than in the diagonally matching approach. In other words, the fraction of non-matching (causal) variants due to the lack of multiple causal variant modeling is low.

      We discuss these findings in Supplementary File 1 Section S2 (bottom of p.2).

      (5) I wonder if you can combine the stability-based and the residualization-based approach, i.e., using the residualized phenotypes for the stability-based approach. Would that further improve the accuracy or not?

      This is a good idea, thank you for suggesting it. We pursued this combined approach on simulated gene expression phenotypes, but did not observe significant gains in causal variant recovery (Figure 2B; Figure 2—figure supplements 2, 13 and 15). We reported this Results “Searching for matching variants between Top PICS and Stable PICS improves causal variant Recovery.”

      “We thus explore ways to combine the residualization and stability-driven approaches, by considering (i) combining them into a single fine-mapping algorithm (we call the resulting procedure Combined PICS); and (ii) prioritizing matching variants between the two algorithms. Comparing the performance of Combined PICS against both Top and Stable PICS, however, we find no significant difference in its ability to recover causal variants (Figure 2B)...”

      However, we also confirmed in our simulations that prioritizing matching variants between the two approaches led to gains in causal variant recovery (Figure 2D; Figure 2—figure supplements 4, 19, 20 and 22). We reported this Results “Searching for matching variants between Top PICS and Stable PICS improves causal variant Recovery.”

      “On the other hand, matching variants between Top and Stable PICS are significantly more likely to be causal. Across all simulations, a matching variant in Potential Set 1 is 2.5X as likely to be causal than either a non-matching top or stable variant (Figure 2D) — a result that was qualitatively consistent even when we stratified simulations by SNR and number of causal variants simulated (Figure 2—figure supplements 19, 20 and 22)...”

      This finding is consistent with our analysis of real GEUVADIS gene expression data, where we reported larger functional significance of matching variants relative to non-matching variants returned by either Top of Stable PICS.

      (6) The authors state that confounding in cohorts with diverse ancestries poses potential difficulties in identifying the correct causal variants. However, I don't see that they directly address whether the stability approach is mitigating this. It is hard to say whether the stability approach is helping beyond what simpler post-hoc QC (e.g., thresholding) can do.

      Thank you for raising this fair point. Here is a model we have in mind. Gene expression phenotypes (Y) can be explained by both genotypic effects (G, as in genotypic allelic dosage) and the environment (E): Y = G + E. However, both G and E depend on ancestry (A), so that Y = G|A+E|A. Suppose that the causal variants are shared across ancestries, so that (G|A=a)=G for all ancestries a. Suppose however that environments are heterogeneous by ancestry: (E|A=a) = e(a) for some function e that depends non-trivially on a. This would violate the exchangeability of exogenous E in the full sample, but by performing fine-mapping on each ancestry stratum, the exchangeability of exogenous E is preserved. This provides theoretical justification for the stability approach.

      We next turned to simulations, where we investigated 1,440 simulated gene expression phenotypes capturing various ways in which ancestry induces heterogeneity in the exogenous E variable (simulation details in Lines 576-610 of Materials and Methods). We ran Stable PICS, as well as a version of PICS that did not residualize phenotypes or apply the stability principle. We observed that (i) causal variant recovery performance was not significantly different between the two approaches (Figure 2—figure supplements 24-32); but (ii) disagreement between the approaches can be considerable, especially when the signal-to-noise ratio is low (Supplementary File 2A). For example, in a set of simulations with three causal variants, with SNR = 0.11 and E heterogeneous by ancestry by letting E be drawn from N(2σ,σ<sup>2</sup>) for only GBR individuals (rest are N(0,σ<sup>2</sup>)), there was disagreement between Potential Set 1 and 2 variants in 25% of simulations — though recovery rates were similar (Probability of recovering at least one causal variant: 75% for Plain PICS and 80% for Stable PICS). These points suggest that confounding in cohorts can reduce power in methods not adjusting or accounting for ancestral heterogeneity, but can be remedied by approaches that do so. We report this analysis in Results “Simulations justify exploration of stability guidance”

      In the current version of our work, we have evaluated, using both simulations and empirical evidence, different ways to combine approaches to boost causal variant recovery. Our simulation study shows that prioritizing matching variants across multiple methods improves causal variant recovery. On GEUVADIS data, where we might not know which variants are causal, we already demonstrated that matching variants are enriched for functional annotations. Therefore, our analyses justify that the adverse consequence of confounding on reducing fine-mapping accuracy can be mitigated by prioritizing matching variants between algorithms including those that account for stability.

      (7) For non-matching variants, I wonder what the difference of posterior probabilities is between the stable and top variants in each method. If the difference is small, maybe it is due to noise rather than signal.

      We have reported differences in posterior probabilities returned by Stable and Top PICS for GEUVADIS data; see Figure 3—figure supplement 1. For completeness, we compute the differences in posterior probabilities and summarize these differences both as histograms and as numerical summary statistics.

      Potential Set 1

      - Number of non-matching variants = 9,921

      - Table of Summary Statistics of (Stable Posterior Probability – Top Posterior Probability)

      Author response table 1.

      - Histogram of (Stable Posterior Probability – Top Posterior Probability)

      Author response image 1.

      Potential Set 2

      - Number of non-matching variants = 14,454

      - Table of Summary Statistics of (Stable Posterior Probability – Top Posterior Probability)

      Author response table 2.

      - Histogram of (Stable Posterior Probability – Top Posterior Probability)

      Author response image 2.

      Potential Set 3

      - Number of non-matching variants = 16,814

      - Table of Summary Statistics of (Stable Posterior Probability – Top Posterior Probability)

      Author response table 3.

      - Histogram of (Stable Posterior Probability – Top Posterior Probability)

      Author response image 3.

      We also compared the difference in posterior probabilities between non-matching variants returned by Stable PICS and Top PICS for our 2,400 simulated gene expression phenotypes. Focusing on just Potential Set 1 variants, we find two equally likely scenarios, as demonstrated by two distinct clusters of points in a “posterior probability-posterior probability” plot. The first is, as pointed out, a small difference in posterior probability (points lying close to y=x). The second, however, reveals stable variants with very small posterior probability (of order 4 x 10<sup>–5</sup> to 0.05) but with a non-matching top variant taking on posterior probability well distributed along [0,1]. Moving down to Potential Sets 2 and 3, the distribution of pairs of posterior probabilities appears less clustered, indicating less tendency for posterior probability differences to be small ( Figure 2—figure supplement 8).

      Here are the histograms and numerical summary statistics.

      Potential Set 1

      - Number of non-matching variants = 663 (out of 2,400)

      - Table of Summary Statistics of (Stable Posterior Probability – Top Posterior Probability)

      Author response table 4.

      - Histogram of (Stable Posterior Probability – Top Posterior Probability)

      Author response image 4.

      Potential Set 2

      Number of non-matching variants = 1,429 (out of 2,400)

      - Table of Summary Statistics of (Stable Posterior Probability – Top Posterior Probability)

      Author response table 5.

      - Histogram of (Stable Posterior Probability – Top Posterior Probability)

      Author response image 5.

      Potential Set 3

      - Number of non-matching variants = 1,810 (out of 2,400)

      - Table of Summary Statistics of (Stable Posterior Probability – Top Posterior Probability)

      Author response table 6.

      - Histogram of (Stable Posterior Probability – Top Posterior Probability)

      Author response image 6.

      (8) It's a bit surprising that you observed matching variants with (stable) posterior probability ~ 0 (SFig. 1). What are the interpretations for these variants? Do you observe functional enrichment even for low posterior probability matching variants?

      Thank you for this question. We have performed a thorough analysis of matching variants with very low stable posterior probability, which we define as having a posterior probability < 0.01 (Supplementary File 1 Section S11). Here, we briefly summarize the analysis and key findings.

      Analysis

      First, such variants occur very rarely — only 8 across all three potential sets in simulations, and 17 across all three potential sets for GEUVADIS (the latter variants are listed in Supplementary 2E). We begin interpreting these variants by looking at allele frequency heterogeneity by ancestry, support size — defined as the number of variants with positive posterior probability in the ALL slice* — and the number of slices including the stable variant (i.e., the stable variant reported positive posterior probability for the slice).

      *Note that the stable variant posterior probability need not be at least 1/(Support Size). This is because the algorithm may have picked a SNP that has a lower posterior probability in the ALL slice (i.e., not the top variant) but happens to appear in the most number of other slices (i.e., a stable variant).

      For variants arising from simulations, because we know the true causal variants, we check if these variants are causal. For GEUVADIS fine-mapped variants, we rely on functional annotations to compare their relative enrichment against other matching variants that did not have very low stable posterior probability.

      Findings

      While we caution against generalizing from observations reported here, which are based on very small sample sizes, we noticed the following. In simulations, matching variants with very low stable posterior probability are largely depleted in causal variants, although factors such as the number of slices including the stable variant may still be useful. In GEUVADIS, however, these variants can still be functionally enriched. We reported three examples in Supplementary File 1 Section S11 (pp. 8-9 of Supplement), where the variants were enriched in either VEP or biologically interpretable functional annotations, and were also reported in earlier studies. We partially reproduce our report below for convenience.

      “However, we occasionally found variants that stand out for having large functional annotation scores. We list one below for each potential set.

      - Potential Set 1 reported the variant rs12224894 from fine-mapping ENSG00000255284.1 (accession code AP006621.3) in Chromosome 11. This variant stood out for lying in the promoter flanking region of multiple cell types and being relatively enriched for GC content with a 75bp flanking region. This variant has been reported as a cis eQTL for AP006632 (using whole blood gene expression, rather than lymphoblastoid cell line gene expression in this study) in a clinical trial study of patients with systemic lupus erythematosus (Davenport et al., 2018). Its nearest gene is GATD1, a ubiquitously expressed gene that codes for a protein and is predicted to regulate enzymatic and catabolic activity. This variant appeared in all 6 slices, with a moderate support size of 23.

      - Potential Set 2 reported the variant rs9912201 from fine-mapping ENSG00000108592.9 (mapped to FTSJ3) in Chromosome 17. Its FIRE score is 0.976, which is close to the maximum FIRE score reported across all Potential Set 2 matching variants. This variant has been reported as a SNP in high LD to a GWAS hit SNP rs7223966 in a pan-cancer study (Gong et al., 2018). This variant appeared in all 6 slices, with a moderate support size of 32.

      - Potential Set 3 reported the variant rs625750 from fine-mapping ENSG00000254614.1 (mapped to CAPN1-AS1, an RNA gene) in Chromosome 11. Its FIRE score is 0.971 and its B statistic is 0.405 (region under selection), which lie at the extreme quantiles of the distributions of these scores for Potential Set 3 matching variants with stable posterior probability at least 0.01. Its associated mutation has been predicted to affect transcription factor binding, as computed using several position weight matrices (Kheradpour and Kellis, 2014). This variant appeared in just 3 slices, possibly owing to the considerable allele frequency difference between ancestries (maximum AF difference = 0.22). However, it has a small support size of 4 and a moderately high Top PICS posterior probability of 0.64.

      To summarize, our analysis of GEUVADIS fine-mapped variants demonstrates that matching variants with very low stable posterior probability could still be functionally important, even for lower potential sets, conditional on supportive scores in interpretable features such as the number of slices containing the stable variant and the posterior probability support size…”

    1. Author response:

      The following is the authors’ response to the original reviews

      eLife Assessment

      This manuscript presents useful insights into the molecular basis underlying the positive cooperativity between the co-transported substrates (galactoside sugar and sodium ion) in the melibiose transporter MelB. Building on years of previous studies, this work improves on the resolution of previously published structures and reports the presence of a water molecule in the sugar binding site that would appear to be key for its recognition, introduces further structures bound to different substrates, and utilizes HDX-MS to further understand the positive cooperativity between sugar and the co-transported sodium cation. Although the experimental work is solid, the presentation of the data lacks clarity, and in particular, the HDX-MS data interpretation requires further explanation in both methodology and discussion, as well as a clearer description of the new insight that is obtained in relation to previous studies. The work will be of interest to biologists and biochemists working on cation-coupled symporters, which mediate the transport of a wide range of solutes across cell membranes.

      We express our gratitude to the associate editor, review editor, and reviewers for their favorable evaluation of this manuscript, as well as their constructive comments and encouragement. Their feedback has been integrated to fortify the evidence, refine the data analysis, and elevate the presentation of the results, thereby enhancing the overall quality and clarity of the manuscript.

      A brief summary of the modifications in this revision:

      (a) We performed four new experiments: 1) intact cell [<sup>3</sup>H]raffinose transport assay; 2) intact cell p-nitrophenol detection to demonstrate α-NPG transport; 3) ITC binding assay for the D59C mutant; and 4) molecular dynamics to simulate the water-1 in sugar-binding site and the dynamics of side chains in the Na<sup>+</sup>- and melibiose-binding pockets. All data consistently support the conclusion draw in this article.

      (b) We have added a new figure to show the apo state dynamics (the new Fig. 5a,b) and annotated the amino acid residue positions and marked positions in sugar- or Na<sup>+</sup>-binding pockets.

      (c) As suggested by reviewer-3, we have moved the individual mapping of ligand effects on HDX data to the main figure, combined with the residual plots, and marked the amino-acid residue positions.

      (d) We have added more deuterium uptake plots to cover all residues in the sugar- or Na<sup>+</sup>-binding pockets in the current figure 7 (previously figure 6).

      (e) We have added a new figure 8 showing the positions at the well-studied cytoplasmic gating salt-bridge network and other loops likely important for conformational changes, along with a membrane topology marked with the HDX data. We have added a new figure 9 from MD simulations.

      Reviewer #1:

      While the structure of the melibiose permease in both outward and inward-facing forms has been solved previously, there remain unanswered questions regarding its mechanism. Hariharan et al set out to address this with further crystallographic studies complemented with ITC and hydrogen-deuterium exchange (HDX) mass spectrometry.

      (1) They first report 4 different crystal structures of galactose derivatives to explore molecular recognition, showing that the galactose moiety itself is the main source of specificity. Interestingly, they observe a water-mediated hydrogen bonding interaction with the protein and suggest that this water molecule may be important in binding.

      We thank you for understanding what we've presented in this manuscript.

      (2) The results from the crystallography appear sensible, though the resolution of the data is low, with only the structure with NPG better than 3Å. However, it is a bit difficult to understand what novel information is being brought out here and what is known about the ligands. For instance, are these molecules transported by the protein or do they just bind? They measure the affinity by ITC, but draw very few conclusions about how the affinity correlates with the binding modes. Can the protein transport the trisaccharide raffinose?

      The four structures with bound sugars of different sizes were used to identify the binding motif on both the primary substrate (sugar) and the transporter (MelB<sub>St</sub>). Although the resolutions of the structures complexed with melibiose, raffinose, or a-MG are relatively low, the size and shape of the densities at each structure are consistent with the corresponding sugar molecules, which provide valuable data for confirming the pose of the bound sugar proposed previously. In this revision, we further refine the α-NPG-bound structure to 2.60 Å. The identified water-1 in this study further confirms the orientation of C4-OH. Notably, this transporter does not recognize or transport glucosides in which the orientation of the C4-OH at the glucopyranosyl ring is opposite. To verify the water in the sugar-binding site, we initiated a new collaborative study using MD simulations. Results showed that Wat-1 exhibited nearly full occupancy when melibiose was present, regardless of whether Na<sup>+</sup> was bound at the cation-binding site.

      As detailed in the Summary, we added two additional sets of transport assays and confirmed that raffinose and α-NPG are transportable substrates of MelB<sub>St</sub>. For α-NPG transport, we measured the end products of the process—enzyme hydrolysis and membrane diffusion of p-nitrophenol released from intracellular α-NPG.

      As a bonus, based on the WT-like downhill α-NPG transport activity by the D59C uniporter mutant that failed in active transport against a sugar concentration gradient, we further emphasized that the sugar translocation pathway is isolated from the cation-binding site. The new data strongly support the allosteric effects of cation binding on sugar-binding affinity. Thank you for this helpful suggestion.

      A meaningful analysis of ITC data heavily depends on the quality of the data. My laboratory has extensive experience with ITC and has gained rich, insightful mechanistic knowledge of MelB<sub>St</sub>. Because of the low affinity in raffinose and a-MG, unfortunately, no further information can be convincingly obtained. Therefore, we did not dissect the enthalpic and entropic contributions but focused on the Kd value and binding stoichiometry.

      (3) The HDX also appears to be well done; however, in the manuscript as written, it is difficult to understand how this relates to the overall mechanism of the protein and the conformational changes that the protein undergoes.

      We are sorry for not presenting our data clearly in the initial submission. In this revised manuscript, we have made numerous improvements, as described in the Summary. These enhancements in the HDX data analysis provided new mechanistic insights into the allosteric effects, leading us to conclude that protein dynamics and conformational transitions are coupled with sugar-binding affinity. Na<sup>+</sup> binding restricts protein conformational flexibility, thereby increasing sugar-binding affinity. The HDX study revealed that the major dynamic region includes a sugar-binding residue, Arg149, which also plays a gating role. Structurally, this dual-function residue undergoes significant displacement during the sugar-affinity-coupled conformational transition, thereby coupling the sugar binding and structural dynamics.

      Reviewer #2:

      This manuscript from Hariharan, Shi, Viner, and Guan presents x-ray crystallographic structures of membrane protein MelB and HDX-MS analysis of ligand-induced dynamics. This work improves on the resolution of previously published structures, introduces further sugar-bound structures, and utilises HDX to explore in further depth the previously observed positive cooperatively to cotransported cation Na<sup>+</sup>. The work presented here builds on years of previous study and adds substantial new details into how Na<sup>+</sup> binding facilitates melibiose binding and deepens the fundamental understanding of the molecular basis underlying the symport mechanism of cation-coupled transporters. However, the presentation of the data lacks clarity, and in particular, the HDX-MS data interpretation requires further explanation in both methodology and discussion.

      We appreciate this reviewer's time in reading our previous articles related to this manuscript.

      Comments on Crystallography and biochemical work:

      (1) It is not clear what Figure 2 is comparing. The text suggests this figure is a comparison of the lower resolution structure to the structure presented in this work; however, the figure legend does not mention which is which, and both images include a modelled water molecule that was not assigned due to poor resolution previously, as stated by the authors, in the previously generated structure. This figure should be more clearly explained.

      This figure is a stereo view of a density map created in cross-eye style. In this revision, we changed this figure to Fig. 3 and showed only the density for sugar and water-1. 

      (2) It is slightly unclear what the ITC measurements add to this current manuscript. The authors comment that raffinose exhibiting poor binding affinity despite having more sugar units is surprising, but it is not surprising to me. No additional interactions can be mapped to these units on their structure, and while it fits into the substrate binding cavity, the extra bulk of additional sugar units is likely to reduce affinity. In fact, from their listed ITC measurements, this appears to be the trend. Additionally, the D59C mutant utilised here in structural determination is deficient in sodium/cation binding. The reported allostery of sodium-sugar binding will likely influence the sugar binding motif as represented by these structures. This is clearly represented by the authors' own ITC work. The ITC included in this work was carried out on the WT protein in the presence of Na<sup>+</sup>. The authors could benefit from clarifying how this work fits with the structural work or carrying out ITC with the D59C mutant, or additionally, in the absence of sodium.

      Thank this reviewer for your helpful suggestions. We have performed the suggested ITC measurements with the D59C mutant. The purpose of the ITC experiments was to demonstrate that MelB<sub>St</sub> can bind raffinose and α-MG to support the crystal structures.

      Comments on HDX-MS work:

      While the use of HDX-MS to deepen the understanding of ligand allostery is an elegant use of the technique, this reviewer advises the authors to refer to the Masson et al. (2019) recommendations for the HDX-MS article (https://doi.org/10.1038/s41592-019-0459-y) on how to best present this data. For example:

      All authors value this reviewer's comments and suggestions, which have been included in this revision.

      (1) The Methodology includes a lipid removal step. Based on other included methods, I assumed that the HDX-MS was being carried out in detergent-solubilised protein samples. I therefore do not see the need for a lipid removal step that is usually included for bilayer reconstituted samples. I note that this methodology is the same as previously used for MelB. It should be clarified why this step was included, if it was in fact used, aka, further details on the sample preparation should be included.

      Yes, a lipid/detergent removal step was included in this study and previous ones, and this information was clearly described in the Methods.

      (2) A summary of HDX conditions and results should be given as recommended, including the mean peptide length and average redundancy per state alongside other included information such as reaction temperature, sequence coverage, etc., as prepared for previous publications from the authors, i.e., Hariharan et al., 2024.

      We have updated the Table S2 and addressed the reviewer’ request for the details of HDX experiments.

      (3) Uptake plots per peptide for the HDX-MS data should be included as supporting information outside of the few examples given in Figure 6.

      We have prepared and presented deuterium uptake time-course plots for any peptides with ΔD > threshold in Fig. S5a-c.

      (4) A reference should be given to the hybrid significance testing method utilised. Additionally, as stated by Hageman and Weis (2019) (doi:10.1021/acs.analchem.9b01325), the use of P < 0.05 greatly increases the likelihood of false positive ΔD identifications. While the authors include multiple levels of significance, what they refer to as high and lower significant results, this reviewer understands that working with dynamic transporters can lead to increased data variation; a statement of why certain statistical criteria were chosen should be included, and possibly accompanied by volcano plots. The legend of Figure 6 should include what P value is meant by * and ** rather than statistically significant and highly statistically significant.

      We appreciate this comment and have cited the suggested article on the hybrid significance method. We fully acknowledge that using a cutoff of P < 0.05 can increase the likelihood of false-positive identifications. By applying multiple levels of statistical testing, we determined that P < 0.05 is an appropriate threshold for this study. The threshold values were presented in the residual plots and explained in the text. For the previous Fig. 6 (renamed Fig. S4b in the current version), we have reported the P value. *, < 0.05; **, < 0.01. (The text for 0.01 was not visible in the previous version. Sorry for the confusion.)

      (5) Line 316 states a significant difference in seen in dynamics, how is significance measured here? There is no S.D. given in Table S4. Can the authors further comment on the potential involvement in solvent accessibility and buried helices that might influence the overall dynamics outside of their role in sugar vs sodium binding? An expected low rate of exchange suggests that dynamics are likely influenced by solvent accessibility or peptide hydrophobicity. The increased dynamics at peptides covering the Na binding site on overall more dynamic helices suggests that there is no difference between the dynamics of each site.

      The current Table S3 (combined from previous Tables S3 and S4 as suggested) was prepared to provide an overall view of the dynamic regions with SD values provided. For other questions, if we understand correctly, this reviewer asked us to comment on the effects of solvent accessibility or hydrophobic regions on the overall dynamics outside the binding residues of the peptides that cover them. Since HDX rates are influenced by two linked factors: solvent accessibility and hydrogen-bonding interactions that reflect structural dynamics, poor solvent accessibility in buried regions should result in low deuterium uptakes. The peptides in our dataset that include the Na<sup>+</sup>-binding site showed lower HDX, likely due to limited solvent accessibility and lower structural stability. It is unclear what this reviewer meant by "increased dynamics at peptides covering the Na binding site on overall more dynamic helices." We did not observe increased dynamics in peptides covering the Na<sup>+</sup>-binding site; instead, all Na<sup>+</sup>-binding residues and nearby sugar-binding residues have lower degrees of deuteriation.

      (6) Previously stated HDX-MS results of MelB (Hariharan et al., 2024) state that the transmembrane helices are less dynamic than polypeptide termini and loops with similar distributions across all transmembrane bundles. The previous data was obtained in the presence of sodium. Does this remove the difference in dynamics in the sugar-binding helices and the cation-binding helices? Including this comparison would support the statement that the sodium-bound MelB is more stable than the Apo state, along with the lack of deprotection observed in the differential analysis.

      Thanks for this suggestion. The previous datasets were collected in the presence of Na<sup>+</sup>. In the current study, we also have two Na<sup>+</sup>-containing datasets. Both showed similar results: the multiple overlapping peptides covering the sugar-binding residues on helices I and V have higher HDX rates than those peptides covering the Na<sup>+</sup>-binding residues, even when Na<sup>+</sup> was present.

      (7) Have the authors considered carrying out an HDX-MS comparison between the WT and the D59C mutant? This may provide some further information on the WT structure (particularly a comparison with sugar-bound). This could be tied into a nice discussion of their structural data.

      Thank you for this suggestion. Comparing HDX-MS between the WT and the D59C mutant is certainly interesting, especially with the increasing amount of structural, biochemical, and biophysical data now available for this mutant. However, due to limited resources, we might consider it later.

      (8) Have the authors considered utilising Li<sup>+</sup> to infer how cation selectivity impacts the allostery? Do they expect similar stabilisation of a higher-affinity sugar binding state with all cations?

      We have shown that Li<sup>+</sup> also works positively with melibiose. Li<sup>+</sup> binds to MelB<sub>St</sub> with a higher affinity than Na<sup>+</sup> and modifies MelB<sub>St</sub> differently. It is important to study this thoroughly and separately. To answer the second question, H<sup>+</sup> is a weak coupling cation with little effect on melibiose binding. Since its pKa is around 6.5, only a small population of MelB<sub>St</sub> is protonated at pH 7.5. The order of sugar-binding cooperativity is highest with Na<sup>+</sup>, then Li<sup>+</sup>, and finally H<sup>+</sup>.

      (9) MD of MelB suggests all transmembrane helices are reorientated during substrate translocation, yet substrate and cotransporter ligand binding only significantly impacts a small number of helices. Can the authors comment on the ensemble of states expected from each HDX experiment? The data presented here instead shows overall stabilisation of the transporter. This data can be compared to that of HDX on MFS sugar cation symporter XylE, where substrate binding induces a transition to the OF state. There is no discussion of how this HDX data compares to previous MFS sugar transporter HDX. The manuscript could benefit from this comparison rather than a comparison to LacY. It is unlikely that there are universal mechanisms that can be inferred even from these model proteins. Highlighting differences between these transport systems provides broader insights into this protein class. Doi: 10.1021/jacs.2c06148 and 10.1038/s41467-018-06704-1.

      The sugar translocation free-energy landscape simulations showed that both helix bundles move relative to the membrane plane. This analysis aimed to clarify a hypothesis in the field—that the MFS transporter can use an asymmetric mode to perform the conformational transition between inward- and outward-facing states. In the case of MelB<sub>St</sub>, we clearly demonstrated that both domains move and each helix bundle moves as a unit. So only a small number of helices and loops showed labeling changes. Thanks for the suggestion about comparing with XylE. We have included that in the discussion.

      (10) Additionally, the recent publication of SMFS data (by the authors: doi:10.1016/j.str.2022.11.011) states the following: "In the presence of either melibiose or a coupling Na<sup>+</sup>-cation, however, MelB increasingly populates the mechanically less stable state which shows a destabilized middle-loop C3." And "In the presence of both substrate and co-substrate, this mechanically less stable state of MelB is predominant.". It would benefit the authors to comment on these data in contrast to the HDX obtained here. Additionally, is the C3 loop covered, and does it show the destabilization suggested by these studies? HDX can provide a plethora of results that are missing from the current analysis on ligand allostery. The authors instead chose to reference CD and thermal denaturation methods as comparisons.

      Thank this reviewer for reading the single-molecule force spectroscopy (SMFS) study on MelB<sub>St</sub>.  The C3 loop mentioned in this SMFS article is partially covered in the dataset Mel or Mel plus Na<sup>+</sup> vs. apo, and there is more coverage in the Na<sup>+</sup> vs. apo dataset. In either condition, no deprotection was detected. The labeling time point might not be long enough to detect it.

      Reviewer #3:

      Summary:

      The melibiose permease from Salmonella enterica serovar Typhimurium (MelB<sub>St</sub>) is a member of the Major Facilitator Superfamily (MFS). It catalyzes the symport of a galactopyranoside with Na<sup>+</sup>, H<sup>+</sup>, or Li<sup>+</sup>, and serves as a prototype model system for investigating cation-coupled transport mechanisms. In cation-coupled symporters, a coupling cation typically moves down its electrochemical gradient to drive the uphill transport of a primary substrate; however, the precise role and molecular contribution of the cation in substrate binding and translocation remain unclear. In a prior study, the authors showed that the binding affinity for melibiose is increased in the presence of Na<sup>+</sup> by about 8-fold, but the molecular basis for the cooperative mechanism remains unclear. The objective of this study was to better understand the allosteric coupling between the Na<sup>+</sup> and melibiose binding sites. To verify the sugar-recognition specific determinants, the authors solved the outward-facing crystal structures of a uniport mutant D59C with four sugar ligands containing different numbers of monosaccharide units (α-NPG, melibiose, raffinose, or α-MG). The structure with α-NPG bound has improved resolution (2.7 Å) compared to a previously published structure and to those with other sugars. These structures show that the specificity is clearly directed toward the galactosyl moiety. However, the increased affinity for α-NPG involves its hydrophobic phenyl group, positioned at 4 Å-distance from the phenyl group of Tyr26, which forms a strong stacking interaction. Moreover, a water molecule bound to OH-4 in the structure with α-NPG was proposed to contribute to the sugar recognition and appears on the pathway between the two specificity-determining pockets. Next, the authors analyzed by hydrogen-to-deuterium exchange coupled to mass spectrometry (HDX-MS) the changes in structural dynamics of the transporter induced by melibiose, Na<sup>+</sup>, or both. The data support the conclusion that the binding of the coupling cation at a remote location stabilizes the sugar-binding residues to switch to a higher-affinity state. Therefore, the coupling cation in this symporter was proposed to be an allosteric activator.

      Strengths:

      (1) The manuscript is generally well written.

      (2) This study builds on the authors' accumulated knowledge of the melibiose permease and integrates structural and HDX-MS analyses to better understand the communication between the sodium ion and sugar binding sites. A high sequence coverage was obtained for the HDX-MS data (86-87%), which is high for a membrane protein.

      Thank this reviewer for your positive comments.

      Weaknesses:

      (1) I am not sure that the resolution of the structure (2.7 Å) is sufficiently high to unambiguously establish the presence of a water molecule bound to OH-4 of the α-NPG sugar. In Figure 2, the density for water 1 is not obvious to me, although it is indeed plausible that water mediates the interaction between OH4/OH6 and the residues Q372 and T373.

      A water molecule can be modeled at a resolution ranging from 2.4 to 3.2 Å, and the quality of the model depends on the map quality and water location. In this revision, we refined the resolution to 2.6 Å using the same dataset and also performed all-atom MD simulations. All results support the occupancy of water-1 in the sugar-bound MelB<sub>St</sub>.

      (2) Site-directed mutagenesis could help strengthen the conclusions of the authors. Would the mutation(s) of Q372 and/or T373 support the water hypothesis by decreasing the affinity for sugars? Mutations of Thr121, Arg 295, combined with functional and/or HDX-MS analyses, may also help support some of the claims of the authors regarding the allosteric communication between the two substrate-binding sites.

      The authors thank this reviewer for the thoughtful suggestions. MelB<sub>St</sub> has been subjected to Cys-scanning mutagenesis (https://doi.org/10.1016/j.jbc.2021.101090). Placing a Cys residue at Gln372 significantly decreased the transport initial rate, accumulation, and melibiose fermentation, with minimal effect on protein expression, as shown in Figure 2 of this JBC article, which could support its role in the binding pocket. The T373C mutant retained most of the WT's activities. Our previous studies showed that Thr121 is only responsible for Na<sup>+</sup> binding in MelB<sub>St</sub>, and mutations decreased protein stability; now, HDX reveals that this is the rigid position. Additionally, our previous studies indicated that Arg295 is another conformationally important residue. In this version, we have added more HDX analysis to explore the relationship between the two substrate-binding sites with conformational dynamics, especially focusing on the gating salt-bridge network including Arg295, which has provided meaningful new insights.

      (3) The main conclusion of the authors is that the binding of the coupling cation stabilizes those dynamic sidechains in the sugar-binding pocket, leading to a high-affinity state. This is visible when comparing panels c and a from Figure S5. However, there is both increased protection (blue, near the sugar) and decreased protection in other areas (red). The latter was less commented, could the increased flexibility in these red regions facilitate the transition between inward- and outward-facing conformations? The HDX changes induced by the different ligands were compared to the apo form (see Figure S5). It might be worth it for data presentation to also analyze the deuterium uptake difference by comparing the conditions sodium ion+melibiose vs melibiose alone. It would make the effect of Na<sup>+</sup> on the structural dynamics of the melibiose-bound transporter more visible. Similarly, the deuterium uptake difference between sodium ion+melibiose vs sodium ion alone could be analyzed too, in order to plot the effect of melibiose on the Na<sup>+</sup>-bound transporter.

      Thanks for this important question. We have added more discussion of the deprotected data and prepared a new Fig. 8b to highlight the melibiose-binding-induced flexibility in several loops, especially the gating area on both sides of the membrane. We also proposed that these changes might facilitate the formation of the transition-competent state. The overall effects induced by substrate binding are relatively small, and the datasets for apo and Na were collected separately, so comparing melibiose&Na<sup>+</sup> versus Na<sup>+</sup> might not be as precise. In fact, the Na<sup>+</sup> effects on the sugar-binding site can be clearly seen in the deuterium uptake plots shown in Figures 7-8, by comparing the first and last panels.

      (4) For non-specialists, it would be beneficial to better introduce and explain the choice of using D59C for the structural analyses.

      Asp59 is the only site that responds to the binding of all coupling cations: Na<sup>+</sup>, Li<sup>+</sup>, or H<sup>+</sup>. Notably, this thermostable mutant D59C selectively abolishes all cation binding and associated cotransport activities, but it maintains intact sugar binding and exhibits conformational transition as the WT, as demonstrated by electroneutral transport reactions including α-NPG transport showed in this articles, and melibiose exchange and fermentation showed previously. Therefore, the structural data derived from this mutant are significant and offer important mechanistic insights into sugar transport, which supports the conclusion that the Na<sup>+</sup> functions as allosteric activator.

      (5) In Figure 5a, deuterium changes are plotted as a function of peptide ID number. It is hardly informative without making it clearer which regions it corresponds to. Only one peptide is indicated (213-226). I would recommend indicating more of them in areas where deuterium changes are substantial.

      We appreciate this comment and have modified the plots by marking the residue position as well as labeled several peptides of significant HDX in the Fig 5b. We also provided a deuteriation map based on peptide coverage (Fig. 5a).

      (6) From prior work of the authors, melibiose binding also substantially increases the affinity of the sodium ion. Can the authors interpret this observation based on the HDX data?

      This is an intriguing mechanistic question. In this HDX study, we found that the cation-binding pocket and nearby sugar-binding residues are conformationally rigid, while some sugar-binding residues farther from the cation-binding pocket are flexible. We concluded that conformational dynamics regulate sugar-binding affinity, but the increase in Na-binding affinity caused by melibiose is not related to protein dynamics. Our previous interpretation based on structural data remains our preferred explanation; therefore, the bound melibiose physically prevents the release of Na<sup>+</sup> or Li<sup>+</sup> from the cation-binding pocket. We also proposed the mechanism of intracellular NA<sup>+</sup> release in the 2024 JBC paper (https://doi.org/10.1016/j.jbc.2024.107427); after sugar release, the rotamer change of Asp55 will help NA<sup>+</sup> exit the cation pocket into the empty sugar pocket, and the negative membrane potential inside the cell will further facilitate movement from MelB<sub>St</sub> to the cytosol.

      Recommendations for the authors:

      Reviewing Editor Comments:

      (1) It would help the reader if the previous work were introduced more clearly, and if the results of the experiments reported in this manuscript were put into the context of the previous work. Lines 283-296 discuss observations that are similar to previous reported structures as well as novel interpretations. It would help the reader to be clearer about what the new observations are.

      Thank you for the important comment. We have revised accordingly by adding related citations and words “as showed previously” when we stated our previous observations.

      (2) The affinity by ITC is measured for various ligands, but very few conclusions are drawn about how the affinity correlates with the binding modes. Are the other ligands that are investigated in this study transported by the protein, or do they just bind? Can the protein transport the trisaccharide raffinose? The authors comment that raffinose exhibiting poor binding affinity despite having more sugar units is surprising, but this is not surprising to me. No additional interactions can be mapped to these units on their structure, and while it fits into the substrate binding cavity, the extra bulk of additional sugar units is likely to reduce affinity. In fact, from their listed ITC measurements, this appears to be the trend.

      Additionally, the D59C mutant utilized here in structural determination is deficient in sodium/cation binding. The reported allostery of sodium-sugar binding will likely influence the sugar binding motif as represented by these structures. This is clearly represented by the authors' own ITC work. The ITC included in this work was carried out on the WT protein in the presence of Na<sup>+</sup>. The authors could benefit from clarifying how this work fits with the structural work or carrying out ITC with the D59C mutant, or additionally, in the absence of sodium. For non-specialists, please better introduce and explain the choice of using D59C for the structural analyses.

      Thank you for the meaningful comments. We have comprehensively addressed all the concerns and suggestions as listed in the summary of this revision. Notably, the D59C mutant does not catalyze any electrogenic melibiose transport involved in a cation transduction but catalyze downhill transport location of the galactosides, as shown by the downhill α-NPG transport assay in Fig. 1a. The intact downhill transport results from D59C mutant further supports the allosteric coupling between the cation- and sugar-binding sites.

      The binding isotherm and poor affinity of the ITC measurements do not support to further analyze the binding mode since none showed sigmoidal curve, so the enthalpy change cannot be accurately determined. But authors thank this comment.

      (3) It is not clear what Figure 2 is comparing. The text suggests this figure is a comparison of the lower resolution structure to the structure presented in this work; however, the figure legend does not mention which is which, and both images include a modelled water molecule that was not assigned due to poor resolution previously, as stated by the authors, in the previously generated structure. This figure should be more clearly explained.

      We have addressed these concerns in the response to the Public Reviews at reviewer-2 #1.

      (4) I am not sure that the resolution of the structure (2.7 Å) is sufficiently high to unambiguously establish the presence of a water molecule bound to OH-4 of the α-NPG sugar. In Figure 2, the density for water 1 is not obvious to me, although it is indeed plausible that water mediates the interaction between OH4/OH6 and the residues Q372 and T373. Please change line 278 to state "this OH-4 water molecule is likely part of sugar binding".

      We have addressed these concerns in the response to the Public Reviews at reviewer-3 #1.

      (5) Line 290-296: The Thr121 is not represented in any figures, while the Lys377 is. Their relative positioning between sugar water and sodium is not made clear by any figure.

      Thanks for this comment. This information has been clearly presented in the Figs. 7-8. Lys377 is closer to the cation site and related far from the sugar-binding site.

      (6) Methodology includes a lipid removal step. Based on other included methods, I assumed that the HDX-MS was being carried out in detergent-solubilized protein samples. I therefore do not see the need for a lipid removal step that is usually included for bilayer reconstituted samples. I note that this methodology is the same as previously used for MelB. It should be clarified why this step was included, if it was in fact used, aka, further details on the sample preparation should be included.

      (7) A summary of HDX conditions and results should be given as recommended, including the mean peptide length and average redundancy per state alongside other included information such as reaction temperature, sequence coverage, etc., as prepared for previous publications from the authors, i.e., Hariharan et al., 2024.

      We have addressed these concerns in the response to the Public Reviews at reviewer-2 #4.

      (8) Uptake plots per peptide for the HDX-MS data should be included as supporting information outside of the few examples given in Figure 6.

      We have addressed these concerns in the response to the Public Reviews at reviewer-2 #4.

      (9) A reference should be given to the hybrid significance testing method utilised. Additionally, as stated by Hageman and Weis (2019) (doi:10.1021/acs.analchem.9b01325), the use of P < 0.05 greatly increases the likelihood of false positive ΔD identifications. While the authors include multiple levels of significance, what they refer to as high and lower significant results, and this reviewer understands that working with dynamic transporters can lead to increased data variation, a statement of why certain statistical criteria were chosen should be included, and possibly accompanied by volcano plots. The legend of Figure 6 should include what P value is meant by * and ** rather than statistically significant and highly statistically significant.

      We have addressed these concerns in the response to the Public Reviews at reviewer-2 #4.

      (10) The table (S3) and figure (S4) showing uncovered residues is an unclear interpretation of the data; this would be better given as a peptide sequence coverage heat map. This would also be more informative for the redundancy in covered regions, too. In this way, S3 and S4 can be combined.

      We have addressed these concerns in the response to the Public Reviews at reviewer-2 #4.

      (11) Residual plots in Figure 5 could be improved by a topological map to indicate how peptide number resembles the protein amino acid sequence.

      Thanks for the request, due to the figure 6 is big so that we add a transmembrane topology plot colored with the HDX results in Fig. 8c.

      (12) The presentation of data in S5 could be clarified. Does the number of results given in the brackets indicate overlapping peptides? What are the lengths of each of these peptides? Classical HDX data presentation utilizes blue for protection and red for deprotection. The use of yellow ribbons to show protection in non-sugar binding residues takes some interpretation and could be clarified by also depicting in a different blue. I also don't see the need to include ribbon and cartoon representation when also using colors to depict protection and deprotection. The authors should change or clarify this choice.

      We have moved this figure into the current Fig. 6b as suggested by Reviewer-3. To address your questions listed in the figure legend, the number of results shown in brackets indeed indicates overlapping peptides. What are the lengths of each of these peptides? The sequences of each peptide are shown in Figures 7-8 and are also included in Supplemental Figure S5. Regarding the use of color, both blue and green were used to distinguish peptides protecting the substrate-binding site from other regions. The ribbon and cartoon representations are provided for clarity, as the cartoon style hides many helices.

      (13) In Table S5, the difference between valid points and protection is unclear. And what is indicated by numbers in brackets or slashes? Additionally, it should be highlighted again here that single-residue information is inferred from peptide-level data. By value, are the authors referring to peptide-level differential data?

      Please review our responses in the Public Reviews at reviewer-2 #5.

      (14) Line 316 states a significant difference in seen in dynamics, how is significance measured here? There is no S.D. given in Table S4. Can the authors further comment on the potential involvement in solvent accessibility and buried helices that might influence the overall dynamics outside of their role in sugar vs sodium binding? An expected low rate of exchange suggests that dynamics are likely influenced by solvent accessibility or peptide hydrophobicity? The increased dynamics at peptides covering the Na binding site on overall more dynamic helices suggests that there isn't a difference between the dynamics of each site.

      Please review our responses in the Public Reviews at reviewer-2 #5.

      (15) Previously stated HDX-MS results of MelB (Hariharan et al., 2024) state that the transmembrane helices are less dynamic than polypeptide termini and loops with similar distributions across all transmembrane bundles. The previous data was obtained in the presence of sodium. Does this remove the difference in dynamics in the sugar-binding helices and the cation-binding helices? Including this comparison would support the statement that the sodium-bound MelB is more stable than the Apo state, along with the lack of deprotection observed in the differential analysis.

      Please review our responses in the Public Reviews.

      (16) MD of MelB suggests all transmembrane helices are reorientated during substrate translocation, yet substrate and cotransporter ligand binding only significantly impacts a small number of helices. Can the authors comment on the ensemble of states expected from each HDX experiment? The data presented here instead shows overall stabilisation of the transporter. This data can be compared to that of HDX on MFS sugar cation symporter XylE, where substrate binding induces a transition to the OF state. There is no discussion of how this HDX data compares to previous MFS sugar transporter HDX. The manuscript could benefit from this comparison rather than a comparison to LacY. It is unlikely that there are universal mechanisms that can be inferred even from these model proteins. Highlighting differences instead between these transport systems provides broader insights into this protein class. Doi: 10.1021/jacs.2c06148 and 10.1038/s41467-018-06704-1.

      Please review our responses in the Public Reviews.

      (17) Additionally, the recent publication of SMFS data (by the authors: doi:10.1016/j.str.2022.11.011) states the following: "In the presence of either melibiose or a coupling Na<sup>+</sup>-cation, however, MelB increasingly populates the mechanically less stable state which shows a destabilized middle-loop C3." And "In the presence of both substrate and co-substrate this mechanically less stable state of MelB is predominant.". It would benefit the authors to comment on these data in contrast to the HDX obtained here. Additionally, is the C3 loop covered, and does it show the destabilization suggested by these studies? HDX can provide a plethora of results that are missing from the current analysis on ligand allostery. The authors instead chose to reference CD and thermal denaturation methods as comparisons.

      Please review our responses in the Public Reviews.

      (18) The main conclusion of the authors is that the binding of the coupling cation stabilizes those dynamic sidechains in the sugar-binding pocket, leading to a high-affinity state. This is visible when comparing panels c and a from Figure S5. However, there is both increased protection (blue, near the sugar) and decreased protection in other areas (red). The latter was less commented, could the increased flexibility in these red regions facilitate the transition between inward- and outward-facing conformations? The HDX changes induced by the different ligands were compared to the apo form (see Figure S5). It might be worth it for data presentation more visible to also analyze the deuterium uptake difference by comparing the conditions sodium ion+melibiose vs melibiose alone. You would make the effect of Na<sup>+</sup> on the structural dynamics of the melibiose-bound transporter. Similarly, the deuterium uptake difference between sodium ion+melibiose vs sodium ion alone could be analyzed too, in order to plot the effect of melibiose on the Na<sup>+</sup>-bound transporter.

      Please review our responses in the Public Reviews.

      (19) In Figure 5a, deuterium changes are plotted as a function of peptide ID number. It is hardly informative without making it clearer which regions it corresponds to. Only one peptide is indicated (213-226); I would recommend indicating more of them, in areas where deuterium changes are substantial.

      Please review our responses in the Public Reviews.

      (20) Figure 6, please indicate in the legend what the black and blue lines are (I assume black is for the apo?)

      We are sorry that we did not make it clear. Yes, the black was used for apo state and blue was used for all bound states

      (21) From prior work of the authors, melibiose binding also substantially increases the affinity of the sodium ion. Can the authors interpret this observation based on the HDX data?

      Please review our responses in the Public Reviews.

      Addressing the following three points would strengthen the manuscript, but also involve a significant amount of additional experimental work. If the authors decide not to carry out the experiments described below, they can still improve the assessment by focusing on points (1-21) described above.

      (22) Have the authors considered carrying out an HDX-MS comparison between the WT and the D59C mutant? This may provide some further information on the WT structure (particularly a comparison with sugar-bound). This could be tied into a nice discussion of their structural data.

      Please review our responses in the Public Reviews.

      (23) Have the authors considered utilising Li<sup>+</sup> to infer how cation selectivity impacts the allostery? Do they expect similar stabilisation of a higher-affinity sugar binding state with all cations?

      Please review our responses in the Public Reviews.

      (24) Site-directed mutagenesis could help strengthen the conclusions. Would the mutation(s) of Q372 and/or T373 support the water hypothesis by decreasing the affinity for sugars? Mutations of Thr 121 and Arg 295, combined with functional and/or HDX-MS analyses, may also help support some of the authors' claims regarding allosteric communication between the two substrate-binding sites.

      Please review our responses in the Public Reviews.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewing Editor Comment:

      The reviewers felt that the study could be improved by (1) better integrating the results with the existing literature in the field

      (1) In the Introduction and Results section of the manuscript, we had made every attempt to cite the relevant literature. (Reviewer 1 stated that “The literature is appropriately cited”). We agree with the Reviewing Editor that rather than simply cite the relevant literature, we could have done a better job of integrating our findings with what has been previously discovered by others. We have attempted to do this in the revised manuscript. Also, we have included many additional citations in the Introduction and in the first section of the Results where work by others has provided a framework for interpreting our single-cell studies.

      and (2) manipulating Trib expression and analyzing the expression of 1-2 HIX genes.

      (2) We are grateful for this suggestion. As suggested by the Reviewing Editor we have attempted to increase and decrease trbl expression and assess the effect on expression of two genes, Swim and CG15784.

      We increased trbl levels in the wing pouch using rn-Gal4, tub-Gal80<sup>ts</sup> and UAS-trbl. By transferring larvae for 24 h from 18oC to 31oC, we were able to induce trbl expression in the wing pouch. When these larvae were irradiated at 4000 rad, we found reduced levels of apoptosis in the wing pouch of discs that overexpressed trbl (Figure 7-figure supplement 1). This indicated that upregulation of trbl is radioprotective. Consistent with our findings, others have previously shown that upregulation of trbl and stalling in the G2 phase of the cells cycle protects cells from JNK-induced apoptosis (Cosolo et al., 2019, PMID:30735120) or that downregulating the G2/M progression promoting factor string protects cells from X-ray radiation induced apoptosis (Ruiz-Losada et al., 2021, PMID:34824391).

      As suggested by the Reviewing Editor, we also examined the effect of trbl overexpression on the induction of two “highly induced by X-ray irradiation (HIX)” gene, Swim and CG15784. Increasing trbl expression had no effect on the induction of Swim and only a modest decrease in the induction of CG15784 (Figure 7-figure supplement 2). Thus, increasing trbl expression, is in itself, insufficient to promote HIX gene expression indicating that other factors are necessary for HIX gene induction.

      We also attempted to reduce trbl expression, using three different RNAi lines. While some of these lines have been used previously by others to reduce trbl expression under unirradiated conditions (Cosolo et al., 2019, PMID:30735120), we nevertheless wanted to check if they reduced trbl induction following irradiation. For each of the three lines, we observed no obvious reduction in trbl RNA following irradiation when visualized using HCR (Author response image 1). Thus, any effects on gene expression that we observe could not be attributed to a decrease in trbl expression. We have therefore included the images showing a lack of knockdown in this Response to Reviews document but not included these experiments in the revised manuscript.

      Author response image 1.

      RNA in situ hybridizations using the hybridization chain reaction performed using probes to trbl. In A-F, the RNAi is expressed using nubbin-Gal4. In G-I the RNAi is expressed using rn-Gal4, tub-Gal80<sup>ts</sup>. white-RNAi was used as a control (A, B, G, H). Three different RNAi lines directed against trbl were tested: Vienna lines VDRC 106774 (C, D) and VDRC 22113 (E, F), and Bloomington line BL42523. In no case was a reduction in trbl RNA upregulation in the wing pouch following 4000 rad observed, except for one disc (n = 6) of VDRC 106774 crossed to nubbin-gal4.

      Reviewer #1 (Public review):

      Summary:

      The authors analyze transcription in single cells before and after 4000 rads of ionizing radiation. They use Seuratv5 for their analyses, which allows them to show that most of the genes cluster along the proximal-distal axis. Due to the high heterogeneity in the transcripts, they use the Herfindahl-Hirschman index (HHI) from Economics, which measures market concentration. Using the HHI, they find that genes involved in several processes (like cell death, response to ROS, DNA damage response (DDR)) are relatively similar across clusters. However, ligands activating the JAK/STAT, Pvr, and JNK pathways and transcription factors Ets21C and dysf are upregulated regionally. The JAK/STAT ligands Upd1,2,3 require p53 for their upregulation after irradiation, but the normal expression of Upd1 in unirradiated discs is p53-independent. This analysis also identified a cluster of cells that expressed tribbles, encoding a factor that downregulates mitosis-promoting String and Twine, that appears to be G2/M arrested and expressed numerous genes involved in apoptosis, DDR, the aforementioned ligands, and TFs. As such, the tribbles-high cluster contains much of the heterogeneity.

      Strengths:

      (1) The authors have used robust methods for rearing Drosophila larvae, irradiating wing discs, and analyzing the data with Seurat v5 and HHI.

      (2) These data will be informative for the field.

      (3) Most of the data is well-presented

      (4) The literature is appropriately cited.

      We thank the reviewer for these comments.

      Weaknesses:

      (1) The data in Figure 1 are single-image representations. I assume that counting the number of nuclei that are positive for these markers is difficult, but it would be good to get a sense of how representative these images are and how many discs were analyzed for each condition in B-M.

      For each condition at least 5 discs were imaged but we imaged up to 15 discs in some cases. We tried to choose a representative disc for each condition after looking at all of them. All discs imaged under each condition are shown below; the disc chosen for the figure is indicated with an asterisk. All scale bars are 100 mm.

      Author response image 2.

      Images for discs shown in Manuscript Figure 1panels B, C

      Author response image 3.

      Images for discs shown in Manuscript Figure 1panels D, E

      Author response image 4.

      Images used in Manuscript Figure 1, F, G

      Author response image 5.

      Images used in Manuscript Figure 1H, I

      Author response image 6.

      Images used in Manuscript Figure 1J, K

      Author response image 7.

      Images used in Manuscript Figure 1L, M

      (2) Some of the figures are unclear.

      It is unclear to us exactly which figures the Reviewer is referring to. Perhaps this is the same issue mentioned below in “Recommendations for the authors”. We address it below.

      Reviewer #1 (Recommendations for the authors):

      (1) Regarding Figure 1, what is stained in blue? Is it DAPI? If so, this should be added to the figure legend.

      Thank you for pointing out this omission. This has been addressed in the revised manuscript.

      It is very difficult to see blue on black, so could the authors please outline the discs?

      Alternatively, they could show DAPI in green and the markers (pH2Av, etc) in magenta.

      We used DAPI (blue) as a way of outlining the discs. While we appreciate the reviewer’s concern, after reviewing the images, we found that the blue is clearly visible when the document is viewed on the screen. It is less obvious if the document is printed on some kinds or printers. Since boosting this channel would make the signal from the channels more difficult to see, we left the images as they were.

      (2) Figure 3, Figure Supplement 2, panel B. It is not possible to read the gene names in the panel's current form. Please break this up into 4 lines (as much as possible from the current 2).

      Thank you for this suggestion. We have done this in the revised manuscript.

      Reviewer #2 (Public review):

      This manuscript investigates the question of cellular heterogeneity using the response of Drosophila wing imaginal discs to ionizing radiation as a model system. A key advance here is the focus on quantitatively expressing various measures of heterogeneity, leveraging single-cell RNAseq approaches. To achieve this goal, the manuscript creatively uses a metric from the social sciences called the HHI to quantify the spatial heterogeneity of expression of individual genes across the identified cell clusters. Inter- and intra-regional levels of heterogeneity are revealed. Some highlights include the identification of spatial heterogeneity in the expression of ligands and transcription factors after IR. Expression of some of these genes shows dependence on p53. An intriguing finding, made possible by using an alternative clustering method focusing on cell cycle progression, was the identification of a high-trbl subset of cells characterized by concordant expression of multiple apoptosis, DNA damage repair, ROS-related genes, certain ligands, and transcription factors, collectively representing HIX genes. This high-trbl set of cells may correspond to an IR-induced G2/M arrested cell state.

      Overall, the data presented in the manuscript are of high quality but are largely descriptive. This study is therefore perceived as a resource that can serve as an inspiration for the field to carry out follow-up experiments.

      Thank you for your assessment of the work.

      Reviewer #2 (Recommendations for the authors):

      I suggest two major points for improvement:

      (1) It is important to test whether manipulation of trbl levels (i.e., overexpression, knockdown, mutation) would result in measurable biological outcomes after IR, such as altered HIX gene expression, altered cell cycle progression, or both. This may help disentangle the question of whether high trbl expression and correlated HIX gene expression are a cause or consequence of G2/M stalling.

      We have described these experiments at the beginning of this Response to Reviews document when addressing the comments made by the Reviewing Editor. Please see Figure 7, figure supplements 1 and 2. These experiments suggest that upregulation of trbl offers some protection from radiation-induced death, yet it is itself insufficient to induce expression of two HIX genes tested. As we have also described earlier, three different RNAi lines tested did not reduce trbl upregulation after irradiation.

      (2) A more extensive characterization of the high-trbl cell state would also be appropriate, particularly in terms of their relationship to the cell cycle.

      We attempted to address this issue in two ways. First, we used the expression of a trbl-gfp transgene and RNA in-situ hybridization experiments to visualize the distribution of the high-trbl cells (shown in new manuscript figure, Figure 6-figure supplement 3). When examining trbl RNA in irradiated discs, there is no obvious demarcation between cells that express high levels of trbl and other cells. This is also apparent in the UMAP shown in Figure 6A and A’. Most cells seem to express trbl; cells in the “high trbl” cluster simply express more trbl than others. We observed cells expressing trbl and PCNA as well as cells expressing only one of those two genes at detectable levels. Thus, it was not possible to distinguish the “high trbl” cells from other cells by this approach.

      We decided instead to focus on examining the expression of other cell-cycle genes in the high-trbl cluster. We have added a paragraph in the Results section that details our findings. Many transcriptional changes are indeed consistent with stalling in G2 such as high levels of trbl and low levels of string (stg). Additionally, that the cells are likely in G2 is consistent with reduced levels of genes that are normally expressed at other stages of the cell cycle: G1 genes such as E2f1 and Dp, S-phase genes such as several Mcm genes, PCNA and RnrS, and genes that encode mitotic proteins such as polo, Incenp and claspin. There are however, several anomalies such as slightly increased expression of the early-G1 cyclin, CycD, and the retinoblastoma ortholog Rbf. Thus, at least as assessed by the transcriptome, this cluster may not correspond to a cell state that is found under normal physiological conditions.

      (3) Minor: p. 12, line 3. Figure 5A is mentioned, but it seems that it should be 4A instead.

      Thank you for pointing this out. We have addressed this in our revisions.

      Reviewer #3 (Public review):

      Strengths:

      Overall, the manuscript makes a compelling case for heterogeneity in gene expression changes that occur in response to uniform induction of damage by X-rays in a single-layer epithelium. This is an important finding that would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

      Weaknesses:

      This work would be more useful to the field if the authors could provide a more comprehensive discussion of both the impact and the limitations of their findings, as explained below.

      Propidium iodide staining was used as a quality control step to exclude cells with a compromised cell membrane. But this would exclude dead/dying cells that result from irradiation. What fraction of the total do these cells represent? Based on the literature, including works cited by the authors, up to 85% of cells die at 4000R, but this likely happens over a longer period than 4 hours after irradiation. Even if only half of the 85% are PI-positive by 4 hr, this still removes about 40% of the cell population from analysis. The remaining cells that manage to stay alive (excluding PI) at 4 hours and included in the analysis may or may not be representative of the whole disc. More relevant time points that anticipate apoptosis at 4 hr may be 2 hr after irradiation, at which time pro-apoptotic gene expression peaks (Wichmann 2006). Can the authors rule out the possibility that there is heterogeneity in apoptosis gene expression, but cells with higher expression are dead by 4 hours, and what is left behind (and analyzed in this study) may be the ones with more uniform, lower expression? I am not asking the authors to redo the study with a shorter time point, but to incorporate the known schedule of events into their data interpretation.

      We thank the reviewer for these important comments. The generation of single-cell RNA-seq data from irradiated cells is tricky. Many cells have already died. Even those that do not incorporate propidium iodide are likely in early stages of apoptosis or are physiologically unhealthy and likely made it through our FACS filters. Indeed, in irradiated samples up to 57% of sequenced cells were not included in our analysis since their RNA content seemed to be of low quality. It is therefore likely that our data are biased towards cells that are less damaged. As advised by the reviewer, we will include a clearer discussion of these issues as well as the time course of events and how our analysis captures RNA levels only at a single time point.

      If cluster 3 is G1/S, cluster 5 is late S/G2, and cluster 4 is G2/M, what are clusters 0, 1, and 2 that collectively account for more than half of the cells in the wing disc? Are the proportions of clusters 3, 4, and 5 in agreement with prior studies that used FACS to quantify wing disc cells according to cell cycle stage?

      Work by others (Ruiz-Losada et al., 2021, PMID:34824391) has shown that almost 80% of cells have a 4C DNA content 4 h after 4,000 rad X-ray irradiation. The high-trbl cluster accounts for only 18% of cells and can therefore account for a minority of cells with a 4C DNA content.

      Thus clusters 0, 1 and 2 could potentially contain other populations that also have a 4C DNA content. Importantly, similar proportions of cells in these clusters are also observed in unirradiated discs.

      We expect that clusters 1 and 2 are largely comprised of cells in G2/M. Together, these clusters are marked by some genes previously found to be higher in FACS separated G2 cells compared to G1 cells (Liang et al., 2014, PMID: 24684830). These genes include Det, aurA, and ana1. Strangely, cluster 0 is not strongly marked by any of the 175 cell cycle genes used in our clustering (eff being the strongest marker) and has a lower-than-average expression of 165/175 cell cycle genes. Cluster 0 is however marked by the genes ac and sc, which are known to be expressed in proneuronal cell clusters interspersed throughout the disc that stall in G2 and form mitotically quiescent domains (Usui & Kimura 1992, Development, 116 (1992), pp. 601-610 (no PMID); Nègre et al., 2003, PMID: 12559497). Given these observations, we hypothesize that cluster 0 is largely comprised of stalled G2 cells like those found in ac/sc-expressing proneural clusters.

      The EdU data in Figure 1 is very interesting, especially the persistence in the hinge. The authors speculate that this may be due to cells staying in S phase or performing a higher level of repair-related DNA synthesis. If so, wouldn't you expect 'High PCNA' cells to overlap with the hinge clusters in Figures 6G-G'? Again, no new experiments are needed. Just a more thorough discussion of the data.

      We have found that the locations of elevated PCNA expression do not always correlate with the location of EdU incorporation either by examining scRNA-seq data or by using HCR to detect PCNA. PCNA expression is far more widespread as we now show in Figure 6-figure supplement 3.

      Trbl/G2/M cluster shows Ets21C induction, while the pattern of Ets21C induction as detected by HCR in Figures 5H-I appears in localized clusters. I thought G2/M cells are not spatially confined. Are Ets21C+ cells in Figure 5 in G2/M? Can the overlap be confirmed, for example, by co-staining for Trbl or a G2/M marker with Ets21C?

      The data show that the high-trbl cells are higher in Ets21C transcripts relative to other cell-cycle-based clusters after irradiation. This does not imply that high-trbl-cells in all regions of the disc upregulate Ets21C equally. Ets21C expression is likely heterogeneous in both ways – by location in the disc and by cell-cycle state.

      Induction of dysf in some but not all discs is interesting. What were the proportions? Any possibility of a sex-linked induction that can be addressed by separating male and female larvae?

      We can separate the cells in our dataset into male and female cells by expression of lncRNA:roX1/2. When we do this, we see X-ray induced dysf expressed similarly in both male and female cells. We think that it is therefore unlikely that this difference in expression can be attributed to cell sex. Another possibility is that dysf upregulation might be acutely sensitive to the developmental stage of the disc. This would require experiments with very precisely-staged larvae. We have not investigated this further as it is not a central issue in our paper.

      Reviewer #3 (Recommendations for the authors):

      Please check the color-coding in Figure 1A. The region marked as pouch appears to include hinge folds that express Zfh2 (a hinge marker) in Figure 2A (even after accounting for low Zfh2 expression in part of the pouch).

      We have corrected this and have marked the pouch region based on the analysis of expression of different hinge and pouch markers by Ayala-Camargo et al. 2013 (PMID 2398534).

      The statement 'Furthermore, within tissues, stem cells are most sensitive while differentiated cells are relatively radioresistant' needs to be qualified, as there are differences in radiosensitivity of adult versus embryonic stem cells (e.g., PMID: 30588339)

      We thank the reviewer for bringing this point to our attention and for pointing us to an article that addresses this issue in detail. We appreciate that our statement was rather simplistic – we have modified it and added two additional references.

    1. Author response:

      Reviewer #1 (Public review):

      Summary:

      Negreira, G. et al clearly presented the challenges of conducting genomic studies in unicellular pathogens and of addressing questions related to the balance between genome integrity and instability, pivotal for survival under the stressful conditions these organisms face and for their evolutionary success. This underlies the need for powerful approaches to perform single-cell DNA analyses suited to the small and plastic Leishmania genome. Accordingly, their goal was to develop such a novel method and demonstrate its robustness.

      In this study, the authors combined semi-permeable capsules (SPCs) with primary template-directed amplification (PTA) and adapted the system to the Leishmania genome, which is about 100 times smaller than the human genome and exhibits remarkable plasticity and mosaic aneuploidy. Given the size and organization of the Leishmania genome, the challenges were substantial; nevertheless, the authors successfully demonstrated that PTA not only works for Leishmania but also represents a significantly improved whole-genome amplification (WGA) method compared with standard approaches. They showed that SPCs provide a superior alternative for cell encapsulation, increasing throughput. The methodology enabled high-resolution karyotyping and the detection of fine-scale copy number variations (CNVs) at the single-cell level. Furthermore, it allowed discrimination between genotypically distinct cells within mixed populations.

      Strengths:

      This is a high-impact study that will likely contribute to our understanding of DNA replication and the genetic plasticity of Leishmania, including its well-documented aneuploidy, somy variations, CNVs, and SNPs - all key elements for elucidating various aspects of the parasite's biology, such as genome evolution, genetic exchange, and mechanisms of drug resistance.

      Overall, the authors clearly achieved their objectives, providing a solid rationale for the study and demonstrating how this approach can advance the investigation of Leishmania's small, plastic genome and its frequent natural strain mixtures within hosts. This methodology may also prove valuable for genomic studies of other single-celled organisms.

      We thank the reviewer for the positive feedback and appreciation of the potential applications for the methodology we describe here.

      Weaknesses:

      The discussion section could be enriched to help readers understand the significance of the work, for instance, by more clearly pointing out the obstacles to a better understanding of DNA replication in Leishmania. Or else, when they discuss the results obtained at the level of nucleotide information and the relevance of being able to compare, in their case, the two strains, they could refer to the implications of this level of precision to those studying clonal strains or field isolates, drug resistance or virulence in a more detailed way.

      We thank the reviewer for the suggestions. Indeed, single-cell DNA sequencing has successfully revealed cell-to-cell variability in replication timing and fork progression in mammalian cells[1,2] and we believe that the SPC-PTA workflow could be used in similar studies in Leishmania to complement bulk-based observations[3,4]. Regarding nucleotide information, it is indeed of high relevance to detect minor circulating variants with potential virulence impact and/or effect on drug resistance which could be missed by bulk sequencing. This includes the ability to detect co-occurring variants with potential epistatic effects. These topics will be further developed in the revised version. Finally, we will explicitly discuss how this methodology can be applied beyond Leishmania, to investigate genome plasticity, adaptation, and evolutionary processes in other organisms.

      Reviewer #2 (Public review):

      Summary:

      Negreira et al. present an application of a novel single-cell genomics approach to investigate the genetic heterogeneity of Leishmania parasites. Leishmania, while also representing a major global disease with hundreds of thousands of cases annually, serves as a model to test the rigor of the sequencing strategy. Its complex karyotypic nature necessitates a method that is capable of resolving natural variation to better understand genome dynamics. Importantly, an earlier single-cell genomics platform (10x Chromium) is no longer available, and new methods need to be evaluated to fill in this gap.

      The study was designed to evaluate whether a capsule-based cell capture method combined with primary template-directed amplification (PTA) could maintain levels of genomic heterogeneity represented in an equal mixture of two Leishmania strains. This was a high bar, given the relatively small protozoan genome and prior studies that showed limitations of single-cell genomics, especially for gene-level copy number changes. Overall, the study found that semi-permeable capsules (SPC) are an effective way to isolate high-quality single cells. Additionally, short reads from amplified genomes effectively maintained the relative levels of variation in the two strains on the chromosome, gene copy, and individual base level. Thus, this method will be useful to evaluate adaptive strategies of Leishmania. Many researchers will also refer to these studies to set up SPC collection and PTA methods for their organism of choice.

      Strengths:

      (1) The use of SPC and PTA in a non-bacterial organism is novel. The study displays the utility of these methods to isolate and amplify single genomes to a level that can be sequenced, despite being a motile organism with a GC-rich genome.

      (2) The authors clearly outlined their optimization strategy and provided numerous quality-control metrics that inspire confidence in the success of achieving even chromosomal coverage relative to ploidy.

      (3) The use of two distinct Leishmania strains with known clonal status provided strong evidence that PTA-based amplification could reflect genome differences and displayed the utility of the method for studies of rare genotypes.

      (4) Evaluating the SPCs pre- and post-amplification with microscopy is a practical and robust way of determining the success of SPC formation and PTA.

      (5) The authors show that the PTA-based approach easily resolved major genotypic ploidy in agreement with a prior 10x Chromium-based study. The new method had improved resolution of drug resistance genotypes in the form of both copy-number variations and single-nucleotide polymorphisms.

      (6) In general, the authors are very thorough in describing the methods, including those used to optimize PTA lysis and amplification steps (fresh vs frozen cells, naked DNA vs sorted cells, etc). This demonstrates a depth of knowledge about the procedure and leaves few unanswered questions.

      (7) The custom, multifaceted, computational assessment of coverage evenness is a major strength of the study and demonstrates that the authors acknowledge potential computational factors that could impact the analysis.

      We deeply appreciate the positive and encouraging feedback on our manuscript.

      Weaknesses:

      (1) The rationale behind some experimental/analysis choices is not well-described. For example, the rationale behind methanol fixation and heat-lysis is unclear. Additionally, the choice of various methods to assess "evenness" is not justified (e.g. why are multiple methods needed? What is the strength of each method?). Also, there is no justification for using 100k reads for subsampling. Finally, what exactly constitutes a "confidently-called SNP"?

      The methanol fixation prior to lysis is part of the original protocol described in the Single-Microbe Genome Barcoding Kit manual and was meant to facilitate lysis and DNA denaturation in bacterial cells (for which the kit was originally developed). However, in our preliminary tests with bulk samples – described in the supplementary material – we noticed a strong negative effect on lysis efficiency/DNA recovery when parasites were fixed with methanol. Thus, we decided to test the effect of skipping this step in the single-cell DNA workflow. We kept the SPC_STD1 sample to have a safe control where the full workflow described in the kit manual was followed.

      As we were unsure if the standard lysis (25 ˚C for 15 minutes) would work efficiently for Leishmania, we included the heat-lysis (99˚C for 15 minutes) as well as the longer incubation lysis (25 ˚C for 1h). These modifications were listed as validated alternatives in the kit's manual.

      The 100k reads threshold was chosen based on the number of reads found in the 'true cell' with the lowest read count.

      Regarding variant calling, a variant was considered confidently called if it was covered, at single-cell level, by at least one deduplicated read with Phred quality above Q30 and mapping quality (MAPQ) also above 30.

      In the revised version, we will include these explanations and improve the explanation of the metrics used to estimate coverage quality.

      (2) In the methods, the STD protocol lists a 15-minute amplification at 45C whereas the PTA protocol involves 10h at 37C. This is a dramatic difference in incubation time and should be addressed when comparing results from the two methods. It is not really a fair comparison when you look at coverage levels; of course, a 10-hour incubation is going to yield more reads than a 15-minute incubation.

      We agree with the reviewer that the longer incubation period of PTA might explain the higher read count seen in the PTA samples, although the differences in amplification kinetics (linear in PTA, exponential in STD) and potential differences in amplification saturation points make it difficult to compare them. For instance, an updated version of PTA (ResolveDNA V2) uses a lower amplification time (2.5 h) and achieves similar amplification levels compared to the 10h incubation time, suggesting PTA amplification saturates well before the 10h time. In any case, all quality check metrics were done with the cells subsampled to 100 k reads to mitigate the effect of read count differences on the data quality.

      (3) There is a lack of quantitative evaluations of the SPCs. e.g. How many capsules were evaluated to assess doublets? How many capsules were detected as Syto5 positive in a successful vs an unsuccessful experiment?

      We agree with the reviewer but during experimental execution SPCs were only assessed qualitatively via microscopy following the Single-cell microbe DNA barcoding kit manual. No quantitative analysis was done and therefore we do not have this data. Regarding doublet, this was done in silico based on the detection of SPCs containing mixed genomes from the two strains used in the study as described in the Materials and Methods. As pointed by another reviewer, this only allow the detection of inter-strain doublets. In the revised version, we explain this and add an estimation of total doublets based on the inter-strain doublet rate.

      (4) The authors do not address some of the amplification results obtained under various conditions. For example, why did temperature-based lysis of STD4 lead to amplification failure? Also, what is the reason for fewer "true" cells (higher background) in the PTA samples compared to the STD samples? Is this related to issues with barcoding or, alternatively, substandard amplification as indicated by lower read amounts in some capsules (knee plots in Figure 1C)?

      After exchange with the technical support team of the SPC generator kit, it was clarified that the heat lysis done in STD4 should have had a shorter incubation time (10 minutes instead of 15 minutes). We suspect that the longer incubation time, combined with the higher temperature and the harsh lysis condition with 0.8M KOH might have damaged SPCs and therefore DNA might have leaked out of them before WGA. In the microscopy images, SPCs in STD4 show a swollen aspect not seen in the other samples. In the revised version we will explain this more clearly.

      (5) The paper presents limited biological relevance. Without this, the paper describes an improvement in genome amplification methods and some proof-of-concept analyses. Using a 1:1 mixture of parasites with different genotypes, the authors display the utility of the method to resolve genetic diversity, but they don't seek to understand the limits of detecting this diversity. For some, the authors do not comment on the mixed karyotypes from the HU3 cells (Figure 3F) other than to state that this line was not clonal. For CNVs, the two loci evaluated were detected at relatively high copy number (according to Figure 4C, they are between 4 and 20 copies). Thus, the sensitivity of CNV detection from this data remains unclear; can this approach detect lower-level CNVs like duplications, or minor CNVs that do not show up in every cell?

      As described above we will include more discussion on potential biological relevance of the method in the revised version of the manuscript. In the revised version we will attempt to use dedicated bioinformatic tools to discover de novo CNVs, as per the suggestion of other reviewers. This might also allow us to determine the detection limit of the methodology for CNVs.

      (6) The authors state that Leishmania can carry extrachromosomal copies of important genes. There is no discussion about how the presence of these molecules would affect the amplification steps and CNV detection. For example, the phi29 enzyme is very processive with circular molecules; does its presence lead to overamplification and overrepresentation in the data? Is this evident in the current study? This information would be useful for organisms that carry this type of genetic element.

      We believe our data, which uses short-read sequences, does not allow to differentiate between intra-chromosomal CNVs and linear or circular episomal CNVs, so we cannot define if circular CNVs are over-amplified. Of note, we have previously demonstrated that the M-locus CNV in chromosome 36 is intrachromosomal, not circular (episomal)[5].

      (7) The manuscript is missing a comparison with other similar studies in the field. For example, how does this coverage level compare to those achieved for other genomes? Can this method achieve amplification levels needed to assess larger genomes? Has there been any evaluation of base composition effects since Leishmania is a GC-rich genome?

      We believe the SPC-PTA workflow can be applied to organisms with larger genomes as PTA was developed specifically for mammalian cells[6], and also because, in our hands, it outperformed the 10X scDNA solution, which was developed for mammals.

      We believe direct comparison with other studies regarding coverage levels is elusive because other steps in the workflow apart from the WGA, such as the library preparation (PCR-based in our case), as well as genome features like GC content, size, and presence of repetitive regions, can also affect coverage levels and evenness. One strength of our approach was the use a single sample (the 50/50 mix between two L. donovani strain) for all conditions, thus removing potential parasite-specific biases. In addition, the application of a multiplexing system during barcoding allowed us to combine all samples prior to library preparation, thus removing potential differences introduced by this step.

      Regarding the effect of GC-content, we did notice a positive bias in all samples in regions with higher GC content, which had to be corrected in silico. This was the opposite to a negative bias observed in previous study[7] likely due to differences in WGA and/or library preparation. In the revised version, we will include a supplementary figure showing the GC bias.

      (8) Cost is mentioned as a benefit of the SPC platform, and savings are achieved when working in a plate format, but no details are included on how this was evaluated.

      In the revised version we will provide precise cost estimates and the rationale for the estimation.

      (9) The Zenodo link for custom scripts does not exist, and code cannot be evaluated.

      The full Zenodo link (https://doi.org/10.5281/zenodo.17094083) will be included in the revised version.

      Reviewer #3 (Public review):

      Summary

      In this manuscript, Negreira et al. propose a new scDNAseq method, using semi-permeable capsules (SPCs) and primary template-directed amplification (PTA). The authors optimize several metrics to improve their predictions, such as determining GC bias, Intra-Chromosomal fluctuation (ICF -metric to differentiate replicative and non-replicative cells) and Intra-chromosomal coefficient of variation (ICCV - chromosome read distribution). The coverage evenness was evaluated using the fini index and the median absolute pairwise difference between the counts of two consecutive bins. They validate the proposed method using two Leishmania donovani strains isolated from different countries, BPK081 (low genomic variability) and HU3 (high genomic variability). Then, they showed that the method outperforms WGA and has similar accuracy to the discontinued 10X-scDNA (10X Genomics), further improving on short CNV identification. The authors also show that the method can identify somy variations, insertions/deletions and SNP variations across cells. This is a timely and very relevant work that has a wide applicability in copy number variation assessment using single-cell data.

      Strengths

      I really appreciate this work. My congratulations to the authors. All my comments below only aim to improve an already solid manuscript.

      We thank the reviewer for the enthusiasm and positive feedback.

      Weaknesses

      (1) Data availability: Although the authors provide a Zenodo link, the data is restricted. I also could not access the GitHub link in the Zenodo website: https://github.com/gabrielnegreira/2025_scDNA_paper. The authors should make these files available.

      Both the Zenodo (https://doi.org/10.5281/zenodo.17094083) and the GitHub (https://github.com/gabrielnegreira/2025_scDNA_paper) repositories are now publicly available.

      (2) 2-SPC-PTA and SPC-STD cell count comparison: The authors have consistently proven that the SPC-PTA method was superior to SPC-STD. However, there are a few points that should be clarified regarding the SPC-PTA results. Is there an explanation for the lower proportion of SPC to true cells success in SPC-STD, which reflects the bimodal distribution for the reads per cell in SPC-PTA2 and a three-to-multimodal distribution in SPC-PTA1 in Figure 1B? Also, in Table 1, does the number of reads reflect the number of reads in all sequenced SPCs or only in the true cells? If it is in the SPCs, I suggest that the authors add a new column in the table with the "Number of reads in true cells" to account for this discrepancy.

      The reason for the higher presence of 'background' SPCs in the PTA samples is not clear, but we hypothesize that it could be due to PTA favoring amplification of small, free floating DNA molecules that might have been trapped in cell-free SPCs, as PTA works with shorter amplicons. Also, the longer incubation time seen in PTA (10 h) might have allowed enhanced amplification of low quantities of free-floating DNA to detectable levels. Regarding Table 1, indeed it only show the total number of reads per sample. In the revised version we will include the suggested column to Table 1.

      (3) The authors should evaluate the results with a higher coverage for SCP-PTA. I understand that the authors subsampled the total read to 100,000 to allow cross-sample comparisons, especially between SPC-STD and SPC-PTA. However, as they concluded that the SPC-PTA was far superior, and the samples SPC-PTA1 and SPC-PTA2 had an "elbow" of 650,493 and 448,041, respectively, it might be interesting to revisit some of the estimations using only SPC-PTA samples and a higher coverage cutoff, as 400,000.

      We believe the 100.000 cutoff is already high for aneuploidy analysis as we have successfully reconstructed parasite karyotype with 20.000 reads per cell8, so a higher cutoff will likely not improve it. For CNV analysis, in the revised version, we will try to identify de novo CNVs using dedicated bioinformatic tools as per other reviewer suggestions. There, we will also test if a higher CNV detection sensitivity is achieved using the suggested 400,000 reads cutoff for the PTA samples.

      (4) Doublet detection: I suggest that the authors be a little more careful with their definition of doublets. The doublet detection was based on diagnostic SNPs from the two strains, BPK081 and HU3, which identify doublets between two very different and well-characterised strains. However, this method will probably not identify strain-specific doublets. This is of minor importance for cloned and stable strains with few passages, as BPK081, but might be more relevant in more heterogeneous strains, as HU3. Strain-specific doublets might also be relevant in other scenarios, as multiclonal infections with different populations from the same strain in the same geographic area. One positive point is that the "between strain doublet count" was low, so probably the within-strain doublet count should be low too. The manuscript would benefit from a discussion on this regard.

      We fully agree with the reviewer. We will make it clear in the revised version that we quantify inter-strain doublets only, and we will also provide an estimation of total doublets based on the inter-strain doublet rate.

      (5) Nucleotide sequence variants and phylogeny: I believe that a more careful description of the phylogenetic analysis and some limitations of the sequence variant identification would benefit the manuscript.

      (5.1) As described in the methods, the authors intentionally selected two fairly different Leishmania donovani strains, HU3 and BPK081, and confirmed that the sequent variant methodology can separate cells from each strain. It is a solid proof of concept. However, most of the multiclonal infections in natural scenarios would be caused by parasite populations that diverge by fewer SNPs, and will be significantly harder to detect. Hence, I suggest that a short discussion about this is important.

      We will add a short discussion clarifying the limitations, while noting that our data demonstrate the ability of the approach to resolve very closely related cells, as illustrated by the fine-scale genetic differences observed within the clonal BPK081 population and by the detection of rare variants at targeted loci. We will also emphasize that the sensitivity to detect closely related genotypes depends on sequencing depth and the genomic regions considered.

      (5.2) The authors should expand on the description of the phylogenetic tree. In the HU3 on Figure 5F left panel, most of the variation is observed in ~8 cells, which goes from position 0 to position ~28.000. Most of the other cells are in very short branches, from ~29.000 to 30.4000 (5F right panel). Assuming that this representation is a phylogram, as the branches are short, these cells diverge by approximately 100-2000 SNPs. It is unexpected (but not impossible) that such ~8 divergent cells be maintained uniquely (or in very low counts) in the culture, unless this is a multiclonal infection. I would carefully investigate these cells. They might be doublets or have more missing data than other cells. I would also suggest that a quick discussion about this should be added to the manuscript.

      In the revised version we will improve the description of the phylogenetic analysis. We will also investigate deeper the 8 mentioned cells to define if they have confounding factors that might have led to their discrepancy. The possibility of multiclonal infection in HU3 is not excluded as this strain was not cloned after isolation.

      References:

      (1) Dileep, V., Gilbert, D. M., Dileep, V. & Gilbert, D. M. Single-cell replication profiling to measure stochastic variation in mammalian replication timing. Nat. Commun. 9, 427 (2018).

      (2) Miura, H. et al. Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization. Nat. Genet. 51, 1356–1368 (2019).

      (3) Marques, C. A. et al. Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe. Genome Biol. 16, 230 (2015).

      (4) Damasceno, J. D. et al. Leishmania major chromosomes are replicated from a single high-efficiency locus supplemented by thousands of lower efficiency initiation events. Cell Rep. 44, 116094 (2025).

      (5) Imamura, H. et al. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. eLife 5, e12613 (2016).

      (6) Gonzalez-Pena, V. et al. Accurate genomic variant detection in single cells with primary template-directed amplification. Proc. Natl. Acad. Sci. 118, e2024176118 (2021).

      (7) Imamura, H. et al. Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level. Sci. Rep. 10, 15043 (2020).

      (8) Negreira, G. H. et al. High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy in Leishmania donovani. Nucleic Acids Res. 50, 293–305 (2022).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary: 

      This study is an evaluation of patient variants in the kidney isoform of AE1 linked to distal renal tubular acidosis. Drawing on observations in the mouse kidney, this study extends findings to autophagy pathways in a kidney epithelial cell line. 

      Strengths: 

      Experimental data are convincing and nicely done.

      Thank you

      Weaknesses: 

      Some data are lacking or not explained clearly. Mutations are not consistently evaluated throughout the study, which makes it difficult to draw meaningful conclusions.

      We have revised our manuscript to clarify some earlier explanations and provided rationale for focusing on specific variants throughout the study.

      Reviewer #2 (Public review):

      Context and significance: 

      Distal renal tubular acidosis (dRTA) can be caused by mutations in a Cl-/HCO3- exchanger (kAE1) encoded by the SLC4A1 gene. The precise mechanisms underlying the pathogenesis of the disease due to these mutations are unclear, but it is thought that loss of the renal intercalated cells (ICs) that express kAE1 and/or aberrant autophagy pathway function in the remaining ICs may contribute to the disease. Understanding how mutations in SLC4A1 affect cell physiology and cells within the kidney, a major goal of this study, is an important first step to unraveling the pathophysiology of this complex heritable kidney disease. 

      Summary: 

      The authors identify a number of new mutations in the SLC4A1 gene in patients with diagnosed dRTA that they use for heterologous experiments in vitro. They also use a dRTA mouse model with a different SLC4A1 mutation for experiments in mouse kidneys. Contrary to previous work that speculated dRTA was caused mainly by trafficking defects of kAE1, the authors observe that their new mutants (with the exception of Y413H, which they only use in Figure 1) traffic and localize at least partly to the basolateral membrane of polarized heterologous mIMCD3 cells, an immortalized murine collecting duct cell line. They go on to show that the remaining mutants induce abnormalities in the expression of autophagy markers and increased numbers of autophagosomes, along with an alkalinized intracellular pH. They also reported that cells expressing the mutated kAE1 had increased mitochondrial content coupled with lower rates of ATP synthesis. The authors also observed a partial rescue of the effects of kAE1 variants through artificially acidifying the intracellular pH. Taken together, this suggests a mechanism for dRTA independent of impaired kAE1 trafficking and dependent on intracellular pH changes that future studies should explore. 

      Strengths: 

      The authors corroborate their findings in cell culture with a well-characterized dRTA KI mouse and provide convincing quantification of their images from the in vitro and mouse experiments

      Thank you  

      Weaknesses: 

      The data largely support the claims as stated, with some minor suggestions for improving the clarity of the work. Some of the mutants induce different strengths of effects on autophagy and the various assays than others, and it is not clear why this is from the present manuscript, given that they propose pHi and the unifying mechanism

      We have modified our manuscript to discuss the various strengths of the mutants and emphasize that alteration of cytosolic pH by kAE1 variants may not be the only mechanism leading to dRTA.  

      Reviewer #3 (Public review):

      Summary: 

      The authors have identified novel dRTA causing SLC4A1 mutations and studied the resulting kAE1 proteins to determine how they cause dRTA. Based on a previous study on mice expressing the dRTA kAE1 R607H variant, the authors hypothesize that kAE1 variants cause an increase in intracellular pH, which disrupts autophagic and degradative flux pathways. The authors clone these new kAE1 variants and study their transport function and subcellular localization in mIMCD cells. The authors show increased abundance of LC3B II in mIMCD cells expressing some of the kAE1 variants, as well as reduced autophagic flux using eGFP-RFP-LC3. These data, as well as the abundance of autophagosomes, serve as the key evidence that these kAE1 mutants disrupt autophagy. Furthermore, the authors demonstrate that decreasing the intracellular pH abrogates the expression of LC3B II in mIMCD cells expressing mutant SLC4A1. Lastly, the authors argue that mitochondrial function, and specifically ATP synthesis, is suppressed in mIMCD cells expressing dRTA variants and that mitochondria are less abundant in AICs from the kidney of R607H kAE1 mice. While the manuscript does reveal some interesting new results about novel dRTA causing kAE1 mutations, the quality of the data to support the hypothesis that these mutations cause a reduction in autophagic flux can be improved. In particular, the precise method of how the western blots and the immunofluorescence data were quantified, with included controls, would enhance the quality of the data and offer more supportive evidence of the authors' conclusions. 

      Strengths: 

      The authors cloned novel dRTA causing kAE1 mutants into expression vectors to study the subcellular localization and transport properties of the variants. The immunofluorescence images are generally of high quality, and the authors do well to include multiple samples for all of their western blots.

      Thank you

      Weaknesses: 

      Inconsistent results are reported for some of the variants. For example, R295H causes intracellular alkalinization but also has no effect on intracellular pH when measured by BCECF. The authors also appear to have performed these in vitro studies on mIMCD cells that were not polarized, and therefore, the localization of kAE1 to the basolateral membrane seems unlikely, based upon images included in the manuscript. Additionally, there is no in vivo work to demonstrate that these kAE1 variants alter intracellular pH, including the R607H mouse, which is available to the authors. The western blots are of varying quality, and it is often unclear which of the bands are being quantified. For example, LAMP1 is reported at 100kDa, the authors show three bands, and it is unclear which one(s) are used to quantify protein abundance. Strikingly, the authors report a nonsensical value for their quantification of LCRB II in Figure 2, where the ratio of LCRB II to total LCRB (I + II) is greater than one. The control experiments with starvation and bafilomyocin are not supportive and significantly reduce enthusiasm for the authors' findings regarding autophagy. There are labeling errors between the manuscript and the figures, which suggest a lack of vigilance in the drafting process.

      The R295H variant was identified in a dRTA patient and as such, it was important to report it. However, this is the first mutation located in the amino-terminus of the protein, which may be involved in protein-protein interactions, so other mechanisms may cause dRTA for this variant. We have therefore modified our manuscript to state that alteration of cytosolic pH may not be the only mechanism leading to dRTA. At this time, we are not able to measure cytosolic pH in vivo and hope to be able to do it in the future.

      In our revised manuscript, we also show cell surface biotinylation results supporting that plasma membrane abundance of the kAE1 S525F and R589H variants is not significantly different than WT in non-polarized mIMCD3 cells (Figure 3 A&B), in line with the predominant basolateral localization of the variants in polarized cells (Figure 1C). Therefore, these two mutant proteins are not mis-trafficked in non-polarized cells.  Finally, we have clarified which bands have been used for quantification and corrected quantifications (including ratio measurements).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) R295H is recessively inherited, whereas Y413H is dominantly inherited: this is interesting and may be linked to their cellular expression and function. Is this information known for the other mutations examined in this study? 

      The S25F and R589H dRTA variants have both been reported to exhibit autosomal dominant inheritance. This information is now updated in lines 146 and 158-159.

      (2) R589H expression levels are evaluated in the Western blot of Figure 1, but localization and activity are not examined in Figure 2. However, R589H is included in autophagy experiments shown in later figures. Similarly, mutant R607H is the subject of several experiments further into the manuscript, but no initial analysis is provided for this variant. 

      Protein abundance and localization of the R589H mutant in mIMCD3 cells have been shown in our previous publication in Supplementary Fig 5D and Supplementary Fig 2J [1]. This now indicated on lines 158-159. Our previous paper also presented a detailed study of the R607H dRTA mutant, the mouse model corresponding to the human R589H mutation. This is now indicated on lines 70, 118-119 and 180. The present study builds upon those published findings.

      (3) This inconsistency is confusing, detracts from the usefulness of the study, and makes the comparative analysis of mutations incomplete. It is difficult to extrapolate from published studies in MDCK1 cells, which show different results on trafficking. 

      The mIMCD3 cell line, which more closely resembles the physiology of the mouse collecting duct than MDCK cells, was selected for this study and our previous one [1]. Accordingly, the results obtained are better aligned with in vivo evidence. In contrast, differences in mutant protein expression and localization observed in other cell lines, like the MDCK cells, are likely attributable to differences in their cellular origin. 

      (4) In Figure 2, could the authors explain why total LC3B is graphed for the data shown in mouse lysates, whereas the ratio of bands is analysed for cell lysates? Both sets of data show the two LC3B bands.

      Total LC3B levels were significantly increased in the mutant compared to WT; however, no significant difference was observed in the lipidation ratio. For this reason, that graph is not shown in the main paper but has been included in the Supplementary Figure 1D. 

      (5) In Figure 3, representative fluorescence images should be shown for all cell lines.

      We have now included representative immunofluorescence images for all cell lines in Figure 3C.

      (6) pH effects: Suggest that steady state pHi (Figure 3E) and rate of alkalization (Figure 1F) would be more effective together in Figure 1. The authors should show data for the effect of nigericin on cytoplasmic pH in Figure 3. If the rate of alkalinization in the mutant cells is reduced, shouldn't the intracellular steady state pH be more acidic? A cartoon depicting the transporter activity in the cell and the expected changes in pHi would be helpful. Is there a way to activate/inhibit NHE1 and rescue the effect of the mutant kAE1? It is unclear if the link between the mutant kAE1 and mitochondrial ATP production is a consequence of the intracellular pH or an indirect effect.

      We opted to keep the effect of nigericin on pHi in Supplementary Fig1A given that Figure 3 already contains 11 panels. Also, in intercalated cells, the kAE1 protein physiologically exports 1 molecule of bicarbonate in exchange of 1 chloride ion import hence a reduced transport activity would result in a more alkaline intracellular pH. To clarify this point, we have included a diagram in Figure 1E as suggested. However, to calculate the rate of intracellular alkalinisation, the transporter is functioning in the opposite direction, i.e. extruding chloride and importing bicarbonate (see methods protocol for transport assay). Therefore, in this assay (Figure 1G), a defective chloride/bicarbonate activity results in a reduced rate of intracellular alkalinisation rate. This is now explained on lines 169-172.

      Disruption of NHE1 function would impair sodium homeostasis and as such, potentially affect the activity of other proteins associated with acid-base balance and autophagy in collecting duct cells. Therefore, any resulting effects may not be confidently attributed specifically to the mutant kAE1. With nigericin, we aimed to alter pHi while affecting the least possible other ion concentration. Due to space considerations, Figure 1 has been reorganised to include the rate of alkalinisation and pHi (panels F and G). 

      Reviewer #2 (Recommendations for the authors):

      (1) The authors could improve the readability of this manuscript for a general audience by clarifying and summarizing the respective phenotype(s)/effect(s) of the different mutants in some kind of table in the main figures. It is hard to keep track of the different disease mutants alongside the KI mouse mutations, as the text frequently discusses multiple mutants at a time. 

      As requested, we added two tables (Supplementary Tables 1 & 2) in Supplementary files summarizing the data obtained in this study. We hope this will help the readership to keep track of each variant’s phenotype.

      (2) The subtitle of the results section of Figure 2 should be reworded to reflect that  whole kidney lysates are used for the KI mice and not the other mutants.

      As requested, the title in the Results section has been modified (lines 178-179).

      (3) More discussion of why the different mutants cause different strengths of phenotypes should be included.

      Different variants induce different degree of functional defects as seen in Figure 1F & G. The kAE1 R295H, the only amino acid substitution in the amino-terminal cytosol causing dRTA, does not affect the transporter’s function or cells’ pHi. Therefore, this variant may cause dRTA via a different pathway than transport-defective S525F or partially inactive R589H variants that both affect pHi. Our study does not exclude that dRTA may be caused by other defects than pHi alterations, including defective proteinprotein interactions. This discussion is now included in the manuscript on lines 386-391.

      Reviewer #3 (Recommendations for the authors):

      In general, I found the subject matter of this manuscript interesting and of value to the scientific community. The interpretation of the data and how much it supports the conclusion that "kAE1 variants increases pHi which alters mitochondrial function and leads to reduced cellular energy levels that eventually attenuate energy-dependent autophagic pathways" is largely incomplete. There are significant concerns about the quantification of Western blot data. Additionally, including the R607H variant in the in vitro experiments would improve the interpretation and extrapolation of in vitro data to the kidney.

      We apologize for the confusion with R589H and R607H variants. The R607H mutant is the murine ortholog to the human R589H dRTA variation. To clarify this, we have added this information on line 180, in addition to lines 118-119 and line 70.

      Suggestions:

      (1) Can an anion replacement experiment be performed in the mIMCD cells (no Cl or no HCO3) to determine that bicarbonate transport through AE1 is responsible for the reduced ATP rates in Figure 5? Inclusion of WT +dox control would be helpful to convince the reader of the effects.

      Because Seahorse real-time cell metabolism ATP rates measurements require specific and patented buffers with un-specified compositions, it was not possible to modify the Cl⁻ or HCO₃⁻ content during the ATP measurement assay. All cell lines, including empty vector cells (EV) were treated with doxycycline; thus, WT + dox was already included. The empty vector cell line treated with doxycycline allowed the exclusion of specific effects of doxycycline on mitochondrial activity as a control. This is now clarified in Figure 5 legend, lines 655-656.

      (2) Can the authors measure pHi in fresh kidney sections from the R607H mouse?

      Unfortunately, we are not currently able to measure pHi in fresh kidney sections and although we recognize it would benefit greatly to our study, establishing a new collaboration to perform this measurement would significantly delay the publication of this work; therefore, these results will not be available for the present manuscript. 

      (3) Does pH 7.0 media have any effect on autophagy, as shown in Figure 3? Why was pH 6.6 selected?

      The idea was to artificially acidify pHi in mutant cell lines (that have a steady state alkaline pHi) and assess whether this acidification corrects autophagy defects. We first determined that incubation in cell culture medium at pH 6.6 with 0.033 µM nigericin (final potassium concentration: 168 mM) for 2 hours provided optimal conditions, i.e. ensuring cell viability over the 2-hour period while effectively lowering intracellular pH to 6.9, as demonstrated in Supplementary Figure 1A-C.

      (4) In vitro experiments should be performed on polarized cells with kAE1 properly inserted in the basolateral membrane. Experiments on subconfluent, non-polarized cells do not support the hypothesis that transport functions of AE1 initiate the cascade of events attributed to these SLC4A1 mutations.

      To address this point, we have performed cell surface biotinylations on 70-80 % confluent mIMCD3 cells expressing kAE1 WT, S525F or R589H mutants and show that cell surface abundance of the mutants is not significantly different from the WT protein. This is now shown in Figure 3 A&B. As cell surface biotinylation provides a more quantitative assessment of protein cell surface abundance, we have removed the immunofluorescence images from non-polarised cells and replaced them with representative immunoblots from a cell surface biotinylation assay.

      Concerns:

      (1) No information about the B1 ATPase antibody used.

      Now provided in Supplementary Material, ATP6V1B1 Antibody from Bicell cat#20901.

      (2) No actin band in Figure 1E (as prepared).

      Actin bands are provided for each blot in Figure 1D.

      (3) Figures 1E and 1F are labelled wrong in the figure versus the results section. 

      Thank you for letting us know, this is now corrected.

      (4) The cortical sections shown in Figure 4 for the KI/KI do not appear to have the morphology of a CCD. The authors may want to consider including glomeruli to convince the reader of the localization of the tubules. Same concern with Figure 5G and I. The WT image in 5G does not have the morphology of a CCD. Principal cells should be predominant, and ICs should be dispersed.

      Both figures 4 and 5 have been updated with images showing glomeruli (light blue “G” on figure) with neighbour and dispersed IC staining.

      (5) The quantification of LAMP1 in Figure 4 is unclear. How did the authors determine the boundary of AICs, and how did they calculate the volume of lysosomes? If a zstack was used, how are the authors sure that their 10um section includes the entire AIC?

      The quantification of LAMP1 is detailed under “Image analysis”, then “Volocity” sections in Supplementary Material. The boundary of A-IC was manually detected in Volocity based on the presence of the H<sup>+</sup>-ATPase before Volocity analysis for lysosomal volume as described in the Methods.

      The 10 micron sections are expected to include full AIC as well as partial AIC, but the frequency of these events should be the same between WT and variants’ sections, therefore they were all included in the analysis if cells displayed H<sup>+</sup>-ATPase signal. 

      (6) Figure 5: There is no description of how ATP rates are calculated from the provided traces.

      We used Agilent Seahorse XF ATP rate assay kit for this experiment. In this assay, the total ATP rate is the sum of ATP production rate from both glycolysis and oxidative phosphorylation. Glycolysis releases protons in a 1:1 ratio with ATP hence the glycolytic ATP rate is calculated from the glycolytic proton efflux rate (glycoPER). GlycoPER is determined by subtracting respiration linked proton efflux from total proton efflux by inhibiting complex I and III. This information is now added to Supplementary Material, in the “Metabolic Flux analysis” section.

      (7) Figure labels in Figure 5 are wrong. It seems 5H (as presented) should actually be labeled 5G. In 5H (G?), why did some cells not have any TOM20 pixel intensity for S525F and R589H variants?

      Confocal image acquisition in this experiment was kept under the same settings to allow comparison between samples. Therefore, some cells show dimer fluorescence than others. From the figure 5 panels, all cells showed TOM 20 pixel intensity. Figure 5H panel has been relabelled Figure 5G.

      (8) In Figure 2, the summary graphs show analysis of more samples than are visible on the included western blots. What is the rationale for this? Why does S525F have 9 samples in BafA1 while R295H only has 3 (2H)? Yet, R295H has 6 samples in 2I. In 2D, S525F has at least 9 samples. Explain.

      Figure 2A-C shows representative immunoblots, among several ones independently conducted. Therefore, the final number of samples is higher than showed on Figure 2. This is now indicated in Figure 2 legend, line 603. It became clear quite early in our study that the recessive kAE1 R295H variant does not behave similarly to the other variants studied, maybe because it affects the cytosolic domain, so we did not perform as many replicates for this variant as we did for the others. However, we felt it was valuable to the research community to report the characterization of this variant and decided to keep it in our study. 

      (9) In general, the actin loading does not appear to be equal between samples. And some figures show the same actin blot twice (2A, C) while some show independent actin bands for LC3B and p62. Equal loading seems a fairly significant control, considering the importance of quantification in the figures.

      In addition to performing protein assays, we systematically conduct immunoblot with anti-b-actin antibody to control for loading variability. When possible, two or three proteins, including actin, are detected on the same blot, when molecular weight differ enough. This sometimes results in b-actin being used as a loading control for two different proteins, as seen on Figure 2A and 2C. This is now indicated on lines 605606.

      (10) In the Supplemental Figure 2, which band is being quantified for mature CTSD at 33kDa? Same for intermediate CTSD. The quantification of V-ATPase seems questionable based on the actin variance shown in the blot. Surely the ratio of the fourth sample is greater than 1.

      Supplementary Figure 2 has been updated to include arrows indicating which band was selected for the quantification. After verifying the measurements of band intensities from “Image Lab” quantification software, we confirm the results, including that fourth KI/KI sample has a ratio of 0.78 (Adj Total Band Vol (Int), lanes 10). Screen shots of quantifications are attached below.

      Author response image 1.

      Author response image 2.

      (11) Why are the experiments performed on non-confluent IMCD cells? Figure 1D shows good basolateral localization of AE1, yet the other experiments in the manuscript appear to use IMCD cells in low confluent states, without proper localization of AE1. Figure 3A shows AE1 dispersed throughout the cytoplasm. Why have the authors decided to study the effects of an anion exchanger without it being properly localized to the basolateral membrane? Shouldn't all experiments be performed in polarized IMCDs? If AE1 isnt properly in the membrane, and the cells do not have defined apico-basolateral polarity, then what role can AE1-mediated intracellular pH change have on the results of the experiments? Were the pHi experiments in 3E performed on polarized cells? Or even 1F?

      To address this point, we have performed cell surface biotinylations on 70-80 % confluent mIMCD3 cells expressing kAE1 WT, S525F or R589H mutants and show that cell surface abundance of the mutants is not significantly different from the WT protein. This is now shown in Figure 3A & B. As it provides a more quantitative assessment of protein cell surface abundance, we have removed the immunofluorescence images from non-polarised cells and replaced them with a representative immunoblot from a cell surface biotinylation assay.

      (12) As mentioned in the public comments, how is the ratio A/(A+B) greater than 1? With A and B > 0. In Figure 3, the data is reasonable, but in Figure 2, the data is simply impossible. What is the explanation for this phenomenon? Why was this presentation of data approved? Is it supposedly a fold of WT, like 2K and 2L? Is the reader also to believe that total LC3B is 2-fold greater in KI/KI mice, as shown in 2K? My eyes, though not densitometry equipment, cannot confirm this. The actin bands are not equal. Yet again, there are 4 lanes of KI/KI mice, but the quantification shows 5 samples.

      The ratios in figure 2D, 2F, 2H and 2L have been re-calculated and corrected. As indicated above, immunoblots are representative and quantification of additional blots has been included in the graphs.

      (12) Spelling error Figure 4B: cels.

      Corrected

      References 

      (1) Mumtaz, R. et al. Intercalated Cell Depletion and Vacuolar H+-ATPase Mistargeting in an Ae1 R607H Knockin Model. Journal of the American Society of Nephrology 28, 1507–1520 (2017).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Lahtinen et al. evaluated the association between polygenic scores and mortality. This question has been intensely studied (Sakaue 2020 Nature Medicine, Jukarainen 2022 Nature Medicine, Argentieri 2025 Nature Medicine), where most studies use PRS as an instrument to attribute death to different causes. The presented study focuses on polygenic scores of non-fatal outcomes and separates the cause of death into "external" and "internal". The majority of the results are descriptive, and the data doesn't have the power to distinguish effect sizes of the interesting comparisons: (1) differences between external vs. internal (2) differences between PGI effect and measured phenotype. I have two main comments:

      (1) The authors should clarify whether the p-value reported in the text will remain significant after multiple testing adjustment. Some of the large effects might be significant; for example, Figure 2C

      We have now added Benjamini-Hochberg multiple-testing adjusted p-values in the text each time we present nominal p-values. Additionally, supplementary tables S5 and S6 provide multiple-adjusted p-values for all analysed PGIs.

      Although this was not always the case, many comparisons remained significant after multiple testing adjustments, especially in Figure 2C that the reviewer commented on. In the revised version, we have placed more emphasis on describing these HRs that have low p-values after multiple-test adjustment. The revised text for Figure 2C in the Results section now reads:

      Panel C analyses mortality in three age-specific follow-up periods. The PGIs were more predictive of death in younger age groups, although the difference between the 25–64 and 65–79 age groups was small, except for the PGI of ADHD (HR=1.14, 95% CI 1.08; 1.21 for 25–64-year-olds; HR=1.04, 95% CI 1.00; 1.08 for 65–79-year-olds; p=0.008 for difference, p=0.27 after multiple-testing adjustment). PGIs predicted death only negligibly among those aged 80+, and the largest differences between the age groups 25–64 and 80+ were for PGIs of self-rated health (HR 0.87, 95% CI 0.82; 0.93 for 25–64-year-olds, HR 1.00, 95% CI 0.94; 1.04 for 80+ year-olds, p=2*10<sup>-4</sup> for difference, p=0.006 after multiple-testing adjustment), ADHD (HR 1.14, 95% CI 1.08; 1.21 for 25–64-year-olds, HR 0.99, 95% CI 0.95; 1.03 for 80+ year-olds, p=7*10<sup>-4</sup> for difference, p=0.012 after multiple-testing adjustment) and depressive symptoms (HR 1.12, 95% CI 1.06; 1.18 for 25–64-year-olds, HR 1.00, 95% CI 0.96; 1.04 for 80+ year-olds, p=0.002 for difference, p=0.032 after multiple-testing adjustment). Additionally, the difference in HRs between these age groups achieved significance after multiple testing adjustment at the conventional 5% level for PGIs of cigarettes per day, educational attainment, and ever smoking.

      We have also included the recent study by Argentieri et al. (2025) in the literature review, which was missing from our previous version. We appreciate the reference. Other references mentioned were already included in the previous version of the manuscript.

      (note that the small prediction accuracy of PGI in older age groups has been extensively studied, see Jiang, Holmes, and McVean, 2021, PLoS Genetics).

      We would like to thank the reviewer for suggesting the relevant reference by Jiang et al. We have now expanded on the discussion of age-specific differences in the discussion section and included this reference.

      (2) The authors might check if PGI+Phenotype has improved performance over Phenotype only. This is similar to Model 2 in Table 1, but slightly different.

      The reviewer raises an interesting angle to approach the analysis. We have now added an analysis assessing the information criteria and the significance of improvement between nested models in Supplementary table S8. All the tested PGI+phenotype models show improvement over the phenotype-only model that is statistically significant at all conventional levels when tested by likelihood-ratio tests between nested models . Additionally,  improvement was found when using Akaike and Bayesian (Schwarz) information criteria (albeit sometimes modest in size). We have added a passage in the results section briefly summarising this analysis:

      Supplementary table S8 presents information criteria and significance tests on corresponding models. Models with PGI+phenotype (Models 2a–f) showed improvement over models with the phenotype only (Models 1a, 1c, 1e, 1g, 1i, 1k, with a p=0.0006 or lower) in terms of both Akaike information criterion (AIC) as well as Bayesian (Schwarz) information criterion (BIC) with a p=0.0006 or lower in all comparisons. The full Model 4 again showed improvement over the model with all PGIs jointly (Model 3b, with a p=0.0002 or p=0.00002, depending on continuous/categorical phenotype measurement), which had a lower AIC but not BIC.

      Reviewer #2 (Public review): 

      Summary:

      This study provides a comprehensive evaluation of the association between polygenic indices (PGIs) for 35 lifestyle and behavioral traits and all-cause mortality, using data from Finnish population- and family-based cohorts. The analysis was stratified by sex, cause of death (natural vs. external), age at death, and participants' educational attainment. Additional analyses focused on the six most predictive PGIs, examining their independent associations after mutual adjustment and adjustment for corresponding directly measured baseline risk factors.

      Strengths:

      Large sample size with long-term follow-up.

      Use of both population- and family-based analytical approaches to evaluate associations.

      Weaknesses:

      It is unclear whether the PGIs used for each trait represent the most current or optimal versions based on the latest GWAS data.

      To our reading, this comment is closely related to the “recommendations for the author” number 3 by reviewer 2, and we thus address them together. 

      If the Finnish data used in this study also contributed to the development of some of the PGIs, there is a risk of overestimating their associations with mortality due to overfitting or "double-dipping." Similar inflation of effect sizes has been observed in studies using the UK Biobank, which is widely used for PGI construction.

      To our reading, this comment is closely related to the “recommendations for the author” 4 by reviewer 2, and we thus address them together.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Specific comments:

      (1) Cited reference 1 also investigated the PRS association with life span; cited reference 8 explains PRS association with healthy lifespan. Can authors be clearer about what is new in the context of these references? Specifically, what are the PGIs studied here that were not analyzed in the cited analyses?

      Although some previous studies on the topic do exist, our analysis arguably has novelty in touching upon several unstudied or scarcely studied themes. These include:

      A set of PGIs focusing on social, psychological, and behavioural phenotypes or PGIs for typically non-fatal health conditions.

      An assessment of direct genetic effects/ confounding with a within-sibship design.

      An assessment of potential heterogeneous effects by several socio-demographic characteristics.

      An analysis of external causes of deaths (which can be hypothesised to be particularly relevant here, given the choice of our PGIs not focusing directly on typical causes of death).

      A detailed assessment of the interplay of the most predictive PGIs with their corresponding phenotypes.

      We have substantially revised the Introduction section focusing on making these novel contributions more explicit.

      (2) In the Methods section, it is not very clear why the authors specifically study the "within-sibship" samples. Is this for avoiding nurturing effects from parental genotypes or for controlling assortative mating? The authors should clarify the rationale behind the design.

      The substance-related rationale behind this approach was briefly discussed in the Introduction section while in the Methods section, we focused more on the technical description of our analyses. However, it is certainly worthwhile to clarify to the reader why within-sibship methods have been used. The revised passage in the methods section now states:

      “In addition to this population sample, we used a within-sibship analysis sample to assess the extent of direct and indirect genetic associations captured by the PGIs, as discussed in the introduction.”

      (3) Residual correlations of PGIs were no more than 0.050..." As a minor comment, since PGIs is a noisy variable, the correlation would be low; however, I don't think there are better ways to evaluate Cox assumptions, and in many cases, this assumption is not correct for strong predictors.

      Yes, these points are true. Overall, it is often implausible that empirical distributions exactly match distributional assumptions in statistical models. For example, it may not be realistic to expect that the mortality hazards across categories of independent variables stay exactly proportional during long mortality-follow-ups; some deviations from constant proportions are almost inevitable. However, there are reasonable grounds to argue that in case of moderate violations of the proportional hazards assumption, the estimates still remain interpretable for practical uses. They can be read as approximating average relative hazards over the study period (for discussion, see pages 42–47 in Allison P. 2014. Event history and survival analysis: Regression for longitudinal event data (second edition). Thousand Oaks: SAGE).

      (4) "PGI of ADHD (HR=1.08 95%CI 1.04;1.11 among men; HR=1.01 95%CI 0.97;1.05 among women; p=0.012 for difference)." Is this difference significant after multiple testing correction?

      We have presented multiple-testing adjusted p-values together with nominal ones in this and in all other instances where they are mentioned in the text. Additionally, Supplementary tables S5–S6 present multiple-adjusted p-values for each PGIs studied.

      (5) "Panel D displays that most PGIs had stronger associations with external (accidents, violent, suicide, and alcohol related deaths) than natural causes of death." Similar to the comment above, are there any results that are significantly different between internal and external?

      We have added the p-values of those variables that had larger differences in the revised text. Quoting from the revised article: “The HR differences between external and natural causes of death were nominally significant at the conventional 5% level for cannabis use (p=0.016), drinks per week (p=0.028), left out of social activity (p=0.029), ADHD (p=0.031), BMI (p=0.035) and height (p=0.049), but none of these differences remained significant after adjusting for 35 multiple tests. “

      (6) Table 1: The effect of the phenotype is stronger than the PGI; this is expected as PGI is a weak predictor and can be considered as "noised" measurement of true genetic value (Becker 2021 Nature Human behavior). Is there a way to adjust for the impact of noise in PGI at tagging genetic value and compare if the PGI effect is different from the phenotype effect?

      PGIs are certainly imperfect measures that contain a lot of noise. However, extracting new information from what is unknown is an extremely demanding exercise, and still further complicated for example, by that we do not know the exact benchmark of total genetic effect we should be aiming at. Different methods of heritability estimation, for instance, often give dramatically differing results – for reasons that are still up to scrutiny.

      We are thus not familiar with a method that could achieve satisfactory answer for this challenging task.

      Reviewer #2 (Recommendations for the authors):

      (3) Justification and Selection of PGIs:

      For several traits, such as BMI, multiple polygenic indices (PGIs) are currently available. The criteria used to select specific PGIs for this study are not clearly described. A more systematic and reproducible approach-for example, leveraging metadata from the PGS Catalog-could strengthen the justification for PGI selection and enhance the study's generalizability.

      There are numerous PGIs developed in the extensive GWAS literature, but a finite set of PGIs always needs to be chosen for any analysis. The rationale behind our decision to include every PGI from the repository of Becker et al. 2021 (full reference in the manuscript, see also https://www.thessgac.org/pgi-repository) that was available for the Finnish data (including the possibility to exclude overlapping samples, see our response to the next comment for more discussion) was to provide rigorous analysis by limiting the researchers degrees of freedom in arbitrarily choosing PGIs. Although it would have been tempting to not use some PGIs that were not expected to substantially correlate with mortality, we believe that our conservative strategy increases the credibility of the reported p-values, particularly the multiple adjustment should now work as intended. 

      We also mention now this rationale when discussing the chosen PGIs in the methods section: “As the independent variables of main interest, we used 35 different PGIs in the Polygenic Index repository by Becker et al., which were mainly based on GWASes using UK Biobank and 23andMe, Inc. data samples, but also other data collections. They were tailored for the Finnish data, i.e., excluding overlapping individuals between the original GWAS and our analysis and performing linkage-disequilibrium adjustment. We used every single-trait PGI defined in the repository (except for subjective well-being, for which we were unable to obtain a meta-analysis version that excluded the overlapping samples). By limiting the researchers’ freedom in selecting the measures, this conservative strategy should increase the validity of our estimates, particularly with regards to multiple-testing adjusted p-values.”

      (4) Overlap Between PGI Training Data and Study Sample:

      The authors should describe any overlap between the data used to develop the PGIs and the current study sample. If such overlap exists, it may lead to overestimation of effect sizes due to "double-dipping." A discussion of this issue and its potential implications is warranted, as similar concerns have been raised in studies using UK Biobank data.

      This is, fortunately, not a concern of our analysis. Overlapping samples were excluded in creating the PGIs that we used. We have now described this more clearly in the revised methods section.

      (1) Clarify the Methodology for Family-Based Cox Analysis:

      It is unclear what specific method was used to perform Cox regression in the family-based analysis. Please provide additional methodological details. ”

      We have described the method further and added an additional reference in the revision. The text now stands:

      “We compared these models to the corresponding within-sibship models, using the sibship identifier as the strata variable. This method employs a sibship-specific (instead of a whole-sample-wide baseline hazard in the population models) baseline hazard, and corresponds to a fixed-effects model in some other regression frameworks (e.g., linear model with sibship-specific intercepts)”

      (2) Clarify Timing of Measured Risk Factors Relative to Follow-Up:

      The main text should provide more detailed information regarding the timing of data collection for directly measured risk factors. Specifically, it should be clarified whether the measurements used correspond to the first available data for each individual after the start of follow-up, or if a different criterion was applied.

      BMI, self-rated health, alcohol consumption and smoking status were measured at the baseline survey of each dataset. Education was registered as the highest completed degree up to the end of 2019. Depression was a composite of survey self-report (at the time of the baseline survey), as well as depression-related medicine purchases and hospitalizations over a two-year period before the start of the individual’s follow-up.

      We have added more comprehensive information on the measurement of the phenotypes of interest in Supplementary table 2, including the timing of the measurement.

    1. Author response:

      Point-by-point description of the revisions:

      Reviewer #1 (Evidence, reproducibility and clarity):

      Summary

      In this article, the authors used the synthetic TALE DNA binding proteins, tagged with YFP, which were designed to target five specific repeat elements in Trypanosoma brucei genome, including centromere and telomeres-associated repeats and those of a transposon element. This is in order to detect and identified, using YFP-pulldown, specific proteins that bind to these repetitive sequences in T. brucei chromatin. Validation of the approach was done using a TALE protein designed to target the telomere repeat (TelR-TALE) that detected many of the proteins that were previously implicated with telomeric functions. A TALE protein designed to target the 70 bp repeats that reside adjacent to the VSG genes (70R-TALE) detected proteins that function in DNA repair and the protein designed to target the 177 bp repeat arrays (177R-TALE) identified kinetochore proteins associated T. brucei mega base chromosomes, as well as in intermediate and mini-chromosomes, which imply that kinetochore assembly and segregation mechanisms are similar in all T. brucei chromosome.

      Major comments:

      Are the key conclusions convincing?

      The authors reported that they have successfully used TALE-based affinity selection of proteinassociated with repetitive sequences in the T. brucei genome. They claimed that this study has provided new information regarding the relevance of the repetitive region in the genome to chromosome integrity, telomere biology, chromosomal segregation and immune evasion strategies. These conclusions are based on high-quality research, and it is, basically, merits publication, provided that some major concerns, raised below, will be addressed before acceptance for publication.

      (1) The authors used TALE-YFP approach to examine the proteome associated with five different repetitive regions of the T. brucei genome and confirmed the binding of TALE-YFP with Chip-seq analyses. Ultimately, they got the list of proteins that bound to synthetic proteins, by affinity purification and LS-MS analysis and concluded that these proteins bind to different repetitive regions of the genome. There are two control proteins, one is TRF-YFP and the other KKT2-YFP, used to confirm the interactions. However, there are no experiment that confirms that the analysis gives some insight into the role of any putative or new protein in telomere biology, VSG gene regulation or chromosomal segregation. The proteins, which have already been reported by other studies, are mentioned. Although the author discovered many proteins in these repetitive regions, their role is yet unknown. It is recommended to take one or more of the new putative proteins from the repetitive elements and show whether or not they (1) bind directly to the specific repetitive sequence (e.g., by EMSA); (2) it is recommended that the authors will knockdown of one or a small sample of the new discovered proteins, which may shed light on their function at the repetitive region, as a proof of concept.

      The main request from Referee 1 is for individual evaluation of protein-DNA interaction for a few candidates identified in our TALE-YFP affinity purifications, particularly using EMSA to identify binding to the DNA repeats used for the TALE selection. In our opinion, such an approach would not actually provide the validation anticipated by the reviewer. The power of TALE-YFP affinity selection is that it enriches for protein complexes that associate with the chromatin that coats the target DNA repetitive elements rather than only identifying individual proteins or components of a complex that directly bind to DNA assembled in chromatin.

      The referee suggests we express recombinant proteins and perform EMSA for selected candidates, but many of the identified proteins are unlikely to directly bind to DNA – they are more likely to associate with a combination of features present in DNA and/or chromatin (e.g. specific histone variants or histone post-translational modifications). Of course, a positive result would provide some validation but only IF the tested protein can bind DNA in isolation – thus, a negative result would be uninformative.

      In fact, our finding that KKT proteins are enriched using the 177R-TALE (minichromosome repeat sequence) identifies components of the trypanosome kinetochore known (KKT2) or predicted (KKT3) to directly bind DNA (Marciano et al., 2021; PMID: 34081090), and likewise the TelR-TALE identifies the TRF component that is known to directly associate with telomeric (TTAGGG)n repeats (Reis et al 2018; PMID: 29385523). This provides reassurance on the specificity of the selection, as does the lack of cross selectivity between different TALEs used (see later point 3 below). The enrichment of the respective DNA repeats quantitated in Figure 2B (originally Figure S1) also provides strong evidence for TALE selectivity.

      It is very likely that most of the components enriched on the repetitive elements targeted by our TALE-YFP proteins do not bind repetitive DNA directly. The TRF telomere binding protein is an exception – but it is the only obvious DNA binding protein amongst the many proteins identified as being enriched in our TelR-TALE-YFP and TRF-YFP affinity selections.

      The referee also suggests that follow up experiments using knockdown of the identified proteins found to be enriched on repetitive DNA elements would be informative. In our opinion, this manuscript presents the development of a new methodology previously not applied to trypanosomes, and referee 2 highlights the value of this methodological development which will be relevant for a large community of kinetoplastid researchers. In-depth follow-up analyses would be beyond the scope of this current study but of course will be pursued in future. To be meaningful such knockdown analyses would need to be comprehensive in terms of their phenotypic characterisation (e.g. quantitative effects on chromosome biology and cell cycle progression, rates and mechanism of recombination underlying antigenic variation, etc) – simple RNAi knockdowns would provide information on fitness but little more. This information is already publicly available from genome-wide RNAi screens (www.tritrypDB.org), with further information on protein location available from the genome-wide protein localisation resource (Tryptag.org). Hence basic information is available on all targets selected by the TALEs after RNAi knock down but in-depth follow-up functional analysis of several proteins would require specific targeted assays beyond the scope of this study.

      (2) NonR-TALE-YFP does not have a binding site in the genome, but YFP protein should still be expressed by T. brucei clones with NLS. The authors have to explain why there is no signal detected in the nucleus, while a prominent signal was detected near kDNA (see Fig.2). Why is the expression of YFP in NonR-TALE almost not shown compared to other TALE clones?

      The NonR-TALE-YFP immunolocalisation signal indeed is apparently located close to the kDNA and away from the nucleus. We are not sure why this is so, but the construct is sequence validated and correct. However, we note that artefactual localisation of proteins fused to a globular eGFP tag, compared to a short linear epitope V5 tag, near to the kinetoplast has been previously reported (Pyrih et al, 2023; PMID: 37669165).

      The expression of NonR-TALE-YFP is shown in Supplementary Fig. S2 in comparison to other TALE proteins. Although it is evident that NonR-TALE-YFP is expressed at lower levels than other TALEs (the different TALEs have different expression levels), it is likely that in each case the TALE proteins would be in relative excess.

      It is possible that the absence of a target sequence for the NonR-TALE-YFP in the nucleus affects its stability and cellular location. Understanding these differences is tangential to the aim of this study.

      However, importantly, NonR-TALE-YFP is not the only control for used for specificity in our affinity purifications. Instead, the lack of cross-selection of the same proteins by different TALEs (e.g. TelR-TALE-YFP, 177R-TALE-YFP) and the lack of enrichment of any proteins of interest by the well expressed ingiR-TALE-YFP or 147R-TALE-YFP proteins each provide strong evidence for the specificity of the selection using TALEs, as does the enrichment of similar protein sets following affinity purification of the TelR-TALE-YFP and TRF-YFP proteins which both bind telomeric (TTAGGG)n repeats. Moreover, control affinity purifications to assess background were performed using cells that completely lack an expressed YFP protein which further support specificity (Figure 6).

      We have added text to highlight these important points in the revised manuscript:

      Page 8:

      “However, the expression level of NonR-TALE-YFP was lower than other TALE-YFP proteins; this may relate to the lack of DNA binding sites for NonR-TALE-YFP in the nucleus.”

      Page 8:

      “NonR-TALE-YFP displayed a diffuse nuclear and cytoplasmic signal; unexpectedly the cytoplasmic signal appeared to be in the vicinity the kDNA of the kinetoplast (mitochrondria). We note that artefactual localisation of some proteins fused to an eGFP tag has previously been observed in T. brucei (Pyrih et al, 2023).”

      Page 10:

      Moreover, a similar set of enriched proteins was identified in TelR-TALE-YFP affinity purifications whether compared with cells expressing no YFP fusion protein (No-YFP), the NonR-TALE-YFP or the ingiR-TALE-YFP as controls (Fig. S7B, S8A; Tables S3, S4). Thus, the most enriched proteins are specific to TelR-TALE-YFP-associated chromatin rather than to the TALE-YFP synthetic protein module or other chromatin.

      (3) As a proof of concept, the author showed that the TALE method determined the same interacting partners enrichment in TelR-TALE as compared to TRF-YFP. And they show the same interacting partners for other TALE proteins, whether compared with WT cells or with the NonR-TALE parasites. It may be because NonR-TALE parasites have almost no (or very little) YFP expression (see Fig. S3) as compared to other TALE clones and the TRF-YFP clone. To address this concern, there should be a control included, with proper YFP expression.

      See response to point 2, but we reiterate that the ingi-TALE -YFP and 147R-TALE-YFP proteins are well expressed (western original Fig. S3 now Fig. S2) but few proteins are detected as being enriched or correspond to those enriched in TelR-TALE-YFP or TRF-YFP affinity purifications (see Fig. S9). Therefore, the ingi-TALE -YFP and 147R-TALE-YFP proteins provide good additional negative controls for specificity as requested. To further reassure the referee we have also included additional volcano plots which compare TelR-TALE-YFP, 70R-TALE-YFP or 177R-TALE-YFP to the ingiR-TALE-YFP affinity selection (new Figure S8). As with No-YFP or NonR-TALE-YFP controls, the use of ingiR-TALE-YFP as a negative control demonstrates that known telomere associated proteins are enriched in TelR-TALE-YFP affinity purification, RPA subunits enriched with 70R-TALE-YFP and Kinetochore KKT poroteins enriched with 177RTALE-YFP. These analyses demonstrate specificity in the proteins enriched following affinity purification of our different TALE-YFPs and provide support to strengthen our original findings.

      We now refer to use of No-YFP, NonR-TALE-YFP, and ingiR-TALE -YFP as controls for comparison to TelR-TALE-YFP, 70R-TALE-YFP or 177R-TALE-YFP in several places:

      Page10:

      “Moreover, a similar set of enriched proteins was identified in TelR-TALE-YFP affinity purifications whether compared with cells expressing no YFP fusion protein (No-YFP), the NonR-TALE-YFP or the ingiR-TALE-YFP as controls (Fig. S7B, S8A; Tables S3, S4).”

      Page 11:

      “Thus, the nuclear ingiR-TALE-YFP provides an additional chromatin-associated negative control for affinity purifications with the TelR-TALE-YFP, 70R-TALE-YFP and 177R-TALE-YFP proteins (Fig. S8).”

      “Proteins identified as being enriched with 70R-TALE-YFP (Figure 6D) were similar in comparisons with either the No-YFP, NonR-TALE-YFP or ingiR-TALE-YFP as negative controls.”

      Top Page 12:

      “The same kinetochore proteins were enriched regardless of whether the 177R-TALE proteomics data was compared with No-YFP, NonR-TALE or ingiR-TALE-YFP controls.”

      Discussion Page 13:

      “Regardless, the 147R-TALE and ingiR-TALE proteins were well expressed in T. brucei cells, but their affinity selection did not significantly enrich for any relevant proteins. Thus, 147R-TALE and ingiR-TALE provide reassurance for the overall specificity for proteins enriched TelR-TALE, 70R-TALE and 177R-TALE affinity purifications.”

      (4) After the artificial expression of repetitive sequence binding five-TALE proteins, the question is if there is any competition for the TALE proteins with the corresponding endogenous proteins? Is there any effect on parasite survival or health, compared to the control after the expression of these five TALEs YFP protein? It is recommended to add parasite growth curves, for all the TALE proteins expressing cultures.

      Growth curves for cells expressing TelR-TALE-YFP, 177R-TALE-YFP and ingiR-TALE-YFP are now included (New Fig S3A). No deficit in growth was evident while passaging 70R-TALE-YFP, 147R-TALE-YFP, NonR-TALE-YFP cell lines (indeed they grew slightly better than controls).

      The following text has been added page 8:

      “Cell lines expressing representative TALE-YFP proteins displayed no fitness deficit (Fig. S3A).”

      (5) Since the experiments were performed using whole-cell extracts without prior nuclear fractionation, the authors should consider the possibility that some identified proteins may have originated from compartments other than the nucleus. Specifically, the detection of certain binding proteins might reflect sequence homology (or partial homology) between mitochondrial DNA (maxicircles and minicircles) and repetitive regions in the nuclear genome. Additionally, the lack of subcellular separation raises the concern that cytoplasmic proteins could have been co-purified due to whole cell lysis, making it challenging to discern whether the observed proteome truly represents the nuclear interactome.

      In our experimental design, we confirmed bioinformatically that the repeat sequences targeted were not represented elsewhere in the nuclear or mitochondrial genome (kDNA). The absence of subcellular fractionation could result in some cytoplasmic protein selection, but this is unlikely since each TALE targets a specific DNA sequence but is otherwise identical such that cross-selection of the same contaminating protein set would be anticipated if there was significant non-specific binding. We have previously successfully affinity selected 15 chromatin modifiers and identified associated proteins without major issues concerning cytoplasmic protein contamination (Staneva et al 2021 and 2022; PMID: 34407985 and 36169304). Of course, the possibility that some proteins are contaminants will need to be borne in mind in any future follow-up analysis of proteins of interest that we identified as being enriched on specific types of repetitive element in T. brucei. Proteins that are also detected in negative control, or negative affinity selections such as No-YFP, NoR-YFP, IngiR-TALE or 147R-TALE must be disregarded.

      (6) Should the authors qualify some of their claims as preliminary or speculative, or remove them altogether?

      As mentioned earlier, the author claimed that this study has provided new information concerning telomere biology, chromosomal segregation mechanisms, and immune evasion strategies. But there are no experiments that provides a role for any unknown or known protein in these processes. Thus, it is suggested to select one or two proteins of choice from the list and validate their direct binding to repetitive region(s), and their role in that region of interaction.

      As highlighted in response to point 1 the suggested validation and follow up experiments may well not be informative and are beyond the scope of the methodological development presented in this manuscript. Referee 2 describes the study in its current form as “a significant conceptual and technical advancement” and “This approach enhances our understanding of chromatin organization in these regions and provides a foundation for investigating the functional roles of associated proteins in parasite biology.”

      The Referee’s phrase ‘validate their direct binding to repetitive region(s)’ here may also mean to test if any of the additional proteins that we identified as being enriched with a specific TALE protein actually display enrichment over the repeat regions when examined by an orthogonal method. A key unexpected finding was that kinetochore proteins including KKT2 are enriched in our affinity purifications of the 177R-TALE-YFP that targets 177bp repeats (Figure 6F). By conducting ChIP-seq for the kinetochore specific protein KKT2 using YFP-KKT2 we confirmed that KKT2 is indeed enriched on 177bp repeat DNA but not flanking DNA (Figure 7). Moreover, several known telomere-associated proteins are detected in our affinity selections of TelRTALE-YFP (Figure 6B, FigS6; see also Reis et al, 2018 Nuc. Acids Res. PMID: 29385523; Weisert et al, 2024 Sci. Reports PMID: 39681615).

      Would additional experiments be essential to support the claims of the paper? Request additional experiments only where necessary for the paper as it is, and do not ask authors to open new lines of experimentation.

      The answer for this question depends on what the authors want to present as the achievements of the present study. If the achievement of the paper was is the creation of a new tool for discovering new proteins, associated with the repeat regions, I recommend that they add a proof for direct interactions between a sample the newly discovered proteins and the relevant repeats, as a proof of concept discussed above, However, if the authors like to claim that the study achieved new functional insights for these interactions they will have to expand the study, as mentioned above, to support the proof of concept.

      See our response to point 1 and the point we labelled ‘6’ above.

      Are the suggested experiments realistic in terms of time and resources? It would help if you could add an estimated cost and time investment for substantial experiments.

      I think that they are realistic. If the authors decided to check the capacity of a small sample of proteins (which was unknown before as a repetitive region binding proteins) to interacts directly with the repeated sequence, it will substantially add of the study (e.g., by EMSA; estimated time: 1 months). If the authors will decide to check the also the function of one of at least one such a newly detected proteins (e.g., by KD), I estimate the will take 3-6 months.

      As highlighted previously the proposed EMSA experiment may well be uninformative for protein complex components identified in our study or for isolated proteins that directly bind DNA in the context of a complex and chromatin. RNAi knockdown data and cell location data (as well as developmental expression and orthology data) is already available through tritrypDB.org and trtyptag.org

      Are the data and the methods presented in such a way that they can be reproduced? Yes

      Are the experiments adequately replicated, and statistical analysis adequate?

      The authors did not mention replicates. There is no statistical analysis mentioned.

      The figure legends indicate that all volcano plots of TALE affinity selections were derived from three biological replicates. Cutoffs used for significance: P < 0.05 (Student's t-test).

      For ChiP-seq two biological replicates were analysed for each cell line expressing the specific YFP tagged protein of interest (TALE or KKT2). This is now stated in the relevant figure legends – apologies for this oversight. The resulting data are available for scrutiny at GEO: GSE295698.

      Minor comments:

      Specific experimental issues that are easily addressable.

      The following suggestions can be incorporated:

      (1) Page 18, in the material method section author mentioned four drugs: Blasticidine, Phleomycin and G418, and hygromycin. It is recommended to mention the purpose of using these selective drugs for the parasite. If clonal selection has been done, then it should also be mentioned.

      We erroneously added information on several drugs used for selection in our labaoratory. In fact all TALE-YFP construct carry the Bleomycin resistance genes which we select for using Phleomycin. Also, clones were derived by limiting dilution immediately after transfection. We have amended the text accordingly:

      Page 17/18:

      “Cell cultures were maintained below 3 x 106 cells/ml. Pleomycin 2.5 µg/ml was used to select transformants containing the TALE construct BleoR gene.”

      “Electroporated bloodstream cells were added to 30 ml HMI-9 medium and two 10-fold serial dilutions were performed in order to isolate clonal Pleomycin resistant populations from the transfection. 1 ml of transfected cells were plated per well on 24-well plates (1 plate per serial dilution) and incubated at 37°C and 5% CO2 for a minimum of 6 h before adding 1 ml media containing 2X concentration Pleomycin (5 µg/ml) per well.”

      (2) In the method section the authors mentioned that there is only one site for binding of NonR-TALE in the parasite genome. But in Fig. 1C, the authors showed zero binding site. So, there is one binding site for NonR-TALE-YFP in the genome or zero?

      We thank the reviewer for pointing out this discrepancy. We have checked the latest Tb427v12 genome assembly for predicted NonR-TALE binding sites and there are no exact matches. We have corrected the text accordingly.

      Page 7:

      “A control NonR-TALE protein was also designed which was predicted to have no target sequence in the T. brucei genome.”

      Page 17:

      “A control NonR-TALE predicted to have no recognised target in the T. brucei geneome was designed as follows: BLAST searches were used to identify exact matches in the TREU927 reference genome. Candidate sequences with one or more match were discarded.”

      (3) The authors used two different anti-GFP antibodies, one from Roche and the other from Thermo Fisher. Why were two different antibodies used for the same protein?

      We have found that only some anti-GFP antibodies are effective for affinity selection of associated proteins, whereas others are better suited for immunolocalisation. The respective suppliers’ antibodies were optimised for each application.

      (4) Page 6: in the introduction, the authors give the number of total VSG genes as 2,634. Is it known how many of them are pseudogenes?

      This value corresponds to the number reported by Consentino et al. 2021 (PMID: 34541528) for subtelomeric VSGs, which is similar to the value reported by Muller et al 2018 (PMID: 30333624) (2486), both in the same strain of trypanosomes as used by us. Based on the earlier analysis by Cross et al (PMID: 24992042), 80% of the identified VSGs in their study (2584) are pseudogenes. This approximates to the estimation by Consentino of 346/2634 (13%) being fully functional VSG genes at subtelomeres, or 17% when considering VSGs at all genomic locations (433/2872).

      (5) I found several typos throughout the manuscript.

      Thank you for raising this, we have read through the manuscipt several times and hopefully corrected all outstanding typos.

      (6) Fig. 1C: Table: below TOTAL 2nd line: the number should be 1838 (rather than 1828)

      Corrected- thank you.

      - Are prior studies referenced appropriately? Yes

      - Are the text and figures clear and accurate? Yes

      - Do you have suggestions that would help the authors improve the presentation of their data and conclusions? Suggested above

      Reviewer #1 (Significance):

      Describe the nature and significance of the advance (e.g., conceptual, technical, clinical) for the field:

      This study represents a significant conceptual and technical advancement by employing a synthetic TALE DNA-binding protein tagged with YFP to selectively identify proteins associated with five distinct repetitive regions of T. brucei chromatin. To the best of my knowledge, it is the first report to utilize TALE-YFP for affinity-based isolation of protein complexes bound to repetitive genomic sequences in T. brucei. This approach enhances our understanding of chromatin organization in these regions and provides a foundation for investigating the functional roles of associated proteins in parasite biology. Importantly, any essential or unique interacting partners identified could serve as potential targets for therapeutic intervention.

      - Place the work in the context of the existing literature (provide references, where appropriate). I agree with the information that has already described in the submitted manuscript, regarding its potential addition of the data resulted and the technology established to the study of VSGs expression, kinetochore mechanism and telomere biology.

      - State what audience might be interested in and influenced by the reported findings. These findings will be of particular interest to researchers studying the molecular biology of kinetoplastid parasites and other unicellular organisms, as well as scientists investigating chromatin structure and the functional roles of repetitive genomic elements in higher eukaryotes.

      - (1) Define your field of expertise with a few keywords to help the authors contextualize your point of view. Protein-DNA interactions/ chromatin/ DNA replication/ Trypanosomes

      - (2) Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate. None

      Reviewer #2 (Evidence, reproducibility and clarity):

      Summary

      Carloni et al. comprehensively analyze which proteins bind repetitive genomic elements in Trypanosoma brucei. For this, they perform mass spectrometry on custom-designed, tagged programmable DNA-binding proteins. After extensively verifying their programmable DNA-binding proteins (using bioinformatic analysis to infer target sites, microscopy to measure localization, ChIP-seq to identify binding sites), they present, among others, two major findings: 1) 14 of the 25 known T. brucei kinetochore proteins are enriched at 177bp repeats. As T. brucei's 177bp repeatcontaining intermediate-sized and mini-chromosomes lack centromere repeats but are stable over mitosis, Carloni et al. use their data to hypothesize that a 'rudimentary' kinetochore assembles at the 177bp repeats of these chromosomes to segregate them. 2) 70bp repeats are enriched with the Replication Protein A complex, which, notably, is required for homologous recombination. Homologous recombination is the pathway used for recombination-based antigenic variation of the 70bp-repeat-adjacent variant surface glycoproteins.

      Major Comments

      None. The experiments are well-controlled, claims well-supported, and methods clearly described. Conclusions are convincing.

      Thank you for these positive comments.

      Minor Comments

      (1) Fig. 2 - I couldn't find an uncropped version showing multiple cells. If it exists, it should be linked in the legend or main text; Otherwise, this should be added to the supplement.

      The images presented represent reproducible analyses, and independently verified by two of the authors. Although wider field of view images do not provide the resolution to be informative on cell location, as requested we have provided uncropped images in new Fig. S4 for all the cell lines shown in Figure 2A.

      In addition, we have included as supplementary images (Fig. S3B) additional images of TelRTALE-YFP, 177R-TALE-YFP and ingiR-TALE YFP localisation to provide additional support their observed locations presented in Figure 1. The set of cells and images presented in Figure 2A and in Fig S3B were prepared and obtained by a different authors, independently and reproducibly validating the location of the tagged protein.

      (2) I think Suppl. Fig. 1 is very valuable, as it is a quantification and summary of the ChIP-seq data. I think the authors could consider making this a panel of a main figure. For the main figure, I think the plot could be trimmed down to only show the background and the relevant repeat for each TALE protein, leaving out the non-target repeats. (This relates to minor comment 6.) Also, I believe, it was not explained how background enrichment was calculated.

      We are grateful for the reviewer’s positive view of original Fig. S1 and appreciate the suggestion. We have now moved these analysis to part B of main Figure 2 in the revised manuscript – now Figure 2B. We have also provided additional details in the Methods section on the approaches used to assess background enrichment.

      Page 19:

      “Background enrichment calculation

      The genome was divided into 50 bp sliding windows, and each window was annotated based on overlapping genomic features, including CIR147, 177 bp repeats, 70 bp repeats, and telomeric (TTAGGG)n repeats. Windows that did not overlap with any of these annotated repeat elements were defined as "background" regions and used to establish the baseline ChIP-seq signal. Enrichment for each window was calculated using bamCompare, as log₂(IP/Input). To adjust for background signal amongst all samples, enrichment values for each sample were further normalized against the corresponding No-YFP ChIP-seq dataset.”

      Note: While revising the manuscript we also noticed that the script had a nomalization error. We have therefore included a corrected version of these analyses as Figure 2B (old Fig. S1)

      (3) Generally, I would plot enrichment on a log2 axis. This concerns several figures with ChIP-seq data.

      Our ChIP-seq enrichment is calculated by bamCompare. The resulting enrichment values are indeed log2 (IP/Input). We have made this clear in the updated figures/legends.

      (4) Fig. 4C - The violin plots are very hard to interpret, as the plots are very narrow compared to the line thickness, making it hard to judge the actual volume. For example, in Centromere 5, YFP-KKT2 is less enriched than 147R-TALE over most of the centromere with some peaks of much higher enrichment (as visible in panel B), however, in panel C, it is very hard to see this same information. I'm sure there is some way to present this better, either using a different type of plot or by improving the spacing of the existing plot.

      We thank the reviewer for this suggestion; we have elected to provide a Split-Violin plot instead. This improves the presentation of the data for each centromere. The original violin plot in Figure 4C has been replaced with this Split-Violin plot (still Figure 4C).

      (5) Fig. 6 - The panels are missing an x-axis label (although it is obvious from the plot what is displayed).

      Maybe the "WT NO-YFP vs" part that is repeated in all the plot titles could be removed from the title and only be part of the x-axis label?

      In fact, to save space the X axis was labelled inside each volcano plot but we neglected to indicate that values are a log2 scale indicating enrichment. This has been rectified – see Figure 6, and Fig. S7, S8 and S9.

      (6) Fig. 7 - I would like to have a quantification for the examples shown here. In fact, such a quantification already exists in Suppl. Figure 1. I think the relevant plots of that quantification (YFPKKT2 over 177bp-repeats and centromere-repeats) with some control could be included in Fig. 7 as panel C. This opportunity could be used to show enrichment separated out for intermediate-sized, mini-, and megabase-chromosomes. (relates to minor comment 2 & 8)

      The CIR147 sequence is found exclusively on megabase-sized chromosomes, while the 177 bp repeats are located on intermediate- and mini-sized chromosomes. Due to limitations in the current genome assembly, it is not possible to reliably classify all chromosomes into intermediate- or mini- sized categories based on their length. Therefore, original Supplementary Fig. S1 presented the YFP-KKT2 enrichment over CIR147 and 177 bp repeats as a representative comparison between megabase chromosomes and the remaining chromosomes (corrected version now presented as main Figure 2B). Additionally, to allow direct comparison of YFP-KKT2 enrichment on CIR147 and 177 bp repeats we have included a new plot in Figure 7C which shows the relative enrichment of YFP-KKT2 on these two repeat types.

      We have added the following text , page 12:

      “Taking into account the relative to the number of CIR147 and 177 bp repeats in the current T.brucei genome (Cosentino et al., 2021; Rabuffo et al., 2024), comparative analyses demonstrated that YFP-KKT2 is enriched on both CIR147 and 177 bp repeats (Figure 7C).”

      (7) Suppl. Fig. 8 A - I believe there is a mistake here: KKT5 occurs twice in the plot, the one in the overlap region should be KKT1-4 instead, correct?

      Thanks for spotting this. It has been corrected

      (8) The way that the authors mapped ChIP-seq data is potentially problematic when analyzing the same repeat type in different regions of the genome. The authors assigned reads that had multiple equally good mapping positions to one of these mapping positions, randomly.

      This is perfectly fine when analysing repeats by their type, independent of their position on the genome, which is what the authors did for the main conclusions of the work.

      However, several figures show the same type of repeat at different positions in the genome. Here, the authors risk that enrichment in one region of the genome 'spills' over to all other regions with the same sequence. Particularly, where they show YFP-KKT2 enrichment over intermediate- and mini-chromosomes (Fig. 7) due to the spillover, one cannot be sure to have found KKT2 in both regions.

      Instead, the authors could analyze only uniquely mapping reads / read-pairs where at least one mate is uniquely mapping. I realize that with this strict filtering, data will be much more sparse. Hence, I would suggest keeping the original plots and adding one more quantification where the enrichment over the whole region (e.g., all 177bp repeats on intermediate-/mini-chromosomes) is plotted using the unique reads (this could even be supplementary). This also applies to Fig. 4 B & C.

      We thank the reviewer for their thoughtful comments. Repetitive sequences are indeed challenging to analyze accurately, particularly in the context of short read ChIP-seq data. In our study, we aimed to address YFP-KKT2 enrichment not only over CIR147 repeats but also on 177 bp repeats, using both ChIP-seq and proteomics using synthetic TALE proteins targeted to the different repeat types. We appreciate the referees suggestion to consider uniquely mapped reads, however, in the updated genome assembly, the 177 bp repeats are frequently immediately followed by long stretches of 70 bp repeats which can span several kilobases. The size and repetitive nature of these regions exceeds the resolution limits of ChIP-seq. It is therefore difficult to precisely quantify enrichment across all chromosomes.

      Additionally, the repeat sequences are highly similar, and relying solely on uniquely mapped reads would result in the exclusion of most reads originating from these regions, significantly underestimating the relative signals. To address this, we used Bowtie2 with settings that allow multi-mapping, assigning reads randomly among equivalent mapping positions, but ensuring each read is counted only once. This approach is designed to evenly distribute signal across all repetitive regions and preserve a meaningful average.

      Single molecule methods such as DiMeLo (Altemose et al. 2022; PMID: 35396487) will need to be developed for T. brucei to allow more accurate and chromosome specific mapping of kinetochore or telomere protein occupancy at repeat-unique sequence boundaries on individual chromosomes.

      Reviewer #2 (Significance):

      This work is of high significance for chromosome/centromere biology, parasitology, and the study of antigenic variation. For chromosome/centromere biology, the conceptual advancement of different types of kinetochores for different chromosomes is a novelty, as far as I know. It would certainly be interesting to apply this study as a technical blueprint for other organisms with minichromosomes or chromosomes without known centromeric repeats. I can imagine a broad range of labs studying other organisms with comparable chromosomes to take note of and build on this study. For parasitology and the study of antigenic variation, it is crucial to know how intermediate- and mini-chromosomes are stable through cell division, as these chromosomes harbor a large portion of the antigenic repertoire. Moreover, this study also found a novel link between the homologous repair pathway and variant surface glycoproteins, via the 70bp repeats. How and at which stages during the process, 70bp repeats are involved in antigenic variation is an unresolved, and very actively studied, question in the field. Of course, apart from the basic biological research audience, insights into antigenic variation always have the potential for clinical implications, as T. brucei causes sleeping sickness in humans and nagana in cattle. Due to antigenic variation, T. brucei infections can be chronic.

      Thank you for supporting the novelty and broad interest of our manuscript

      My field of expertise / Point of view:

      I'm a computer scientist by training and am now a postdoctoral bioinformatician in a molecular parasitology laboratory. The laboratory is working on antigenic variation in T. brucei. The focus of my work is on analyzing sequencing data (such as ChIP-seq data) and algorithmically improving bioinformatic tools.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors assess the role of map3k1 in adult Planaria through whole body RNAi for various periods of time. The authors' prior work has shown that neoblasts (stem cells that can regenerate the entire body) for various tissues are intermingled in the body. Neoblasts divide to produce progenitors that migrate within a "target zone" to the "differentiated target tissues" where they differentiate into a specific cell type. Here the authors show that map3k1-i animals have ectopic eyes that form along the "normal" migration path of eye progenitors (Fig. 1), ectopic neurons and glands along the AP axis (Fig. 2) and pharynx in ectopic anterior positions (Fig. 3). The rest of the study show that positional information is largely unaffected by loss of map3k1 (Fig. 4,5). However, loss of map3k1 leads to premature differentiated of progenitors along their normal migratory route (Fig. 6). They also show that an ill-defined "long-term" whole body depletion of map3k1 results in mis-specified organs and teratomas.

      Strengths:

      (1) The study has appropriate controls, sample sizes and statistics.

      (2) The work appears to be high-quality.

      (3) The conclusions are supported by the data.

      (4) Planaria is a good system to analyze the function of map3k1, which exists in mammals but not in other invertebrates.

      Weaknesses:

      (1) The paper is largely descriptive with no mechanistic insights. 

      The mechanistic insights we aim to address are primarily at the cellular systems level – how adult progenitor cells produce pattern. Specifically, we uncovered strong evidence that regulation of differentiation is an active process occurring in migratory progenitors and that this regulation is a major component of pattern formation during the adult processes of tissue turnover and regeneration. The map3k1 phenotype provided a tool used to reveal the existence of this regulation, and to understand the patterning abnormalities prevented by this regulatory mechanism. We updated the text in several places to make clearer some of this emphasis. For example, in the Discussion: "We suggest that differentiation is restricted during migratory targeting as an essential component of pattern formation, with the map3k1 RNAi phenotype indicating the existence and purpose of this element of patterning." 

      Naturally, identifying a particular molecule involved in this process is of interest for understanding molecular mechanism; this would allow for comparison to other cellular systems in other organisms and would focus future molecular inquiry. Future molecular studies into the mechanism of Map3k1 regulation and its downstream signaling will be fascinating as next steps towards understanding the process at the molecular level more deeply. We also added some discussion considering the types of upstream activation cues that could potentially be associated with Map3k1 regulation to suppress differentiation. 

      (2) Given the severe phenotypes of long-term depletion of map3k1, it is important that this exact timepoint is provided in the methods, figures, figure legends and results. 

      We removed the use of the term “long-term” and instead added timepoints used to all figure legends. We also added a summary of timepoints used in the methods section and included RNAi timepoint labels in figures where a phenotype progression over time is relevant to interpretation. For timecourses, we also added suitable time information to text in the results. 

      (3) Figure 1C, the ectopic eyes are difficult to see, please add arrows. 

      To improve visualization, we replaced the example animal in the original Figure 1C with one that has a stronger phenotype, including arrows pointing to every ectopic event. Additionally, we included magnified images of optic cup cells and photoreceptor neurons in the trunk and tail region. This is now Figure 1B.

      (4) line 217 - why does the n=2/12 animals not match the values in Figure 3B, which is 11/12 and 12/12. The numbers don't add up. Please correct/explain. 

      In Figure 3B in the submitted version (3/18 had cells in the tail) had more animals scored (6 animals from a replicate experiment where 1/6 showed the cells in the tail) than the total scored (2/12 had cells in the tail) in the text, which did not have the animals from the replicate added during writing. The results are the same, just different sample sizes were noted in those locations and we fixed this issue. In the updated Figure 3, the order of presentation has shifted (e.g., prior 3B is now in 3C and Figure 3_figure supplement 1). We made sure to include numbers to all figure panels. 

      (5) Figure panels do not match what is written in the results section. There is no Figure 6E. Please correct.

      Thank you for catching this. We have gone through figures and text after editing to make sure that text callouts are appropriately matched to the figures. 

      Reviewer #2 (Public review):

      Summary:

      The flatworm planarian Schmidtea mediterranea is an excellent model for understanding cell fate specification during tissue regeneration and adult tissue maintenance. Planarian stem cells, known as neoblasts, are continuously deployed to support cellular turnover and repair tissues damaged or lost due to injury. This reparative process requires great precision to recognize the location, timing, and cellular fate of a defined number of neoblast progeny. Understanding the molecular mechanisms driving this process could have important implications for regenerative medicine and enhance our understanding of how form and function are maintained in long-lived organisms such as humans. Unfortunately, the molecular basis guiding cell fate and differentiation remains poorly understood.

      In this manuscript, Canales et al. identified the role of the map3k1 gene in mediating the differentiation of progenitor cells at the proper target tissue. The map3k1 function in planarians appears evolutionarily conserved as it has been implicated in regulating cell proliferation, differentiation, and cell death in mammals. The results show that the downregulation of map3k1 with RNAi leads to spatial patterning defects in different tissue types, including the eye, pharynx, and the nervous system. Intriguingly, long-term map3k1-RNAi resulted in ectopic outgrowths consistent with teratomas in planarians. The findings suggest that map3k1 mediates signaling, regulating the timing and location of cellular progenitors to maintain correct patterning during adult tissue maintenance.

      Strengths:

      The authors provide an entry point to understanding molecular mechanisms regulating progenitor cell differentiation and patterning during adult tissue maintenance.

      The diverse set of approaches and methods applied to characterize map3k1 function strengthens the case for conserved evolutionary mechanisms in a selected number of tissue types. The creativity using transplantation experiments is commendable, and the findings with the teratoma phenotype are intriguing and worth characterizing.

      Thank you to the reviewer for the positive feedback

      Weaknesses:

      The article presents a provocative idea related to the importance of positional control for organs and cells, which is at least in part regulated by map3k1. Nonetheless, the role of map3k1 or its potential interaction with regulators of the anterior-posterior, mediolateral axes, and PCGs is somewhat superficial. The authors could elaborate or even speculate more in the discussion section and the different scenarios incorporating these axial modulators into the map3k1 model presented in Figure 8 

      First, to strengthen the support for our finding that positional information is largely unaffected in map3k1 RNAi animals, we added data regarding the expression of additional relevant position control genes (PCGs) –ndl-4, ptk7, sp5, and wnt11-1 – to the PCG panel in Figure 5. The expression domain of ndl-4, an FGF receptor-like protein family member that contributes to head patterning and anterior pole maintenance, was normal in map3k1 RNAi. wnt11-1, a PCG with expression concentrated in the posterior end of the animal and with expression dependent on general Wnt activity, was also normal in map3k1 RNAi animals. ptk7, RNAi of which can result in supernumerary pharynges, also showed normal expression in map3k1 RNAi animals. Finally, sp5, a Wnt-activated gene with expression in the tail, also showed normal expression in map3k1 RNAi animals. 

      Second, to further support the conclusion that cells are not suitably responding to positional information after map3k1 RNAi, which we argue normally dictates where differentiation should occur, we added examples of differentiated cell types that are ectopically positioned within an atypical PCG expression domain for that cell type (Figure 5C). This underscores that following map3k1 RNAi the PCG expression domains do not change, but the pattern of differentiated cell types relative to these domains does shift. We also added data showing that regenerating tails had a proper wntP-2 gradient, but an anterior regenerating pharynx appeared outside of this wntP-2<sup>+</sup> zone and inside of an ndl-5<sup>+</sup> zone (Figure 5- figure supplement 1E). We added some discussion of these new data in the Figure 5 results section. We also noted, regarding independent recent map3k1 work (Lo, 2025), some evidence exists that a minor posterior shift in ndl-5 expression can occur after map3k1 RNAi.

      Next, we added a new element to the model figure (Figure 8B) depicting that PCG expression domains remain normal after map3k1 RNAi, with ectopic differentiation occurring in an incorrect positional information environment. We refer to this new panel in the discussion: "We suggest that map3k1 is not required for the spatial distribution of progenitor-extrinsic differentiation-promoting cues themselves, but for progenitors to be restricted from differentiating until these cues are received (Figure 8B)."; we then follow this statement with a summary in the Discussion of six pieces of evidence that support this model.

      Finally, we added some additional text to the discussion section about candidate mechanisms by which extrinsic cues could potentially regulate Map3k1, pointing to potential future inquiry directions. We suggest that map3k1 is not involved in regulating PCG activity domains themselves, but instead acts as a brake on differentiation within migratory progenitors through active signaling. This brake is then lifted when the progenitors hit their correct PCG-based migratory target, or when they hit their target tissue. How that occurs mechanistically is unknown. One scenario is that each progenitor is tuned to respond to a particular PCG-regulated environment (such as a particular ECM or signaling environment) to generate a molecular change that inactivates Map3K1 signaling, such as by inactivating or disengaging an RTK signal. Alternatively, the migratory process in progenitors could engage the Map3K1 signal, enabling signal cessation with arrival at a target location. When Map3K1 is active it could result in a transcriptional state that prevents full expression of differentiated factors required for maturation, tissue incorporation, and cessation of migration. These considerations are now added to the discussion.

      The article can be improved by addressing inconsistencies and adding details to the results, including the main figures and supplements. This represents one of the most significant weaknesses of this otherwise intriguing manuscript. Below are some examples of a few figures, but the authors are expected to pay close attention to the remaining figures in the paper.

      Details associated with the number of animals per experiment, statistical methods used, and detailed descriptions of figures appear inconsistent or lacking in almost all figures. In some instances, the percentage of animals affected by the phenotype is shown without detailing the number of animals in the experiment or the number of repeats. Figures and their legends throughout the paper lack details on what is represented and sometimes are mislabeled or unrelated. 

      We endeavored to ensure that these noted details are present throughout the legends and figures for all figure panels.

      Specifically, the arrows in Figure 1A are different colors. Still, no reasoning is given for this, and in the exact figure, the top side (1A) shows the percentages and the number of animals below. 

      The only reason for the different colored arrows was for visibility purposes. To avoid confusion, we now use white arrows for all FISH images in figure 1, and where ever else possible. We also replaced the percentages with n numbers in the bottom left corner of the live images in Figure 1A. 

      Conversely, in Figures 1B, C, and D, no details on the number of animals or percentages are shown, nor an explanation of why opsin was used in Figure 1A but not 1B. 

      The original Figure 1B represented a few different examples of ectopic eye/eye cell patterns in the map3k1 RNAi animals to demonstrate the variable and disorganized nature of the phenotype. To address this, we added further explanation in the legend. We also merged 1A and 1B for simplicity of interpretation. opsin was used in Figure 1A to label cell bodies of photoreceptors. anti-Arrestin was used in the example FISH images to see if these cells were interconnected via projections, which we now clarify in the legend and in the text. 

      Is Figure 1B missing an image for the respective control? Figure 1C needs details regarding what the two smaller boxes underneath are. 

      The control for Figure 1B was in Figure 1A; the merger of Figures 1A/B should address this. Boxes in Figure 1C were labelled with numbers corresponding to the image above them.

      Figure 1C could use an AP labeling map in 10 days (e.g., AP6 has one optic cup present). Figure 1C and F counts do not match. 

      We added a cartoon to 1C to show the region imaged. Note that the 36d trunk image (now Fig. 1B) has now been replaced with a full animal image and magnified boxes that show locations of example ectopic cells. That cell in 1C was categorized as in AP5. Note that additional animals were analyzed and data added to the distribution (now Fig. 1D). 

      In Figure 1C, we do not know the number of animals tested, controls used, the scale bar sizes in the first two images, nor the degree of magnification used despite the pharynx region appearing magnified in the second image.  Figure 1C is also shown out of chronological order; 36 days post RNAi is shown before 10 days post RNAi. Moreover, the legends for Figures 1C and 1D are swapped.

      We have endeavored to ensure sample numbers, control images, and appropriate scale bar notation in legends are present for all images. Figure 1C has now been split into two panels: Figure 1B and Figure 1C. It does not follow a chronological order in presentation for the following logic flow: we uncover and describe the phenotype; then, with knowledge of the defect, we walk back to see how early the phenotype starts after RNAi and what the pattern of ectopic cell distribution is when the phenotype starts to emerge (using the knowledge of which cells are affected from the overt phenotype described in 1A/B). 

      Additionally, Figure 1F and many other figures throughout the paper lack overall statistical considerations. Furthermore, Figure 1F has three components, but only one is labeled. Labeling each of them individually and describing them in the corresponding figure legend may be more appropriate.

      The main point of the graphs in 1F (now 1D) was the overt overall pattern difference with the wild-type, which never has ectopic eye cells in the midbody or tail, and that the ectopic eye cells progress throughout the entire AP axis. However, we concur that a statistical test is a reasonable thing to show here and that is now included in the legend. The 3 components (in Figure 1F, now Figure 1D) where kept together with one figure label (D) for simplicity, but were rearranged (top and bottom) with a cartoon to the side and with modified labeling for extra clarity. 

      Figure 2C shows images of gene expression for two genes, but the counts are shown for only one in Figure 2D. It is challenging to follow the author's conclusions without apparent reasoning and by only displaying quantitative considerations for one case but not the other. These inconsistencies are also observed in different figures. 

      In Figure 2C, FISH images of cintillo+ and dd_17258+ neurons are shown to display the specificity of this effect to some neurons and not others. Because cintillo+ cells did not expand at all (n=24/24 animals), the counts for them would all be zero values. We only counted data for dd_17258 cells because it was the neuron that expanded compared to the control animals. We have now added a note in the legend explaining this.

      In Figure 2D, 24/24 animals were reported to show the phenotype, but only eight were counted (is there a reason for this?).

      8 animals were used to quantitatively characterize the spread of cells along the AP axis, as it was deemed an adequate sample size to capture the change in distribution of 17258+ cells from being head restricted to being present throughout the body. Through multiple cohorts of animals in replicates, a total of 24/24 examined animals showed this expansion phenotype. Double FISH experiments were additionally carried out using dd_17258 and various PCGs; these data are now included in Figure 5C, and these animals were added to the total counts regarding quantitative analysis of the phenotype in Figure 2D. 

      In Figure 2E, the expression for three genes is shown, with some displaying anterior and posterior regions while others only show the anterior picture. Is there a particular reason for this? 

      The original first panel in Figure 2E showed an example of a non-expanding gland cell type, dd_9223, which is very restricted to the head in both control and map3k1 RNAi animals. Because we did not observe a phenotype for this cell type (no cells in all control and map3k1 RNAi animal tails), we only included tail images of cell types that showed an abnormal phenotype with clear expanded to the posterior (dd_8476 and dd_7131). However, we have now included tail images of dd_9223 cells and added data for dd_9223 to the graph in Figure 2E. 

      Also, in Figure 2F, the counts are shown for only the posterior region of two genes out of the three displayed in Figure 2E. It is unclear why the authors do not show counts for the anterior areas considered in Figure 2E. Furthermore, the legend for Figure 2D is missing, and the legend for 2F is mislabeled as a description for Figure 2D.

      We now include tail images for dd_9223 in Figure 2E to show that there are no ectopic cells in tails. We did not originally include counts of dd_9223 because there was no phenotype observed. dd_7131 and dd_8476 cell types appeared in the posterior of even control animals at a low frequency, unlike dd_9223 cells. However, we did now add counts for dd_9223 tail regions in the graph. We did not count the anterior regions of the animal because our goal was to show data for the visible phenotype (ectopic cells in the tail) not only with an example image, but also by showing the number of cells in the tail with a graph and statistical test. Legends have been updated with correct details.

      Supplement Figure 1 B reports data up to 6 weeks, but no text in the manuscript or supplement mentions any experiment going up to 6 weeks. There are no statistics for data in Supplement Figure 1E. Any significance between groups is unclear.

      More details about the RNAi feeding schedules have been added in the methods section. All RNAi timepoints are now specified specifically in the legends. The Figure 1F and Figure 1- figure supplement 1E (additional data: ovo<sup>+</sup>; smedwi-1<sup>-</sup> cell counts) and legends now mention the statistical tests performed and annotations (not significant *ns) or p values have been added to the graphs. For simplicity, we decided to include all smedwi-1+ counts together rather than splitting them into low and high smedwi-1+ cells, because we weren't really making any claims about low and high cells. 

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      It would be good to acknowledge in the discussion the recent paper from the Petersen lab on map3k1, published in PLoS Genet 2025, especially if the results differ between the two labs.

      We added reference/discussion regarding the recent PLoS Genetics Lo, 2025 map3k1 paper at several suitable points in the manuscript.

      Reviewer #2 (Recommendations for the authors):

      Please pay close attention to the description of experimental details and the consistency throughout the paper. It seems like the reader has to assume or come across information that is not readily available from the text or the legends in the paper. This is an interesting paper with intriguing findings. However, the version presented here appears rushed or put together on the flight.

      Thank you for your thorough feedback. We have endeavored to ensure all appropriate details are present in figures and/or figure legends.

    1. Author response:

      We thank all reviewers for their overall assessment, thoughtful comments, and suggestions. We are working to address each reviewer’s comment in detail. In this provisional response, we provide clarifications regarding our experimental approach and the novelty of our work, and include additional analyses that we have performed since the submission of the manuscript. We are also happy to report that we have now shared the raw data, intermediate analysis files, and the complete repository to facilitate replication of the analysis and figures.

      Code repo: github.com/LorenFrankLab/ms_stim_analysis

      Data repo: dandiarchive.org/dandiset/001634

      Docker containers (see GitHub repo for use instructions):

      Database: https://hub.docker.com/r/samuelbray32/spyglass-db-ms_stim_analysis

      Python notebooks: https://hub.docker.com/r/samuelbray32/spyglass-hub-ms_stim_analysis

      (1) Novelty and contrast with earlier manipulations:

      We thank the reviewers for suggesting that we explicitly contrast our results with prior pharmacological (Wang et al., 2016; Wang et al., 2015; Koenig et al., 2011; Brandon et al., 2014), systemic (Robbe & Buzsaki 2009; Petersen and Buzsáki 2020), and behavioral (Drieu et al., 2018) manipulations that also assessed some of the physiological features we evaluated. We will add a discussion of these studies, which will help us emphasize both the insights and discrepancies observed using these prior approaches. We will also more clearly explain the the novelty and importance of our specific approach for temporally and physiologically precise manipulation. Specifically, our approach (closed-loop theta-phase stimulation during locomotion) provides a level of physiological specificity that made it possible to dissociate theta-state dynamics from other hippocampal processes. This in turn allowed us to address a question that has remained unresolved across prior studies: Are hippocampal spatial sequences during locomotion (i.e., theta sequences) necessary to learn a novel hippocampal-dependent task?

      (2) Additional analysis on SWRs during rest:

      since submitting the manuscript, we have conducted additional analysis on the rate and length of SWRs in the rest box and found that their rate and length are also indistinguishable between targeted and control animals (effect of manipulation between control and targeted animals; rSWR rate: p=0.45; rSWR length: p=0.94, mixed effect model). We also find evidence for sequential neural representations in the rest box, when the encoding was performed in the behavioral arena. Example trajectories are shown below. These results are consistent with our observations on SWRs rate, length, and content in the behavioral arena. Additionally, we are in the process of evaluating and quantifying the results of decoding the rSWRs and will include those in the next version of the manuscript.

      Author response image 1.

      Sequential replay events observed in the rest box

      (3) Theta sequence measurement in the absence of theta:

      In the next version of the manuscript, we will explicitly explain why our manipulation makes it is more appropriate to measure sequential hippocampal representations during locomotion (i.e., theta sequences) without using theta oscillation or an epoch-averaged relatively large sliding window as a reference. The key insight here is that our manipulation suppresses theta and thus makes it difficult or impossible to accurately identify theta phase. We understand that theta-phase based approaches were used in prior work; however, these prior analyses may have confounded the absence of hippocampal theta sequences during locomotion by the inability to detect theta oscillatory phase reliably. We will show that our method of using clusterless Bayesian decoding in which we estimate the decoded position at every 2ms timestep is indeed able to capture endogenous hippocampal sequences even without imposing any requirements of aligning to theta oscillations, thus providing an unbiased estimate of the rhythmicity of hippocampal spatial representations.

      (4) Additional analysis on place cell stability and tuning:

      We thank the reviewer for this question. For the KL divergence analysis, we have imposed a spike-count criterion (100 spikes for each interval type —stimulation-off, stimulation-on, and the stimulus sub-interval) and a coverage criterion (50% HPD of the units’ spatial firing distribution was contained within 40cm on the linear track and 100cm on the w-track). These criteria were chosen to ensure that spatial tuning curves were sufficiently well sampled and localized to allow reliable estimation of KL divergence, which is particularly sensitive to noise arising from low spike counts or diffuse firing. Based on the reviewer’s suggestion, we have relaxed the unit inclusion criteria for KL divergence by relaxing the criteria for number of spikes and spatial coverage criterion to include more weakly tuned place cells and replicated our results (p=.146). Further, we have also evaluated the stability of place field order between stimulation-on and stimulation-off conditions using more standard methods (as in Wang et. al., 2015; spearman correlation of place field order, control vs targeted, p = .920, t-test). These results are consistent with our observations about place field stability during stimulation-off and stimulation-on conditions (Fig. 2F).

      Author response image 2.

      Spearman correlation of place field order during stimulation-on and stimulation-off conditions.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public reviews:

      Reviewer #1 (Public review):

      Summary: 

      The authors provide a resource to the systems neuroscience community, by offering their Python-based CLoPy platform for closed-loop feedback training. In addition to using neural feedback, as is common in these experiments, they include a capability to use real-time movement extracted from DeepLabCut as the control signal. The methods and repository are detailed for those who wish to use this resource. Furthermore, they demonstrate the efficacy of their system through a series of mesoscale calcium imaging experiments. These experiments use a large number of cortical regions for the control signal in the neural feedback setup, while the movement feedback experiments are analyzed more extensively.

      Strengths:

      The primary strength of the paper is the availability of their CLoPy platform. Currently, most closed-loop operant conditioning experiments are custom built by each lab and carry a relatively large startup cost to get running. This platform lowers the barrier to entry for closed-loop operant conditioning experiments, in addition to making the experiments more accessible to those with less technical expertise.

      Another strength of the paper is the use of many different cortical regions as control signals for the neurofeedback experiments. Rodent operant conditioning experiments typically record from the motor cortex and maybe one other region. Here, the authors demonstrate that mice can volitionally control many different cortical regions not limited to those previously studied, recording across many regions in the same experiment. This demonstrates the relative flexibility of modulating neural dynamics, including in non-motor regions.

      Finally, adapting the closed-loop platform to use real-time movement as a control signal is a nice addition. Incorporating movement kinematics into operant conditioning experiments has been a challenge due to the increased technical difficulties of extracting real-time kinematic data from video data at a latency where it can be used as a control signal for operant conditioning. In this paper they demonstrate that the mice can learn the task using their forelimb position, at a rate that is quicker than the neurofeedback experiments.

      Weaknesses:

      There are several weaknesses in the paper that diminish the impact of its strengths. First, the value of the CLoPy platform is not clearly articulated to the systems neuroscience community. Similarly, the resource could be better positioned within the context of the broader open-source neuroscience community. For an example of how to better frame this resource in these contexts, I recommend consulting the pyControl paper. Improving this framing will likely increase the accessibility and interest of this paper to a less technical neuroscience audience, for instance by highlighting the types of experimental questions CLoPy can enable.

      We appreciate the editor’s feedback regarding the clarity of the CLoPy platform's value and its positioning within the broader neuroscience community. We agree and understand the importance of effectively communicating the utility of CLoPy to both the systems neuroscience field and the wider open-source neuroscience community.

      To address this, we have revised the introduction and discussion sections of the manuscript to more clearly articulate the unique contributions of the CLoPy platform. Specifically:

      (1) We have emphasized how CLoPy can address experimental questions in systems neuroscience by highlighting its ability to enable real-time closed-loop experiments, such as investigating neural dynamics during behavior or studying adaptive cortical reorganization after injury. These examples are aimed at demonstrating its practical utility to the neuroscience audience.

      (2) We have positioned CLoPy within the broader open-source neuroscience ecosystem, drawing comparisons to similar resources like pyControl. We describe how CLoPy complements existing tools by focusing on real-time optical feedback and integration with genetically encoded indicators, which are becoming increasingly popular in systems neuroscience. We also emphasize its modularity and ease of adoption in experimental settings with limited resources.

      (3) To make the manuscript more accessible to a less technically inclined audience, we have restructured certain sections to focus on the types of experiments CLoPy enables, rather than the technical details of the implementation.

      We have consulted the pyControl paper, as suggested, and have used it as a reference point to improve the framing of our resource. We believe these changes will increase the accessibility and appeal of the paper to a broader neuroscience audience.

      While the dataset contains an impressive amount of animals and cortical regions for the neurofeedback experiment, and an analysis of the movement-feedback experiments, my excitement for these experiments is tempered by the relative incompleteness of the dataset, as well as its description and analysis in the text. For instance, in the neurofeedback experiment, many of these regions only have data from a single mouse, limiting the conclusions that can be drawn. Additionally, there is a lack of reporting of the quantitative results in the text of the document, which is needed to better understand the degree of the results. Finally, the writing of the results section could use some work, as it currently reads more like a methods section.

      Thank you for your thoughtful and constructive feedback on our manuscript. We appreciate the time and effort you took to review our work and provide detailed suggestions for improvement. Below, we address the key points raised in your review:

      (1) Dataset Completeness: We acknowledge that some of the neurofeedback experiments include data from only a single mouse for some cortical regions while for some cortical regions, there are several animals. This was due to practical constraints during the study, and we understand the limitations this poses for drawing broad conclusions. We felt it was still important to include these data sets with smaller sample sizes as they might be useful for others pursuing this direction in the future. To address this, we have revised the text to explicitly acknowledge these limitations and clarify that the results for some regions are exploratory in nature. We believe our flexible tool will provide a means for our lab and others include more animals representing additional cortical regions in future studies. Importantly, we have included all raw and processed data as well as code for future analysis.

      (2) Quantitative Results: We recognize the importance of reporting quantitative results in the text for better clarity and interpretation. In response, we have added more detailed description of the quantitative findings from both the neurofeedback and movement-feedback experiments. This will include effect sizes, statistical measures, and key numerical results to provide a clearer understanding of the degree and significance of the observed effects.

      (3) Results Section Writing: We appreciate your observation that parts of the results section read more like a methods section. To improve clarity and focus, we have restructured the results section to present the findings in a more concise and interpretative manner, while moving overly detailed descriptions of experimental procedures to the methods section.

      Suggestions for improved or additional experiments, data or analyses:

      Not necessary for this paper, but it would be interesting to see if the CLNF group could learn without auditory feedback.

      This is a great suggestion and certainly something that could be done in the future.

      There are no quantitative results in the results section. I would add important results to help the reader better interpret the data. For example, in: "Our results indicated that both training paradigms were able to lead mice to obtain a significantly larger number of rewards over time," You could show a number, with an appropriate comparison or statistical test, to demonstrate that learning was observed.

      Thank you for pointing this out. We have mentioned quantification values in the results now, along with being mentioned in the figure legends, and we are quoting it in following sentences. “A ΔF/F0 threshold value was calculated from a baseline session on day 0 that would have allowed 25% performance. Starting from this basal performance of around 25% on day 1, mice (CLNF No-rule-change, N=23, n=60 and CLNF Rule-change, N=17, n=60) were able to discover the task rule and perform above 80% over ten days of training (Figure 4A, RM ANOVA p=2.83e-5), and Rule-change mice even learned a change in ROIs or rule reversal (Figure 4A, RM ANOVA p=8.3e-10, Table 5 for different rule changes). There were no significant differences between male and female mice (Supplementary Figure 3A).”

      For: "Performing this analysis indicated that the Raspberry Pi system could provide reliable graded feedback within ~63 {plus minus} 15 ms for CLNF experiments." The LED test shows the sending of the signal, but the actual delay for the audio generation might be longer. This is also longer than the 50 ms mentioned in the abstract.

      We appreciate the reviewer’s insightful comment. The latency reported (~63ms) was measured using the LED test, which captures the time from signal detection to output triggering on the Raspberry Pi GPIO. We agree that the total delay for auditory feedback generation could include an additional latency component related to the digital-to-analog conversion and speaker response. In our setup, we employ a fast Audiostream library written in C to generate the audio signal and expect the delay contribution to be negligible compared to the GPIO latency. Though we did not do this, it can be confirmed by an oscilloscope-based pilot measurement (for additional delay calculation). We have updated the manuscript to clarify that the 63 ± 15 ms value reflects the GPIO-triggered output latency, and we have revised the abstract to accurately state the delay as “~63 ms” rather than 50 ms. This ensures consistency and avoids underestimation of the latency. We have corrected the LED latency for CLNF and CLMF experiments in the abstract as well.

      It could be helpful to visualize an individual trial for each experiment type, for instance how the audio frequency changes as movement speed / calcium activity changes.

      We have added Supplementary Figure 8 that contains this data where you can see the target cortical activity trace, target paw speed, rewards, along with the audio frequency generated.

      The sample sizes are small (n=1) for a few groups. I am excited by the variety of regions recorded, so it could be beneficial for the authors to collect a few more animals to beef up the sample sizes.

      We've acknowledged that some of the sample sizes are small. Importantly, we have included raw and processed data as well as code for future analysis. We felt it was still important to still include these data sets with smaller sample sizes as they might be useful for others pursuing this direction in the future.

      I am curious as to why 60 trials sessions were used. Was it mostly for the convenience of a 30 min session, or were the animals getting satiated? If the former, would learning have occurred more rapidly with longer sessions?

      This is a great observation and the answer is it was mostly due to logistical reasons. We tried to not keep animals headfixed for more than 45 minutes in each session as they become less engaged with long duration headfixed sessions. After headfixing them, it takes about 15 minutes to get the experiment going and therefore 30 - 40 minutes long recorded sessions seemed appropriate before they stop being engaged or before they get satiated in the task. We provided supplemental water after the sessions and we observed that they consumed water after the sessions so they were not fully satiated during the sessions even when they performed well in the task and got maximum rewards. We also had inter-trial rest periods of 10s that elongated the session duration. We think it would be interesting to explore the relationship between session duration(number of trials) and task learning progression over the days in a separate study.

      Figure 4E is interesting, it seems like the changes in the distribution of deltaF was in both positive and negative directions, instead of just positive. I'd be curious as to the author's thoughts as to why this is the case. Relatedly, I don't see Figure 4E, and a few other subplots, mentioned in the text. As a general comment, I would address each subplot in the text.

      We have split Figure 4 into two to keep the figures more readable. Previous Figure 4E-H are now Figure 5A-D in the revised manuscript. The online real-time CLNF sessions were using a moving window average to calculate ΔF/F<sub>0</sub>  and the figures were generated by averaging the whole recorded sessions. We have added text in Methods under “Online ΔF/F<sub>0</sub>calculation” and “Offline ΔF/F<sub>0</sub> calculation” sections making it clear about how we do our ΔF/F<sub>0</sub> normalization based on average fluorescence over the entire session. Using this method of normalization does increase the baseline so that some peaks appear to be below zero. Additionally, it is unclear what strategy animals are employing to achieve the rule specific target activity. The task did not constrain them to have a specific strategy for cortical activation - they were rewarded as long as they crossed the threshold in target ROI(s). For example, in 2-ROI experiments, to increase ROI1-ROI2 target activity, they could increase activity of ROI1 relative to ROI2 or decreased activity of ROI1 relative to ROI1 - both would have led to a reward as long as the result crossed the threshold.

      We have now addressed and added reference to the figures in the text in Results under “Mice can explore and learn an arbitrary task, rule, and target conditions” and “Mice can rapidly adapt to changes in the task rule” sections - thanks for pointing this out.

      For: "In general, all ROIs assessed that encompassed sensory, pre-motor, and motor areas were capable of supporting increased reward rates over time," I would provide a visual summary showing the learning curves for the different types of regions.

      We have rewritten this section to emphasize that these conclusions were based on pooled data from multiple regions of interest. The sample sizes for each type of region are different and some are missing. We believe it would be incomplete and not comparable to present this as a regular analysis since the sample sizes were not balanced. We would be happy to dive deeper into this and point to the raw and processed dataset if anyone would like to explore this further by GitHub or other queries.

      Relatedly, I would further explain the fast vs slow learners, and if they mapped onto certain regions.

      Mice were categorized into fast or slow learners based on the slope of learning over days (reward progression over the days) as shown in Supplementary Figure 3C,D. Our initial aim was not to probe cortical regions that led to fast vs slow learning but this was a grouping we did afterwards. Based on the analysis we did, the fast learners included the sensory (V1), somatosensory (BC, HL), and motor (M1, M2) areas, while the slow learners included the motor (M1, M2), and higher order (TR, RL) cortical areas. Testing all dorsal cortical areas would be prudent to establish their role in fast or slow learning and it is an interesting future direction.

      Also I would make the labels for these plots (e.g. Supp Fig3) more intuitive, versus the acronyms currently used.

      We have made more expressive labels and explained the acronyms below the Supplementary Figure 3.

      The CLMF animals showed a decrease in latency across learning, what about the CLNF animals? There is currently no mention in the text or figures.

      We have now incorporated the CLNF task latency data into both the Results text and Figure 4C. Briefly, task latency decreased as performance improved, increased following a rule change, and then decreased again as the animals relearned the task. The previous Figure 4C has been updated to Figure 4D, and the former Figure 4D has been moved to Supplementary Figure 4E.

      Reviewer #2 (Public review):

      Summary:

      In this work, Gupta & Murphy present several parallel efforts. On one side, they present the hardware and software they use to build a head-fixed mouse experimental setup that they use to track in "real-time" the calcium activity in one or two spots at the surface of the cortex. On the other side, the present another setup that they use to take advantage of the "real-time" version of DeepLabCut with their mice. The hardware and software that they used/develop is described at length, both in the article and in a companion GitHub repository. Next, they present experimental work that they have done with these two setups, training mice to max out a virtual cursor to obtain a reward, by taking advantage of auditory tone feedback that is provided to the mice as they modulate either (1) their local cortical calcium activity, or (2) their limb position.

      Strengths:

      This work illustrates the fact that thanks to readily available experimental building blocks, body movement and calcium imaging can be carried using readily available components, including imaging the brain using an incredibly cheap consumer electronics RGB camera (RGB Raspberry Pi Camera). It is a useful source of information for researchers that may be interested in building a similar setup, given the highly detailed overview of the system. Finally, it further confirms previous findings regarding the operant conditioning of the calcium dynamics at the surface of the cortex (Clancy et al. 2020) and suggests an alternative based on deeplabcut to the motor tasks that aim to image the brain at the mesoscale during forelimb movements (Quarta et al. 2022).

      Weaknesses:

      This work covers 3 separate research endeavors: (1) The development of two separate setups, their corresponding software. (2) A study that is highly inspired from the Clancy et al. 2020 paper on the modulation of the local cortical activity measured through a mesoscale calcium imaging setup. (3) A study of the mesoscale dynamics of the cortex during forelimb movements learning. Sadly, the analyses of the physiological data appears uncomplete, and more generally the paper tends to offer overstatements regarding several points:

      In contrast to the introductory statements of the article, closed-loop physiology in rodents is a well-established research topic. Beyond auditory feedback, this includes optogenetic feedback (O'Connor et al. 2013, Abbasi et al. 2018, 2023), electrical feedback in hippocampus (Girardeau et al. 2009), and much more.

      We have included and referenced these papers in our introduction section (quoted below) and rephrased the part where our previous text indicated there are fewer studies involving closed-loop physiology.

      “Some related studies have demonstrated the feasibility of closed-loop feedback in rodents, including hippocampal electrical feedback to disrupt memory consolidation (Girardeau et al.2009), optogenetic perturbations of somatosensory circuits during behavior (O'Connor et al.2013), and more recent advances employing targeted optogenetic interventions to guide behavior (Abbasi et al. 2023).”

      The behavioral setups that are presented are representative of the state of the art in the field of mesoscale imaging/head fixed behavior community, rather than a highly innovative design. In particular, the closed-loop latency that they achieve (>60 ms) may be perceived by the mice. This is in contrast with other available closed-loop setups.

      We thank the reviewer for this thoughtful comment and fully agree that our closed-loop latency is larger than that achieved in some other contemporary setups. Our primary aim in presenting this work, however, is not to compete with the lowest possible latencies, but to provide an open-source, accessible, and flexible platform that can be readily adopted by a broad range of laboratories. By building on widely available and lower-cost components, our design lowers the barrier of entry for groups that wish to implement closed-loop imaging and behavioral experiments, while still achieving latencies well within the range that can support many biologically meaningful applications.

      For example, our latency (~60 ms) remains compatible with experimental paradigms such as:

      Motor learning and skill acquisition, where sensorimotor feedback on the scale of tens to hundreds of milliseconds is sufficient to modulate performance.

      Operant conditioning and reward-based learning, in which reinforcement timing windows are typically broader and not critically dependent on sub-20 ms latencies.

      Cortical state dependent modulation, where feedback linked to slower fluctuations in brain activity (hundreds of milliseconds to seconds) can provide valuable insight.

      Studies of perception and decision-making, in which stimulus response associations often unfold on behavioral timescales longer than tens of milliseconds.

      We believe that emphasizing openness, affordability, and flexibility will encourage widespread adoption and adaptation of our setup across laboratories with different research foci. In this way, our contribution complements rather than competes with ultra-low-latency closed-loop systems, providing a practical option for diverse experimental needs.

      Through the paper, there are several statements that point out how important it is to carry out this work in a closed-loop setting with an auditory feedback, but sadly there is no "no feedback" control in cortical conditioning experiments, while there is a no-feedback condition in the forelimb movement study, which shows that learning of the task can be achieved in the absence of feedback.

      We fully agree that such a control would provide valuable insight into the contribution of feedback to learning in the CLNF paradigm. In designing our initial experiments, we envisioned multiple potential control conditions, including No-feedback and Random-feedback. However, our first and primary objective was to establish whether mice could indeed learn to modulate cortical ROI activation through auditory feedback, and to further investigate this across multiple cortical regions. For this reason, we focused on implementing the CLNF paradigm directly, without the inclusion of these additional control groups. To broaden the applicability of the system, we subsequently adapted the platform to the CLMF experiments, where we did incorporate a No-feedback group. These results, as the reviewer notes, strengthen the evidence for the role of feedback in shaping task performance. We agree that the inclusion of a No-feedback control group in the CLNF paradigm will be crucial in future studies to further dissect the specific contribution of feedback to cortical conditioning.

      The analysis of the closed-loop neuronal data behavior lacks controls. Increased performance can be achieved by modulating actively only one of the two ROIs, this is not clearly analyzed (for instance looking at the timing of the calcium signal modulation across the two ROIs. It seems that overall ROIs1 and 2 covariate, in contrast to Clancy et al. 2020. How can this be explained?

      We agree that the possibility of increased performance being driven by modulation of a single ROI is an important consideration. Our study indeed began with 1-ROI closed-loop experiments. In those early experiments, while we did observe animals improving performance across days, we realized that daily variability in ongoing cortical GCaMP activity could lead to fluctuations in threshold-crossing events. The 2-ROI design was subsequently introduced to reduce this variability, as the target activity was defined as the relative activity between the two ROIs (e.g., ROI1 – ROI2). This approach offered a more stable signal by normalizing ongoing fluctuations. In our analysis of the early 2-ROI experiments, we observed that animals adopted diverging strategies to achieve threshold crossings. Specifically, some animals increased activity in ROI1 relative to ROI2, while others decreased activity in ROI2 to accomplish the same effect. Once discovered, each animal consistently adhered to its chosen strategy throughout subsequent training sessions. This was an early and intriguing observation, but as the experiments were not originally designed to systematically test this effect, we limited our presentation to the analysis of a small number of animals (shown in Figure 11). We have added details about this observation in our Results section as well, quoted below-

      “In the 2-ROI experiment where the task rule required “ROI1 - ROI2” activity to cross a threshold for reward delivery, mice displayed divergent strategies. Some animals predominantly increased ROI1 activity, whereas others reduced ROI2 activity, both approaches leading to successful threshold crossing (Figure 11)”.

      We hope this clarifies how the use of two ROIs helps explain the apparent covariation of the signals, and why some divergence from the observations of Clancy et al. (2020) may be expected.

      Reviewer #3 (Public review):

      Summary:

      The study demonstrates the effectiveness of a cost-effective closed-loop feedback system for modulating brain activity and behavior in head-fixed mice. Authors have tested real-time closed-loop feedback system in head-fixed mice two types of graded feedback: 1) Closed-loop neurofeedback (CLNF), where feedback is derived from neuronal activity (calcium imaging), and 2) Closed-loop movement feedback (CLMF), where feedback is based on observed body movement. It is a python based opensource system, and authors call it CLoPy. The authors also claim to provide all software, hardware schematics, and protocols to adapt it to various experimental scenarios. This system is capable and can be adapted for a wide use case scenario.

      Authors have shown that their system can control both positive (water drop) and negative reinforcement (buzzer-vibrator). This study also shows that using the close loop system mice have shown better performance, learnt arbitrary task and can adapt to change in the rule as well. By integrating real-time feedback based on cortical GCaMP imaging and behavior tracking authors have provided strong evidence that such closed-loop systems can be instrumental in exploring the dynamic interplay between brain activity and behavior.

      Strengths:

      Simplicity of feedback systems designed. Simplicity of implementation and potential adoption.

      Weaknesses:

      Long latencies, due to slow Ca2+ dynamics and slow imaging (15 FPS), may limit the application of the system.

      We appreciate the reviewer’s comment and agree that latency is an important factor in our setup. The latency arises partly from the inherent slow kinetics of calcium signaling and GCaMP6s, and partly from the imaging rate of 15 FPS (every 66 ms). These limitations can be addressed in several ways: for example, using faster calcium indicators such as GCaMP8f, or adapting the system to electrophysiological signals, which would require additional processing capacity. In our implementation, image acquisition was fixed at 15 FPS to enable real-time frame processing (256 × 256 resolution) on Raspberry Pi 4B devices. With newer hardware, such as the Raspberry Pi 5, substantially higher acquisition and processing rates are feasible (although we have not yet benchmarked this extensively). More powerful platforms such as Nvidia Jetson or conventional PCs would further support much faster data acquisition and processing.

      Major comments:

      (1) Page 5 paragraph 1: "We tested our CLNF system on Raspberry Pi for its compactness, general-purpose input/output (GPIO) programmability, and wide community support, while the CLMF system was tested on an Nvidia Jetson GPU device." Can these programs and hardware be integrated with windows-based system and a microcontroller (Arduino/ Tency). As for the broad adaptability that's what a lot of labs would already have (please comment/discuss)?

      While we tested our CLNF system on a Raspberry Pi (chosen for its compactness, GPIO programmability, and large user community) and our CLMF system on an Nvidia Jetson GPU device (to leverage real-time GPU-based inference), the underlying software is fully written in Python. This design choice makes the system broadly adaptable: it can be run on any device capable of executing Python scripts, including Windows-based PCs, Linux machines, and macOS systems. For hardware integration, we have confirmed that the framework works seamlessly with microcontrollers such as Arduino or Teensy, requiring only minor modifications to the main script to enable sending and receiving of GPIO signals through those boards. In fact, we are already using the same system in an in-house project on a Linux-based PC where an Arduino is connected to the computer to provide GPIO functionality. Furthermore, the system is not limited to Raspberry Pi or Arduino boards; it can be interfaced with any GPIO-capable devices, including those from Adafruit and other microcontroller platforms, depending on what is readily available in individual labs. Since many neuroscience and engineering laboratories already possess such hardware, we believe this design ensures broad accessibility and ease of integration across diverse experimental setups.

      (2) Hardware Constraints: The reliance on Raspberry Pi and Nvidia Jetson (is expensive) for real-time processing could introduce latency issues (~63 ms for CLNF and ~67 ms for CLMF). This latency might limit precision for faster or more complex behaviors, which authors should discuss in the discussion section.

      In our system, we measured latencies of approximately ~63 ms for CLNF and ~67 ms for CLMF. While such latencies indeed limit applications requiring millisecond precision, such as fast whisker movements, saccades, or fine-reaching kinematics, we emphasize that many relevant behaviors, including postural adjustments, limb movements, locomotion, and sustained cortical state changes, occur on timescales that are well within the capture range of our system. Thus, our platform is appropriate for a range of mesoscale behavioral studies that probably needs to be discussed more. It is also important to note that these latencies are not solely dictated by hardware constraints. A significant component arises from the inherent biological dynamics of the calcium indicator (GCaMP6s) and calcium signaling itself, which introduce slower temporal kinetics independent of processing delays. Newer variants, such as GCaMP8f, offer faster response times and could further reduce effective biological latency in future implementations.

      With respect to hardware, we acknowledge that Raspberry Pi provides a low-cost solution but contributes to modest computational delays, while Nvidia Jetson offers faster inference at higher cost. Our choice reflects a balance between accessibility, cost-effectiveness, and performance, making the system deployable in many laboratories. Importantly, the modular and open-source design means the pipeline can readily be adapted to higher-performance GPUs or integrated with electrophysiological recordings, which provide higher temporal resolution. Finally, we agree with the reviewer that the issue of latency highlights deeper and interesting questions regarding the temporal requirements of behavior classification. Specifically, how much data (in time) is required to reliably identify a behavior, and what is the minimum feedback delay necessary to alter neural or behavioral trajectories? These are critical questions for the design of future closed-loop systems and ones that our work helps frame.

      We have added a slightly modified version of our response above in the discussion section under “Experimental applications and implications”.

      (3) Neurofeedback Specificity: The task focuses on mesoscale imaging and ignores finer spatiotemporal details. Sub-second events might be significant in more nuanced behaviors. Can this be discussed in the discussion section?

      This is a great point  and we have added the following to the discussion section. “In the case of CLNF we have focused on regional cortical GCAMP signals that are relatively slow in kinetics. While such changes are well suited for transcranial mesoscale imaging assessment, it is possible that cellular 2-photon imaging (Yu et al. 2021) or preparations that employ cleared crystal skulls (Kim et al. 2016) could resolve more localized and higher frequency kinetic signatures.”

      (4) The activity over 6s is being averaged to determine if the threshold is being crossed before the reward is delivered. This is a rather long duration of time during which the mice may be exhibiting stereotyped behaviors that may result in the changes in DFF that are being observed. It would be interesting for the authors to compare (if data is available) the behavior of the mice in trials where they successfully crossed the threshold for reward delivery and in those trials where the threshold was not breached. How is this different from spontaneous behavior and behaviors exhibited when they are performing the test with CLNF? 

      We would like to emphasize that we are not directly averaging activity over 6 s to compare against the reward threshold. Instead, the preceding 6 s of activity is used solely to compute a dynamic baseline for ΔF/F<sub>0</sub> ( ΔF/F<sub>0</sub> = (F –F<sub>0</sub> )/F<sub>0</sub>). Here, F<sub>0</sub>is calculated as the mean fluorescence intensity over the prior 6 s window and is updated continuously throughout the session. This baseline is then subtracted from the instantaneous fluorescence signal to detect relative changes in activity. The reward threshold is therefore evaluated against these baseline-corrected ΔF/F<sub>0</sub> values at the current time point, not against an average over 6 s. This moving-window baseline correction is a standard approach in calcium imaging analyses, as it helps control for slow drifts in signal intensity, bleaching effects, or ongoing fluctuations unrelated to the behavior of interest. Thus, the 6-s window is not introducing a temporal lag in reward assignment but is instead providing a reference to detect rapid increases in cortical activity.  We have added the term dynamic baseline to the Methods to clarify.

      Recommendations for the authors

      Reviewer #1 (Recommendations for the authors):

      Additional suggestions for improved or additional experiments, data or analyses.

      For: "Looking closely at their reward rate on day 5 (day of rule change), they had a higher reward rate in the second half of the session as compared to the first half, indicating they were adapting to the rule change within one session." It would be helpful to see this data, and would be good to see within-session learning on the rule change day

      Thank you for pointing this out. We had missed referencing the figure in the text, and have now added a citation to Supplementary Figure 4A, which shows the cumulative rewards for each day of training. As seen in the plot for day 5, the cumulative rewards are comparable to those on day 1, with most rewards occurring during the second half of the session.

      For: "These results suggest that motor learning led to less cortical activation across multiple regions, which may reflect more efficient processing of movement-related activity," it could also be the case that the behaviour became more stereotyped over learning, which would lead to more concentrated, correlated activity. To test this, it would be good to look at the limb variability across sessions. Similarly, if it is movement-related, there should be good decoding of limb kinematics.

      Indeed, we observed that behavior became more stereotyped over the course of learning, as shown in Supplementary Figure 4C, 4D. One plausible explanation for the reduction in cortical activation across multiple regions is that behavior itself became more stereotyped, a possibility we have explored in the manuscript. Specifically, forelimb movements during the trial became increasingly correlated as mice improved on the task, particularly in the groups that received auditory feedback (Rule-change and No-rule-change groups; Figure 8). As movements became more correlated, overall body movements during trials decreased and aligned more closely with the task rule (Figure 9D). This suggests that reduced cortical activity may in part reflect changes in behavior. Importantly, however, in the Rule-change group, we observed that on the day of the rule switch (day 5), when the target shifted from the left to the right forelimb, cortical activity increased bilaterally (Figure 9A–C). This finding highlights our central point: groups that received feedback (Rule-change and No-rule-change) were able to identify the task rule more effectively, and both their behavior and cortical activity became more specifically aligned with the rule compared to the No-feedback group. We agree with the reviewers that additional analyses along these lines would be valuable future directions. To facilitate this, we have included the movement data for readers who may wish to pursue further analyses, details can be found under “Data and code availability” in Methods section. However, given the limited sample sizes in our dataset and the need to keep the manuscript focused on the central message, we felt that including these additional analyses here would risk obscuring the main findings.

      For: "We believe the decrease in ΔF/F0peak is unlikely to be driven by changes in movement, as movement amplitudes did not decrease significantly during these periods (Figure 7D CLMF Rule-change)." I would formally compare the two conditions. This is an important control. Also, another way to see if the change in deltaF is related to movement would be to see if you can predict movement from the deltaF.

      Figure 7D in the previous version is Figure 9D in the current revision of the manuscript. We've assessed this for the examples shown based on graphing the movement data, unfortunately there is not enough of that data to do a group analysis of movement magnitude. We would suggest that this would be an excellent future direction that would take advantage of the flexible open source nature of our tool.

      Recommendations for improving the writing and presentation.

      In the abstract there is no mention of the rationale for the project, or the resulting significance. I would modify this to increase readership by the behavioral neuroscience community. Similarly, the introduction also doesn't highlight the value of this resource for the field. Again, I think the pyControl paper does a good job of this. For readability, I would add more subheadings earlier in the results, to separate the different technical aspects of the system.

      We have revised the introduction to include the rationale for the project, its potential implications, and its relevance for translational research. We have also framed the work within the broader context of the behavioral and systems neuroscience community. We greatly appreciate this suggestion, as we believe it enhances the clarity and accessibility of the manuscript for the community.

      For: "While brain activity can be controlled through feedback, other variables such as movements have been less studied, in part because their analysis in real time is more challenging." I would highlight research that has studied the control of behavior through feedback, such as the Mathis paper where mice learn to pull a joystick to a virtual box, and adapt this motion to a force perturbation.

      We have added a citation to the Mathis paper and describe this as an additional form of feedback. The text is quoted below:

      “Opportunities also exist in extending real time pose classification (Forys et al. 2020; Kane et al. 2020) and movement perturbation (Mathis et al. 2017) to shape aspects of an animal’s motor repertoire.”

      Some of the results content would be better suited for the methods, one example: "A previous version of the CLNF system was found to have non-linear audio generation above 10 kHz, partly due to problems in the audio generation library and partly due to the consumer-grade speaker hardware we were employing. This was fixed by switching to the Audiostream (https://github.com/kivy/audiostream) library for audio generation and testing the speakers to make sure they could output the commanded frequencies"

      This is now moved to the Methods section.

      For: "There are reports of cortical plasticity during motor learning tasks, both at cellular and mesoscopic scales (17-19), supporting the idea that neural efficiency could improve with learning," not sure I agree with this, the studies on cortical plasticity are usually to show a neural basis for the learning observed, efficiency is separate from this.

      We have modified this statement to remove the concept of efficiency "There are reports of cortical plasticity during motor learning tasks, both at cellular and mesoscopic scales (17-19).”

      The paragraph that opens "Distinct task- and reward-related cortical dynamics" that describes the experiment should appear in the previous section, as the data is introduced there.

      We have moved the mentioned paragraphs in the previous section where we presented the data and other experiment details. This makes the text more readable and contextual.

      I would present the different ROI rules with better descriptors and visualization to improve the readability.

      We have added Supplementary Figure 7, which provides visualizations of the ROIs across all task rules used in the CLNF experiments.

      Minor corrections to the text and figures.

      Figure 1 is a little crowded, combining the CLNF and CLMF experiments, I would turn this into a 2 panel figure, one for each, similar to how you did figure 2.

      We have revised Figure 1 to include two panels, one for CLNF and one for CLMF. The colored components indicate elements specific to each setup, while the uncolored components represent elements shared between CLNF and CLMF. Relevant text in the manuscript is updated to refer to these figures.

      For Figure 2, the organization of the CLMF section is not intuitive for the reader. I would reorder it so it has a similar flow as the CLNF experiment.

      We have revised the figure by updating the layout of panel B (CLMF) to align with panel A (CLNF), thereby creating a more intuitive and consistent flow between the panels. We appreciate this helpful suggestion, which we believe has substantially improved the clarity of the figure. The corresponding text in the manuscript has also been updated to reflect these changes.

      For Figure 3, highlight that C and E are examples. They also seem a little out of place, so they could even be removed.

      We have now explicitly labeled Figures 3C and 3E as representative examples (figure legend and on figure itself). We believe including these panels provides helpful context for readers: Figure 3C illustrates how the ROIs align on the dorsal cortical brain map with segmented cortical regions, while Figure 3E shows example paw trajectories in three dimensions, allowing visualization of the movement patterns observed during the trials.

      In the plots, I would add sample sizes, for instance, in CLNF learning curve in Figure 4A, how many animals are in each group? 

      We have labeled Figure 4 with number of animals used in CLNF (No-rule-change, N=23; Rule-change, N=17), and CLMF (Rule-change, N=8; No-rule-change, N=4; No-feedback, N=4).

      Also, Figure 7 for example, which figures are single-sessions, versus across animals? For Figure 7c, what time bin is the data taken from?

      We have clarified this now and mentioned it in all the figures. Figure 7 in the previous version is Figure 9 in the current updated manuscript. Figure 9A is from individual sessions on different days from the same mouse. Figure 9B is the group average reward centered ΔF/F<sub>0</sub> activity in different cortical regions (Rule-change, N=8; No-rule-change, N=4; No-feedback, N=4). Figure 9C shows average ΔF/F<sub>0</sub> peak values obtained within -1sec to +1sec centered around the reward point (N=8).

      It says "punish" in Figure 3, but there is no punishment?

      Yes, the task did not involve punishment. Each trial resulted in either a success, which is followed by a reward, or a failure, which is followed by a buzzer sound. To better reflect these outcomes, we have updated Figure 3 and replaced the labels “Reward” with “Success” and “Punish” with “Failure.”

      The regression on 5c doesn't look quite right, also this panel is not mentioned in the text.

      The figure referred to by the reviewer as Figure 5 is now presented as Figure 6 in the revised manuscript. Regarding the reviewer’s observation about the regression line in the left panel of Figure 5C, the apparent misalignment arises because the majority of the data points are densely clustered at the center of the scatter plot, where they overlap substantially. The regression line accurately reflects this concentration of overlapping data. To improve clarity, we have updated the figure and ensured that it is now appropriately referenced in the Results section.

      Reviewer #2 (Recommendations for the authors):

      (1) There would be many interesting observations and links between the peripheral and cortical studies if there was a body video available during the cortical study. Is there any such data available?

      We agree that a detailed analysis of behavior during the CLNF task would be necessary to explore any behavior correlates with success in the task. Unfortunately, we do not have a sufficient video of the whole body to perform such an analysis.

      (2) The text (p. 24) states: [intracortical GCAMP transients measured over days became more stereotyped in kinetics and were more correlated (to each other) as the task performance increased over the sessions (Figure 7E).] But I cannot find this quantification in the figures or text?

      Figure 7 in the previous version of the manuscript now appears as Figure 9. In this figure, we present cortical activity across selected regions during trials, and in Figure 9E we highlight that this activity becomes more correlated. Since we did not formally quantify variability, we have removed the previous claim that the activity became stereotyped and revised the text in the updated manuscript accordingly.

      Typos:

      10-serest c (page 13)

      Inverted color codes in figure 4E vs F

      Reviewer #3 (Recommendations for the authors):

      We have mostly attempted to limit the feedback to suggestions and posed a few questions that might be interesting to explore given the dataset the authors have collected.

      Comments:

      In close loop systems the latency is primary concern, and authors have successfully tested the latency of the system (Delay): from detection of an event to the reaction time was less than 67ms.

      We have commented on the issues and limitations caused by latency, and potential future directions to overcome these challenges in responses to some of the previous comments.

      Additional major comments:

      "In general, all ROIs assessed that encompassed sensory, pre-motor, and motor areas were capable of supporting increased reward rates over time (Figure 4A, Animation 1)." Fig 4A is merely showing change in task performance over time and does not have information regarding the changes observed specific to CLNF for each ROI.

      We acknowledge that the sample size for individual ROI rules was not sufficient for meaningful comparisons. To address this limitation, we pooled the data across all the rules tested. The manuscript includes a detailed list of the rules along with their corresponding sample sizes for transparency.

      A ΔF/F<sub>0</sub> threshold value was calculated from a baseline session on day 0 that would have allowed 25% performance. Starting from this basal performance of around 25% on day 1, mice (CLNF No-rule-change, n=28 and CLNF Rule-change, n=13). It is unclear what the replicates here are. Trials or mice? The corresponding Figure legend has a much smaller n value.

      Thank you for pointing this out. We realized that we had not indicated the sample replicates in the figure, and the use of n instead of N for the number of animals may have been misleading. We have now corrected the notation and clarified this information in the figure to resolve the discrepancy.

      What were the replicates for each ROI pairs evaluated?

      Each ROI rule and number of mice and trials are listed in Table 5 and Table 6.

      Our analysis revealed that certain ROI rules (see description in methods) lead to a greater increase in success rate over time than others (Supplementary Figure 3D). The Supplementary figures 3C and 3D are blurry and could use higher resolution images. 

      We have increased the font size of the text that was previously difficult to read and re-exported the figure at a higher resolution (300 DPI). We believe these changes will resolve the issue.

      Also, It will help the reader is a visual representation of the ROI pairs are provided, instead of the text view. One interesting question is whether there are anatomical biases to fast vs slow learning pairs (Directionality - anterior/posterior, distance between the selected ROIs etc). This could be interesting to tease apart.

      We have added Supplementary Figure 7, which provides visualizations of the ROIs across all task rules used in the CLNF experiments. While a detailed investigation of the anatomical basis of fast versus slow learning cortical ROIs is beyond the scope of the present study, we agree that this represents an exciting future direction for further research.

      How distant should the ROIs be to achieve increased task performance?

      We appreciate this insightful question. We did not specifically test this scenario. In our study, we selected 0.3 × 0.3 mm ROIs centered on the standard AIBS mouse brain atlas (CCF). At this resolution, ROIs do not overlap, regardless of their placement in a two-ROI experiment. Furthermore, because our threshold calculations are based on baseline recordings, we expect the system would function for any combination of ROI placements. Nonetheless, exploring this systematically would be an interesting avenue for future experiments.

      Figures:

      I would leave out some of the methodological details such as the protocol for water restriction (Fig. 3) out of the legend. This will help with readability.

      We have removed some of the methodological details, including those mentioned above, from the legend of Figure 3 in the updated manuscript.

      Fig 1 and Fig 2: In my opinion, It would be easier for the reader if the current Fig. 2, which provides a high level description of CLNF and CLBF is presented as Fig. 1. The current Fig. 1, goes into a lot of methodological implementation details, and also includes a lot of programming jargon that is being introduced early in the paper that is hard to digest early on in the paper's narrative.

      Thank you for the suggestion. In the new manuscript, Figure 1 and Figure 2 have been swapped.

      Higher-resolution images/ plots are needed in many instances. Unsure if this is the pdf compression done by the manuscript portal that is causing this.

      All figures were prepared in vector graphics format using the open-source software Inkscape. For this manuscript, we exported the images at 300 DPI, which is generally sufficient for publication-quality documents. The submission portal may apply additional processing, which could have resulted in a reduction in image quality. We will carefully review the final submission files and ensure that all figures are clear and of high quality.

      The authors repeatedly show ROI specific analysis M1_L, F1_R etc. It will be helpful to provide a key, even if redundant in all figures to help the reader.

      We have now included keys to all such abbreviations in all the figures.

      There are also instances of editorialization and interpretation e.g., "Surprisingly, the "Rule-change" mice were able to discover the change in rule and started performing above 70% within a day of the rule change, on day 6" that would be more appropriate in the main body of the paper.

      Thank you for pointing this out in the figure legend, and we have removed it now since we already discussed this in the Results.

      Minor comments

      (1) The description of Figure 1 is hard to follow and can be described better based on how the information is processed and executed in the system from source to processing and back. Using separated colors (instead of shaded of grey) for the neuro feedback and movement feedback would help as well. Common components could have a different color. The specification like the description of the config file should come later.

      Figure 1 in the previous version is Figure 2 in the updated version. We have taken suggestions from other reviewers and made the figure easier to understand and split it into two panels with color coding Green for CLNF, Pink for CLMF specific parts while common shared parts are left without any color.

      (2) Page 20 last paragraph:

      Authors are neglecting that the rule change is done one day prior and the results that you see in the second half on the 6th day are not just because of the first half of the 6th day instead combined training on the 5th day (rule change) and then the first half of the 6th day. Rephrasing this observation is essential.

      We have revised the text for clarity to indicate that the performance increase observed on day 6 is not necessarily attributable to training on that day. In fact, we noted and mentioned that mice began to perform the task better during the second half of the session on day 5 itself.

      (3)  The method section description of the CLMF setup (Page no 39 first paragraph) is more detailed, a diagram of this setup would make it easy to follow and a better read.

      We have made changes to the CLMF setup (Figure 1B) and CLMF schematic (Figure 2B) to make it easier to understand parts of the setup and flow of control.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Bansal et al. present a study on the fundamental blood and nectar feeding behaviors of the critical disease vector, Anopheles stephensi. The study encompasses not just the fundamental changes in blood feeding behaviors of the crucially understudied vector, but then uses a transcriptomic approach to identify candidate neuromodulation pathways which influence blood feeding behavior in this mosquito species. The authors then provide evidence through RNAi knockdown of candidate pathways that the neuromodulators sNPF and Rya modulate feeding either via their physiological activity in the brain alone or through joint physiological activity along the brain-gut axis (but critically not the gut alone). Overall, I found this study to be built on tractable, well-designed behavioral experiments.

      Their study begins with a well-structured experiment to assess how the feeding behaviors of A. stephensi change over the course of its life history and in response to its age, mating, and oviposition status. The authors are careful and validate their experimental paradigm in the more well-studied Ae. aegypti, and are able to recapitulate the results of prior studies, which show that mating is a prerequisite for blood feeding behaviors in Ae. aegypt. Here they find A. Stephensi, like other Anopheline mosquitoes, has a more nuanced regulation of its blood and nectar feeding behaviors.

      The authors then go on to show in a Y-maze olfactometer that ,to some degree, changes in blood feeding status depend on behavioral modulation to host cues, and this is not likely to be a simple change to the biting behaviors alone. I was especially struck by the swap in valence of the host cues for the blood-fed and mated individuals, which had not yet oviposited. This indicates that there is a change in behavior that is not simply desensitization to host cues while navigating in flight, but something much more exciting is happening.

      The authors then use a transcriptomic approach to identify candidate genes in the blood-feeding stages of the mosquito's life cycle to identify a list of 9 candidates that have a role in regulating the host-seeking status of A. stephensi. Then, through investigations of gene knockdown of candidates, they identify the dual action of RYa and sNPF and candidate neuromodulators of host-seeking in this species. Overall, I found the experiments to be well-designed. I found the molecular approach to be sound. While I do not think the molecular approach is necessarily an all-encompassing mechanism identification (owing mostly to the fact that genetic resources are not yet available in A. stephensi as they are in other dipteran models), I think it sets up a rich line of research questions for the neurobiology of mosquito behavioral plasticity and comparative evolution of neuromodulator action.

      We appreciate the reviewer’s detailed summary of our work. We thank them for their positive comments and agree with them on the shortcomings of our approach.

      Strengths:

      I am especially impressed by the authors' attention to small details in the course of this article. As I read and evaluated this article, I continued to think about how many crucial details could potentially have been missed if this had not been the approach. The attention to detail paid off in spades and allowed the authors to carefully tease apart molecular candidates of blood-seeking stages. The authors' top-down approach to identifying RYamide and sNPF starting from first principles behavioral experiments is especially comprehensive. The results from both the behavioral and molecular target studies will have broad implications for the vectorial capacity of this species and comparative evolution of neural circuit modulation.

      We really appreciate that the reviewer has recognised the attention to detail we have tried to put, thank you!

      Weaknesses:

      There are a few elements of data visualizations and methodological reporting that I found confusing on a first few read-throughs. Figure 1F, for example, was initially confusing as it made it seem as though there were multiple 2-choice assays for each of the conditions. I would recommend removing the "X" marker from the x-axis to indicate the mosquitoes did not feed from either nectar, blood, or neither in order to make it clear that there was one assay in which mosquitoes had access to both food sources, and the data quantify if they took both meals, one meal, or no meals.

      We thank the reviewer for flagging the schematic in figure 1F. As suggested, we have removed the “X” markers from the x-axis and revised the axis label from “choice of food” to “choice made” to better reflect what food the mosquitoes chose in the assay. For clarity, we have now also plotted the same data as stacked graphs at the bottom of Fig. 1F, which clearly shows the proportion of mosquitoes fed on each particular choice. We avoid the stacked graph as the sole representation of this data, as it does not capture the variability in the data.

      I would also like to know more about how the authors achieved tissue-specific knockdown for RNAi experiments. I think this is an intriguing methodology, but I could not figure out from the methods why injections either had whole-body or abdomen-specific knockdown.

      The tissue-specific knockdown (abdomen only or abdomen+head) emerged from initial standardisations where we were unable to achieve knockdown in the head unless we used higher concentrations of dsRNA and did the injections in older females. We realised that this gave us the opportunity to isolate the neuronal contribution of these neuropeptides in the phenotype produced. Further optimisations revealed that injecting dsRNA into 0-10h old females produced abdomen-specific knockdowns without affecting head expression, whereas injections into 4 days old females resulted in knockdowns in both tissues. Moreover, head knockdowns in older females required higher dsRNA concentrations, with knockdown efficiency correlating with the amount injected. In contrast, abdominal knockdowns in younger females could be achieved even with lower dsRNA amounts.

      We have mentioned the knockdown conditions- time of injection and the amount dsRNA injected- for tissue-specific knockdowns in methods but realise now that it does not explain this well enough. We have now edited it to state our methodology more clearly (see lines 932-948).

      I also found some interpretations of the transcriptomic to be overly broad for what transcriptomes can actually tell us about the organism's state. For example, the authors mention, "Interestingly, we found that after a blood meal, glucose is neither spent nor stored, and that the female brain goes into a state of metabolic 'sugar rest', while actively processing proteins (Figure S2B, S3)".

      This would require a physiological measurement to actually know. It certainly suggests that there are changes in carbohydrate metabolism, but there are too many alternative interpretations to make this broad claim from transcriptomic data alone.

      We thank the reviewer for pointing this out and agree with them. We have now edited our statement to read:

      “Instead, our data suggests altered carbohydrate metabolism after a blood meal, with the female brain potentially entering a state of metabolic 'sugar rest' while actively processing proteins (Figure S2B, S3). However, physiological measurements of carbohydrate and protein metabolism will be required to confirm whether glucose is indeed neither spent nor stored during this period.” See lines 271-277.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Bansal et al examine and characterize feeding behaviour in Anopheles stephensi mosquitoes. While sharing some similarities to the well-studied Aedes aegypti mosquito, the authors demonstrate that mated females, but not unmated (virgin) females, exhibit suppression in their bloodfeeding behaviour. Using brain transcriptomic analysis comparing sugar-fed, blood-fed, and starved mosquitoes, several candidate genes potentially responsible for influencing blood-feeding behaviour were identified, including two neuropeptides (short NPF and RYamide) that are known to modulate feeding behaviour in other mosquito species. Using molecular tools, including in situ hybridization, the authors map the distribution of cells producing these neuropeptides in the nervous system and in the gut. Further, by implementing systemic RNA interference (RNAi), the study suggests that both neuropeptides appear to promote blood-feeding (but do not impact sugar feeding), although the impact was observed only after both neuropeptide genes underwent knockdown.

      Strengths and/or weaknesses:

      Overall, the manuscript was well-written; however, the authors should review carefully, as some sections would benefit from restructuring to improve clarity. Some statements need to be rectified as they are factually inaccurate.

      Below are specific concerns and clarifications needed in the opinion of this reviewer:

      (1) What does "central brains" refer to in abstract and in other sections of the manuscript (including methods and results)? This term is ambiguous, and the authors should more clearly define what specific components of the central nervous system was/were used in their study.

      Central brain, or mid brain, is a commonly used term to refer to brain structures/neuropils without the optic lobes (For example: https://www.nature.com/articles/s41586-024-07686-5). In this study we have focused our analysis on the central brain circuits involved in modulating blood-feeding behaviour and have therefore excluded the optic lobes. As optic lobes account for nearly half of all the neurons in the mosquito brain (https://pmc.ncbi.nlm.nih.gov/articles/PMC8121336/), including them would have disproportionately skewed our transcriptomic data toward visual processing pathways. 

      We have indicated this in figure 3A and in the methods (see lines 800-801, 812). We have now also clarified it in the results section for neurotranscriptomics to avoid confusion (see lines 236-237).

      (2) The abstract states that two neuropeptides, sNPF and RYamide are working together, but no evidence is summarized for the latter in this section.

      We thank the reviewer for pointing this out. We have now added a statement “This occurs in the context of the action of RYa in the brain” to end of the abstract, for a complete summary of our proposed model. 

      (3) Figure 1

      Panel A: This should include mating events in the reproductive cycle to demonstrate differences in the feeding behavior of Ae. aegypti.

      Our data suggest that mating can occur at any time between eclosion and oviposition in An. stephensi and between eclosion and blood feeding in Ae. aegypti. Adding these into (already busy) 1A, would cloud the purpose of the schematic, which is to indicate the time points used in the behavioural assays and transcriptomics.

      Panel F: In treatments where insects were not provided either blood or sugar, how is it that some females and males had fed? Also, it is unclear why the y-axis label is % fed when the caption indicates this is a choice assay. Also, it is interesting that sugar-starved females did not increase sugar intake. Is there any explanation for this (was it expected)?

      We apologise for the confusion. The experiment is indeed a choice assay in which sugar-starved or sugar-sated females, co-housed with males, were provided simultaneous access to both blood and sugar, and were assessed for the choice made (indicated on the x-axis): both blood and sugar, blood only, sugar only, or neither. The x-axis indicates the choice made by the mosquitoes, not the choice provided in the assay, and the y-axis indicates the percentage of males or females that made each particular choice. We have now removed the “X” markers from the x-axis and revised the axis label from “choice of food” to “choice made” to better reflect what food the mosquitoes chose to take.

      In this assay, we scored females only for the presence or absence of each meal type (blood or sugar) and are therefore unable to comment on whether sugar-starved females consumed more sugar than sugarsated females. However, when sugar-starved, a higher proportion of females consumed both blood and sugar, while fewer fed on blood alone.

      For clarity, we have now also plotted the same data as stacked graphs at the bottom of Fig. 1F, which clearly shows the proportion of mosquitoes fed on each particular choice. We avoid the stacked graph as the sole representation of this data as it does not capture the variability in the data.

      (4) Figure 3

      In the neurotranscriptome analysis of the (central) brain involving the two types of comparisons, can the authors clarify what "excluded in males" refers to? Does this imply that only genes not expressed in males were considered in the analysis? If so, what about co-expressed genes that have a specific function in female feeding behaviour?

      This is indeed correct. We reasoned that since blood feeding is exclusive to females, we should focus our analysis on genes that were specifically upregulated in them. As the reviewer points out, it is very likely that genes commonly upregulated in males and females may also promote blood feeding and we will miss out on any such candidates based on our selection criteria. 

      (5) Figure 4

      The authors state that there is more efficient knockdown in the head of unfed females; however, this is not accurate since they only get knockdown in unfed animals, and no evidence of any knockdown in fed animals (panel D). This point should be revised in the results test as well.

      Perhaps we do not understand the reviewer’s point or there has been a misunderstanding. In figure 4D, we show that while there is more robust gene knockdown in unfed females, blood-fed females also showed modest but measurable knockdowns ranging from 5-40% for RYamide and 2-21% for sNPF. 

      Relatedly, blood-feeding is decreased when both neuropeptide transcripts are targeted compared to uninjected (panel C) but not compared to dsGFP injected (panel E). Why is this the case if authors showed earlier in this figure (panel B) that dsGFP does not impact blood feeding?

      We realise this concern stems from our representation of the data. Since we had earlier determined that dsGFP-injected females fed similarly to uninjected females (fig 4B), we used these controls interchangeably in subsequent experiments. To avoid confusion, we have now only used the label ‘control’ in figure 4 (and supplementary figure S9) and specified which control was used for each experiment in the legend.

      In addition to this, we wanted to clarify that fig 4C and 4E are independent experiments. 4C is the behaviour corresponding to when the neuropeptides were knocked down in both heads and abdomens. 4E is the behaviour corresponding to when the neuropeptides were knocked down in only the abdomens. We have now added a schematic in the plots to make this clearer.

      In addition, do the uninjected and dsGFP-injected relative mRNA expression data reflect combined RYa and sNPF levels? Why is there no variation in these data,…

      In these qPCRs, we calculated relative mRNA expression using the delta-delta Ct method (see line 975). For each neuropeptide its respective control was used. For simplicity, we combined the RYa and sNPF control data into a single representation. The value of this control is invariant because this method sets the control baseline to a value of 1.

      …and how do transcript levels of RYa and sNPF compare in the brain versus the abdomen (the presentation of data doesn't make this relationship clear).

      The reviewer is correct in pointing out that we have not clarified this relationship in our current presentation. While we have not performed absolute mRNA quantifications, we extracted relative mRNA levels from qPCR data of 96h old unmanipulated control females. We observed that both sNPF and RYa transcripts are expressed at much lower levels in the abdomens, as compared to those in the heads, as shown in Author response Image 1 below. 

      Author response image 1.

      (6) As an overall comment, the figure captions are far too long and include redundant text presented in the methods and results sections.

      We thank the reviewer for flagging this and have now edited the legends to remove redundancy.  

      (7) Criteria used for identifying neuropeptides promoting blood-feeding: statement that reads "all neuropeptides, since these are known to regulate feeding behaviours". This is not accurate since not all neuropeptides govern feeding behaviors, while certainly a subset do play a role.

      We agree with the reviewer that not all neuropeptides regulate feeding behaviours. Our statement refers to the screening approach we used: in our shortlist of candidates, we chose to validate all neuropeptides.

      (8) In the section beginning with "Two neuropeptides - sNPF and RYa - showed about 25% and 40% reduced mRNA levels...", the authors state that there was no change in blood-feeding and later state the opposite. The wording should be clarified as it is unclear.

      Thank you for pointing this out. We were referring to an unchanged proportion of the blood fed females. We have now edited the text to the following: 

      “Two neuropeptides - sNPF and RYa - showed about 25% and 40% reduced mRNA levels in the heads but the proportion of females that took blood meals remained unchanged”. See lines 338-340.

      (9) Just before the conclusions section, the statement that "neuropeptide receptors are often ligandpromiscuous" is unjustified. Indeed, many studies have shown in heterologous systems that high concentrations of structurally related peptides, which are not physiologically relevant, might cross-react and activate a receptor belonging to a different peptide family; however, the natural ligand is often many times more potent (in most cases, orders of magnitude) than structurally related peptides. This is certainly the case for various RYamide and sNPF receptors characterized in various insect species.

      We agree with the reviewer and apologise for the mistake. We have now removed the statement.

      (10) Methods

      In the dsRNA-mediated gene knockdown section, the authors could more clearly describe how much dsRNA was injected per target. At the moment, the reader must carry out calculations based on the concentrations provided and the injected volume range provided later in this section.

      We have now edited the section to reflect the amount of dsRNA injected per target. Please see lines 921-931.

      It is also unclear how tissue-specific knockdown was achieved by performing injection on different days/times. The authors need to explain/support, and justify how temporal differences in injection lead to changes in tissue-specific expression. Does the blood-brain barrier limit knockdown in the brain instead, while leaving expression in the peripheral organs susceptible?

      To achieve tissue-specific knockdowns of sNPF and RYa, we optimised both the time of injection as well as the dsRNA concentration to be injected. Injecting dsRNA into 0-10h females produced abdomen-specific knockdowns without affecting head expression, whereas injections into 96h old females resulted in knockdowns in both tissues. Head knockdowns in older females required higher dsRNA concentrations, with knockdown efficiency correlating with the amount injected. In contrast, abdominal knockdowns in younger females could be achieved even with lower dsRNA amounts, reflecting the lower baseline expression of sNPF in abdomens compared to heads and the age-dependent increase in head expression (as confirmed by qPCR). It is possible that the blood-brain barrier also limits the dsRNA entering the brain, thereby requiring higher amounts to be injected for head knockdowns. 

      We have now edited this section to state our methodology more clearly (see lines 932-948).

      For example, in Figure 4, the data support that knockdown in the head/brain is only effective in unfed animals compared to uninjected animals, while there is no evidence of knockdown in the brain relative to dsGFP-injected animals. Comparatively, evidence appears to show stronger evidence of abdominal knockdown mostly for the RYa transcript (>90%) while still significantly for the sNPF transcript (>60%).

      As we explained earlier, this concern likely stems from our representation of the data. Since we had earlier determined that dsGFP-injected females fed similarly to uninjected females (fig 4B), we used these controls interchangeably in subsequent experiments. To avoid confusion, we have now only used the label ‘control’ in figure 4 (and supplementary figure S9) and specified which control was used for each experiment in the legend.

      In addition to this, we wanted to clarify that fig 4C and 4E are independent experiments. 4C is the behaviour corresponding to when the neuropeptides were knocked down in both heads and abdomens.  4E is the behaviour corresponding to when the neuropeptides were knocked down in only the abdomen. We have now added a schematic in the plots to make this clearer.

      Reviewer #3 (Public review):

      Summary:

      This manuscript investigates the regulation of host-seeking behavior in Anopheles stephensi females across different life stages and mating states. Through transcriptomic profiling, the authors identify differential gene expression between "blood-hungry" and "blood-sated" states. Two neuropeptides, sNPF and RYamide, are highlighted as potential mediators of host-seeking behavior. RNAi knockdown of these peptides alters host-seeking activity, and their expression is anatomically mapped in the mosquito brain (sNPF and RYamide) and midgut (sNPF only).

      Strengths:

      (1) The study addresses an important question in mosquito biology, with relevance to vector control and disease transmission.

      (2) Transcriptomic profiling is used to uncover gene expression changes linked to behavioral states.

      (3) The identification of sNPF and RYamide as candidate regulators provides a clear focus for downstream mechanistic work.

      (4) RNAi experiments demonstrate that these neuropeptides are necessary for normal host-seeking behavior.

      (5) Anatomical localization of neuropeptide expression adds depth to the functional findings.

      Weaknesses:

      (1) The title implies that the neuropeptides promote host-seeking, but sufficiency is not demonstrated (for example, with peptide injection or overexpression experiments).

      Demonstrating sufficiency would require injecting sNPF peptide or its agonist. To date, no small-molecule agonists (or antagonists) that selectively mimic sNPF or RYa neuropeptides have been identified in insects. An NPY analogue, TM30335, has been reported to activate the Aedes aegypti NPY-like receptor 7 (NPYLR7; Duvall et al., 2019), which is also activated by sNPF peptides at higher doses (Liesch et al., 2013). Unfortunately, the compound is no longer available because its manufacturer, 7TM Pharma, has ceased operations. Synthesising the peptides is a possibility that we will explore in the future.

      (2) The proposed model regarding central versus peripheral (gut) peptide action is inconsistently presented and lacks strong experimental support.

      The best way to address this would be to conduct tissue-specific manipulations, the tools for which are not available in this species. Our approach to achieve head+abdomen and abdomen only knockdown was the closest we could get to achieving tissue specificity and allowed us to confirm that knockdown in the head was necessary for the phenotype. However, as the reviewer points out, this did not allow us to rule out any involvement of the abdomen. This point has been addressed in lines 364-371.

      (3) Some conclusions appear premature based on the current data and would benefit from additional functional validation.

      The most definitive way of demonstrating necessity of sNPF and RYa in blood feeding would be to generate mutant lines. While we are pursuing this line of experiments, they lie beyond the scope of a revision. In its absence, we relied on the knockdown of the genes using dsRNA. We would like to posit that despite only partial knockdown, mosquitoes do display defects in blood-feeding behaviour, without affecting sugar-feeding. We think this reflects the importance of sNPF in promoting blood feeding.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Overall, I found this manuscript to be well-prepared, visually the figures are great and clearly were carefully thought out and curated, and the research is impactful. It was a wonderful read from start to finish. I have the following recommendations:

      Thank you very much, we are very pleased to hear that you enjoyed reading our manuscript!

      (1) For future manuscripts, it would make things significantly easier on the reviewer side to submit a format that uses line numbers.

      We sincerely apologise for the oversight. We have now incorporated line numbers in the revised manuscript.

      (2) There are a few statements in the text that I think may need clarification or might be outside the bounds of what was actually studied here. For example, in the introduction "However, mating is dispensable in Anophelines even under conditions of nutritional satiety". I am uncertain what is meant by this statement - please clarify.

      We apologise for the lack of clarity in the statement and have now deleted it since we felt it was not necessary.

      (3) Typo/Grammatical minutiae:

      (a) A small idiosyncrasy of using hyphens in compound words should also be fixed throughout. Typically, you don't hyphenate if the words are being used as a noun, as in the case: e.g. "Age affects blood feeding.". However, you would hyphenate if the two words are used as a compound adjective "Age affects blood-feeding behavior". This may not be an all-inclusive list, but here are some examples where hyphens need to either be removed or added. Some examples:

      "Nutritional state also influences other internal state outputs on blood-feeding": blood-feeding -> blood feeding

      "... the modulation of blood-feeding": blood-feeding -> blood feeding

      "For example, whether virgin females take blood-meals...": blood-meals -> blood meals

      ".... how internal and external cues shape meal-choice"-> meal choice

      "blood-meal" is often used throughout the text, but is correctly "blood meal" in the figures.

      There are many more examples throughout.

      We apologise for these errors and appreciate the reviewer’s keen eye. We have now fixed them throughout the manuscript.  

      (b) Figure 1 Caption has a typo: "co-housed males were accessed for sugar-feeding" should be "co-housed males were assessed for sugar feeding"

      We apologise for the typo and thank the reviewer for spotting it. We have now corrected this.  

      (c) It would be helpful in some other figure captions to more clearly label which statement is relevant to which part of the text. For example, in Figure 4's caption.

      "C,D. Blood-feeding and sugar-feeding behaviour of females when both RYa and sNPF are knocked down in the head (C). Relative mRNA expressions of RYa and sNPF in the heads of dsRYa+dssNPF - injected blood-fed and unfed females, as compared to that in uninjected females, analysed via qPCR (D)."

      I found re-referencing C and D at the end of their statements makes it look as thought C precedes the "Relative mRNA expression" and on a first read through, I thought the figure captions were backwards. I'd recommend reformatting here and throughout consistently to only have the figure letter precede its relevant caption information, e.g.:

      "C. Blood-feeding and sugar-feeding behaviour of females when both RYa and sNPF are knocked down in the head. D. Relative mRNA expressions of RYa and sNPF in the heads of dsRYa+dssNPF - injected bloodfed and unfed females, as compared to that in uninjected females, analysed via qPCR."

      We have now edited the legends as suggested.

      Reviewer #2 (Recommendations for the authors):

      Separately from the clarifications and limitations listed above, the authors could strengthen their study and the conclusions drawn if they could rescue the behavioural phenotype observed following knockdown of sNPF and RYamide. This could be achieved by injection of either sNPF or RYa peptide independently or combined following knockdown to validate the role of these peptides in promoting blood-feeding in An. stephensi. Additionally, the apparent (but unclear) regionalized (or tissue-specific) knockdown of sNPF and RYamide transcripts could be visualized and verified by implementing HCR in situ hyb in knockdown animals (or immunohistochemistry using antibodies specific for these two neuropeptides). 

      In a follow up of this work, we are generating mutants and peptides for these candidates and are planning to conduct exactly the experiments the reviewer suggests.

      Reviewer #3 (Recommendations for the authors):

      The loss-of-function data suggest necessity but not sufficiency. Synthetic peptide injection in non-hostseeking (blood-fed mated or juvenile) mosquitoes would provide direct evidence for peptide-induced behavioral activation. The lack of these experiments weakens the central claim of the paper that these neuropeptides directly promote blood feeding.

      As noted above, we plan to synthesise the peptide to test rescue in a mutant background and sufficiency.  

      Some of the claims about knockdown efficiency and interpretation are conflicting; the authors dismiss Hairy and Prp as candidates due to 30-35% knockdown, yet base major conclusions on sNPF and RYamide knockdowns with comparable efficiencies (25-40%). This inconsistency should be addressed, or the justification for different thresholds should be clearly stated.

      We have not defined any specific knockdown efficacy thresholds in the manuscript, as these can vary considerably between genes, and in some cases, even modest reductions can be sufficient to produce detectable phenotypes. For example, knockdown efficiencies of even as low as about 25% - 40% gave us observable phenotypes for sNPF and RYa RNAi (Figure S9B-G).

      No such phenotypes were observed for Hairy (30%) or Prp (35%) knockdowns. Either these genes are not involved in blood feeding, or the knockdown was not sufficient for these specific genes to induce phenotypes. We cannot distinguish between these scenarios. 

      The observation that knockdown animals take smaller blood meals is interesting and could reflect a downstream effect of altered host-seeking or an independent physiological change. The relationship between meal size and host-seeking behavior should be clarified.

      We agree with the reviewer that the reduced meal size observed in sNPF and RYa knockdown animals could result from their inability to seek a host or due to an independent effect on blood meal intake. Unfortunately, we did not measure host-seeking in these animals. We plan to distinguish between these possibilities using mutants in future work.

      Several figures are difficult to interpret due to cluttered labeling and poorly distinguishable color schemes. Simplifying these and improving contrast (especially for co-housed vs. virgin conditions) would enhance readability. 

      We regret that the reviewer found the figures difficult to follow. We have now revised our annotations throughout the manuscript for enhanced readability. For example, “D1<sup>B”</sup> is now “D1<sup>PBM”</sup> (post-bloodmeal) and “D1<sup>O”</sup> is now “D1<sup>PO”</sup> (post-oviposition). Wherever mated females were used, we have now appended “(m)” to the annotations and consistently depicted these females with striped abdomens in all the schematics. We believe these changes will improve clarity and readability.

      The manuscript does not clearly justify the use of whole-brain RNA sequencing to identify peptides involved in metabolic or peripheral processes. Given that anticipatory feeding signals are often peripheral, the logic for brain transcriptomics should be explained.

      The reviewer is correct in pointing out that feeding signals could also emerge from peripheral tissues. Signals from these tissues – in response to both changing nutritional and reproductive states – are then integrated by the central brain to modulate feeding choices. For example, in Drosophila, increased protein intake is mediated by central brain circuitry including those in the SEZ and central complex (Munch et al., 2022; Liu et al., 2017; Goldschmidt et al., 202ti). In the context of mating, male-derived sex peptide further increases protein feeding by acting on a dedicated central brain circuitry (Walker et al., 2015). We, therefore focused on the central brain for our studies.

      The proposed model suggests brain-derived peptides initiate feeding, while gut peptides provide feedback. However, gut-specific knockdowns had no effect, undermining this hypothesis. Conversely, the authors also suggest abdominal involvement based on RNAi results. These contradictions need to be resolved into a consistent model.

      We thank the reviewer for raising this point and recognise their concern. Our reasons for invoking an involvement of the gut were two-fold:

      (1) We find increased sNPF transcript expression in the entero-endocrine cells of the midgut in blood-hungry females, which returns to baseline after a blood-meal (Fig. 4L, M).

      (2) While the abdomen-only knockdowns did not affect blood feeding, every effective head knockdown that affected blood feeding also abolished abdominal transcript levels (Fig. S9C, F). (Achieving a head-only reduction proved impossible because (i) systemic dsRNA delivery inevitably reaches the abdomen and (ii) abdominal expression of both peptides is low, leaving little dynamic range for selective manipulation.) Consequently, we can only conclude the following: 1) that brain expression is required for the behaviour, 2) that we cannot exclude a contributory role for gut-derived sNPF. We have discussed this in lines 364-371.

      The identification of candidate receptors is promising, but the manuscript would be significantly strengthened by testing whether receptor knockdowns phenocopy peptide knockdowns. Without this, it is difficult to conclude that the identified receptors mediate the behavioral effects.

      We agree that functional validation of the receptors would strengthen the evidence for sNPF and RYa-mediated control of blood feeding in An. stephensi. We selected these receptors based on sequence homology. A possibility remains that sNPF neuropeptides activate more than one receptor, each modulating a distinct circuit, as shown in the case of Drosophila Tachykinin (https://pmc.ncbi.nlm.nih.gov/articles/PMC10184743/). This will mean a systematic characterisation and knockdown of each of them to confirm their role. We are planning these experiments in the future.  

      The authors compared the percentage changes in sugar-fed and blood-fed animals under sugar-sated or sugar-starved conditions. Figure 1F should reflect what was discussed in the results.

      Perhaps this concern stems from our representation of the data in figure 1F? We have now edited the xaxis and revised its label from “choice of food” to “choice made” to better reflect what food the mosquitoes chose to take.

      For clarity, we have now also plotted the same data as stacked graphs at the bottom of Fig. 1F, which clearly shows the proportion of mosquitoes fed on each particular choice. We avoid the stacked graph as the sole representation of this data because it does not capture the variability in the data.

      Minor issues:

      (1) The authors used mosquitoes with belly stripes to indicate mated females. To be consistent, the post-oviposition females should also have belly stripes.

      We thank the reviewer for pointing this out. We have now edited all the figures as suggested.

      (2) In the first paragraph on the right column of the second page, the authors state, "Since females took blood-meals regardless of their prior sugar-feeding status and only sugar-feeding was selectively suppressed by prior sugar access." Just because the well-fed animals ate less than the starved animals does not mean their feeding behavior was suppressed.

      Perhaps there has been a misunderstanding in the experimental setup of figure 1F, probably stemming from our data representation. The experiment is a choice assay in which sugar-starved or sugar-sated females, co-housed with males, were provided simultaneous access to both blood and sugar, and were assessed for the choice made (indicated on the x-axis): both blood and sugar, blood only, sugar only, or neither. We scored females only for the presence or absence of each meal type (blood or sugar) and did not quantify the amount consumed.

      (3) The figure legend for Figure 1A and the naming convention for different experimental groups are difficult to follow. A simplified or consistently abbreviated scheme would help readers navigate the figures and text.

      We regret that the reviewer found the figure difficult to follow. We have now revised our annotations throughout the manuscript for enhanced readability. For example, “D1<sup>B”</sup> is now “D1<sup>PBM”</sup> (post-bloodmeal) and “D1<sup>O”</sup> is now “D1<sup>PO”</sup> (post-oviposition).

      (4) In the last paragraph of the Y-maze olfactory assay for host-seeking behaviour in An. stephensi in Methods, the authors state, "When testing blood-fed females, aged-matched sugar-fed females (bloodhungry) were included as positive controls where ever possible, with satisfactory results." The authors should explicitly describe what the criteria are for "satisfactory results".

      We apologise for the lack of clarity. We have now edited the statement to read:

      “When testing blood-fed females, age-matched sugar-fed females (blood-hungry) were included wherever possible as positive controls. These females consistently showed attraction to host cues, as expected.” See lines 786-790.

      (5) In the first paragraph of the dsRNA-mediated gene knockdown section in Methods, dsRNA against GFP is used as a negative control for the injection itself, but not for the potential off-target effect.

      We agree with the reviewer that dsGFP injections act as controls only for injection-related behavioural changes, and not for off-target effects of RNAi. We have now corrected the statement. See lines 919-920.

      To control for off-target effects, we could have designed multiple dsRNAs targeting different parts of a given gene. We regret not including these controls for potential off-target effects of dsRNAs injected. 

      (6) References numbers 48, 89, and 90 are not complete citations.

      We thank the reviewer for spotting these. We have now corrected these citations.

    1. Author response:

      The following is the authors’ response to the original reviews.

      First, we thank the reviewers for the valuable and constructive reviews. Thanks to these, we believe the article has been considerably improved. We have organized our response to address points that are relevant to both reviewers first, after which we address the unique concerns of each individual reviewer separately. We briefly paraphrase each concern and provide comments for clarification, outlining the precise changes that we have made to the text.

      Common Concerns (R1 & R2):

      Can you clarify how NREM and REM sleep relate to the oneirogen hypothesis?

      Within the submission draft we tried to stay agnostic as to whether mechanistically similar replay events occur during NREM or REM sleep; however, upon a more thorough literature review, we think that there is moderately greater evidence in favor of Wake-Sleep-type replay occurring during REM sleep which is related to classical psychedelic drug mechanisms of action.

      First, we should clarify that replay has been observed during both REM and NREM sleep, and dreams have been documented during both sleep stages, though the characteristics of dreams differ across stages, with NREM dreams being more closely tied to recent episodic experience and REM dreams being more bizarre/hallucinatory (see Stickgold et al., 2001 for a review). Replay during sleep has been studied most thoroughly during NREM sharp-wave ripple events, in which significant cortical-hippocampal coupling has been observed (Ji & Wilson, 2007). However, it is critical to note that the quantification methods used to identify replay events in the hippocampal literature usually focus on identifying what we term ‘episodic replay,’ which involves a near-identical recapitulation of neural trajectories that were recently experienced during waking experimental recordings (Tingley & Peyrach, 2020). In contrast, our model focuses on ‘generative replay,’ where one expects only a statistically similar reproduction of neural activity, without any particular bias towards recent or experimentally controlled experience. This latter form of replay may look closer to the ‘reactivation’ observed in cortex by many studies (e.g. Nguyen et al., 2024), where correlation structures of neural activity similar to those observed during stimulus-driven experience are recapitulated. Under experimental conditions in which an animal is experiencing highly stereotyped activity repeatedly, over extended periods of time, these two forms of replay may be difficult to dissociate.

      Interestingly, though NREM replay has been shown to couple hippocampal and cortical activity, a similar study in waking animals administered psychedelics found hippocampal replay without any obvious coupling to cortical activity (Domenico et al., 2021). This could be because the coupling was not strong enough to produce full trajectories in the cortex (psychedelic administration did not increase ‘alpha’ enough), and that a causal manipulation of apical/basal influence in the cortex may be necessary to observe the increased coupling. Alternatively, as Reviewer 1 noted, it may be that psychedelics induce a form of hippocampus-decoupled replay, as one would expect from the REM stage of a recently proposed complementary learning systems model (Singh et al., 2022). 

      Evidence in favor of a similarity between the mechanism of action of classical psychedelics and the mechanism of action of memory consolidation/learning during REM sleep is actually quite strong. In particular, studies have shown that REM sleep increases the activity of soma-targeting parvalbumin (PV) interneurons and decreases the activity of apical dendrite-targeting somatostatin (SOM) interneurons (Niethard et al., 2021), that this shift in balance is controlled by higher-order thalamic nuclei, and that this shift in balance is critical for synaptic consolidation of both monocular deprivation effects in early visual cortex (Zhou et al., 2020) and for the consolidation of auditory fear conditioning in the dorsal prefrontal cortex (Aime et al., 2022). These last studies were not discussed in our previous text–we have added them, in addition to a more nuanced description of the evidence connecting our model to NREM and REM replay. 

      Relevant modifications: Page 4, 1st paragraph; Page 11, 1st paragraph.

      Can you explain how synaptic plasticity induced by psychedelics within your model relates to learning at a behavioral level?

      While the Wake-Sleep algorithm is a useful model for unsupervised statistical learning, it is not a model of reward or fear-based conditioning, which likely occur via different mechanisms in the brain (e.g. dopamine-dependent reinforcement learning or serotonin-dependent emotional learning). The Wake-Sleep algorithm is a ‘normative plasticity algorithm,’ that connects synaptic plasticity to the formation of structured neural representations, but it is not the case that all synaptic plasticity induced by psychedelic administration within our model should induce beneficial learning effects. According to the Wake-Sleep algorithm, plasticity at apical synapses is enhanced during the Wake phase, and plasticity at basal synapses is enhanced during the Sleep phase; under the oneirogen hypothesis, hallucinatory conditions (increased ‘alpha’) cause an increase in plasticity at both apical and basal sites. Because neural activity is in a fundamentally aberrant state when ‘alpha’ is increased, there are no theoretical guarantees that plasticity will improve performance on any objective: psychedelic-induced plasticity within our model could perhaps better be thought of as ‘noise’ that may have a positive or negative effect depending on the context.

      In particular, such ‘noise’ may be beneficial for individuals or networks whose synapses have become locked in a suboptimal local minimum. The addition of large amounts of random plasticity could allow a system to extricate itself from such local minima over subsequent learning (or with careful selection of stimuli during psychedelic experience), similar to simulated annealing optimization approaches. If our model were fully validated, this view of psychedelic-induced plasticity as ‘noise’ could have relevance for efforts to alleviate the adverse effects of PTSD, early life trauma, or sensory deprivation; it may also provide a cautionary note against repeated use of psychedelic drugs within a short time frame, as the plasticity changes induced by psychedelic administration under our model are not guaranteed to be good or useful in-and-of themselves without subsequent re-learning and compensation.

      We should also note that we have deliberately avoided connecting the oneirogen hypothesis model to fear extinction experimental results that have been observed through recordings of the hippocampus or the amygdala (Bombardi & Giovanni, 2013; Jiang et al., 2009; Kelly et al., 2024; Tiwari et al., 2024). Both regions receive extensive innervation directly from serotonergic synapses originating in the dorsal raphe nucleus, which have been shown to play an important role in emotional learning (Lesch & Waider, 2012); because classical psychedelics may play a more direct role in modulating this serotonergic innervation, it is possible that fear conditioning results (in addition to the anxiolytic effects of psychedelics) cannot be attributed to a shift in balance between apical and basal synapses induced by psychedelic administration. We have provided a more detailed review of these results in the text, as well as more clarity regarding their relation to our model.

      Relevant modifications: Page 9, final paragraph; Page 12, final paragraph.

      Reviewer 1 Concerns:

      Is it reasonable to assign a scalar parameter ‘alpha’ to the effects of classical psychedelics? And is your proposed mechanism of action unique to classical psychedelics? E.g. Could this idea also apply to kappa opioid agonists, ketamine, or the neural mechanisms of hallucination disorders?

      We have clarified that within our model ‘alpha’ is a parameter that reflects the balance between apical and basal synapses in determining the activity of neurons in the network. For the sake of simplicity we used a single ‘alpha’ parameter, but realistically, each neuron would have its own ‘alpha’ parameter, and different layers or individual neurons could be affected differentially by the administration of any particular drug; therefore, our scalar ‘alpha’ value can be thought of as a mean parameter for all neurons, disregarding heterogeneity across individual neurons.

      There are many different mechanisms that could theoretically affect this ‘alpha’ parameter, including: 5-HT2a receptor agonism, kappa opioid receptor binding, ketamine administration, or possibly the effects of genetic mutations underlying the pathophysiology of complex developmental hallucination disorders. We focused exclusively on 5-HT2a receptor agonism for this study because the mechanism is comparatively simple and extensively characterized, but similar mechanisms may well be responsible for the hallucinatory symptoms of a variety of drugs and disorders.

      Relevant modifications: Page 4, first paragraph; Page 13, first paragraph.

      Can you clarify the role of 5-HT2a receptor expression on interneurons within your model?

      While we mostly focused on the effects of 5-HT2a receptors on the apical dendrites of pyramidal neurons, these receptors are also expressed on soma-targeting parvalbumin (PV) interneurons. This expression on PV interneurons is consistent with our proposed psychedelic mechanism of action, because it could lead to a coordinated decrease in the influence of somatic and proximal dendritic inputs while increasing the influence of apical dendritic inputs. We have elaborated on this point, and moved the discussion earlier in the text.

      Relevant modifications: Page 1, 1st paragraph; Page 4, 2nd paragraph.

      Discussions of indigenous use of psychedelics over millenia may amount to over-romanticization.

      We ultimately decided to remove these discussions from the main text, as they had little bearing on the content of our work. Within the Ethics Declarations section we softened our claims from “millenia” to “centuries,” as indigenous psychedelic use over this latter period of time is well-substantiated.

      Relevant modifications: removed from introduction; modified Ethics Declarations

      You isolate the 5-HT2a agonism as the mechanism of action underlying ‘alpha’ in your model, but there exist 5-HT2a agonists that do not have hallucinatory effects (e.g. lisuride). How do you explain this?

      Lisuride has much-reduced hallucinatory effects compared to other psychedelic drugs at clinical doses (though it does indeed induce hallucinations at high doses; Marona-Lewicka et al., 2002), and we should note that serotonin (5-HT) itself is pervasive in the cortex without inducing hallucinatory effects during natural function. Similarly, MDMA is a partial agonist for 5-HT2a receptors, but it has much-reduced perceptual hallucination effects relative to classical psychedelics (Green et al., 2003) in addition to many other effects not induced by classical psychedelics.

      Therefore, while we argue that 5-HT2a agonism induces an increase in influence of apical dendritic compartments and a decrease in influence of basal/somatic compartments, and that this change induces hallucinations, we also note that there are many other factors that control whether or not hallucinations are ultimately produced, so that not all 5-HT2a agonists are hallucinogenic. There are two possible additional factors that could contribute to this phenomenon: 5-HT receptor binding affinity and cellular membrane permeability.

      Importantly, many 5-HT2a receptor agonists are also 5-HT1a receptor agonists (e.g. serotonin itself and lisuride), while MDMA has also been shown to increase serotonin, norepinephrine, and dopamine release (Green et al., 2003). While 5-HT2a receptor agonism has been shown to reduce sensory stimulus responses (Michaiel et al., 2019), 5-HT1a receptor agonism inhibits spontaneous cortical activity (Azimi et al., 2020); thus one might expect the net effect of administering serotonin or a nonselective 5-HT receptor agonist to be widespread inhibition of a circuit, as has been observed in visual cortex (Azimi et al., 2020). Therefore, selective 5-HT2a agonism is critical for the induction of hallucinations according to our model, though any intervention that jointly excites pyramidal neurons’ apical dendrites and inhibits their basal/somatic compartments across a broad enough area of cortex would be predicted to have a similar effect. Lisuride has a much higher binding affinity for 5-HT1a receptors than, for instance, LSD (Marona-Lewicka et al., 2002).

      Secondly, it has recently been shown that both the head-twitch effect (a coarse behavioral readout of hallucinations in animals) and the plasticity effects of psychedelics are abolished when administering 5-HT2a agonists that are impermeable to the cellular membrane because of high polarity, and that these effects can be rescued by temporarily rendering the cellular membrane permeable (Vargas et al., 2023). This suggests that the critical hallucinatory effects of psychedelics (apical excitation according to our model) may be mediated by intracellular 5-HT2a receptors. Notably, serotonin itself is not membrane permeable in the cortex.

      Therefore, either of these two properties could play a role in whether a given 5-HT2a agonist induces hallucinatory effects. We have provided an extended discussion of these nuances in our revision.

      Relevant modifications: Page 1, paragraph 2.

      Your model proposes that an increase in top-down influence on neural activity underlies the hallucinatory effects of psychedelics. How do you explain experimental results that show increases in bottom-up functional connectivity (either from early sensory areas or the thalamus)?

      Firstly, we should note that our proposed increase in top-down influence is a causal, biophysical property, not necessarily a statistical/correlative one. As such, we will stress that the best way to test our model is via direct intervention in cortical microcircuitry, as opposed to correlative approaches taken by most fMRI studies, which have shown mixed results with regard to this particular question. Correlative approaches can be misleading due to dense recurrent coupling in the system, and due to the coarse temporal and spatial resolution provided by noninvasive recording technologies (changes in statistical/functional connectivity do not necessarily correspond to changes in causal/mechanistic connectivity, i.e. correlation does not imply causation).

      There are two experimental results that appear to contradict our hypothesis that deserve special consideration. The first shows an increase in directional thalamic influence on the distributed cortical networks after psychedelic administration (Preller et al., 2018). To explain this, we note that this study does not distinguish between lower-order sensory thalamic nuclei (e.g. the lateral and medial geniculate nuclei receiving visual and auditory stimuli respectively) and the higher-order thalamic nuclei that participate in thalamocortical connectivity loops (Whyte et al., 2024). Subsequent more fine-grained studies have noted an increase in influence of higher order thalamic nuclei on the cortex (Pizzi et al., 2023; Gaddis et al., 2022), and in fact extensive causal intervention research has shown that classical psychedelics (and 5-HT2a agonism) decrease the influence of incoming sensory stimuli on the activity of early sensory cortical areas, indicating decoupling from the sensory thalamus (Evarts et al., 1955; Azimi et al., 2020; Michaiel et al. 2019). The increased influence of higher-order thalamic nuclei is consistent with both the cortico-striatal-thalamo-cortical (CTSC) model of psychedelic action as well as the oneirogen hypothesis, since higher-order thalamic inputs modulate the apical dendrites of pyramidal neurons in cortex (Whyte et al., 2024).

      The second experimental result notes that DMT induces traveling waves during resting state activity that propagate from early visual cortex to deeper cortical layers (Alamia et al., 2020). There are several possibilities that could explain this phenomenon: 1) it could be due to the aforementioned difficulties associated with directed functional connectivity analyses, 2) it could be due to a possible high binding affinity for DMT in the visual cortex relative to other brain areas, or 3) it could be due to increases in apical influence on activity caused by local recurrent connectivity within the visual cortex which, in the absence of sensory input, could lead to propagation of neural activity from the visual cortex to the rest of the brain. This last possibility is closest to the model proposed by (Ermentrout & Cowan, 1979), and which we believe would be best explained within our framework by a topographically connected recurrent network architecture trained on video data; a potentially fruitful direction for future research.

      Relevant modifications: Page 9, paragraph 1; Page 10, final paragraph; Page 11, final paragraph.

      Shouldn’t the hallucinations generated by your model look more ‘psychedelic,’ like those produced by the DeepDream algorithm?

      We believe that the differences in hallucination visualization quality between our Wake-Sleep-trained models and DeepDream are mostly due to differences in the scale and power of the models used across these two studies. We are confident that with more resources (and potentially theoretical innovations to improve the Wake-Sleep algorithm’s performance) the produced hallucination visualizations could become more realistic.

      We note that more powerful generative models trained with backpropagation are able to produce surreal images of comparable quality (Rezende et al., 2014; Goodfellow et al., 2020; Vahdat & Kautz, 2020), though these have not yet been used as a model of psychedelic hallucinations. However, the DeepDream model operates on top of large pretrained image processing models, and does not provide an biologically mechanistic/testable interpretation of its hallucination effects. When training smaller models with a local synaptic plasticity rule (as opposed to backpropagation), the hallucination effects are less visually striking due to the reduced quality of our trained generative model, though they are still strongly tied to the statistics of sensory inputs, as quantified by our correlation similarity metric (Fig. 5b).

      To demonstrate that our proposed hallucination mechanism is capable of producing more complex hallucinations in larger, more powerful models, we employed our same hallucination generation mechanism in a pretrained Very Deep Variational Autoencoder (VDVAE) (Child et al., 2021), which is a hierarchical variational autoencoder with a nearly identical structure compared to our Wake-Sleep-trained networks, with both a bottom-up inference pathway and a top-down generative pathway that maps cleanly onto our multicompartmental neuron model. VDVAEs are trained on the same objective function as our Wake-Sleep-trained networks, but using the backpropagation algorithm. The VDVAE models were able to generate much more complex hallucinations (emergence of complex geometric patterns, smooth deformations of objects and faces), whose complexity arguably exceeds those produced by the DeepDream algorithm. Therefore while the VDVAEs are less biologically realistic (they do not learn via local synaptic plasticity), they function as a valuable high-level model of hallucination generation that complements our Wake-Sleep-trained approach. As further validation, we were also able to replicate our key results and testable predictions with these models.

      Relevant modifications: Results section “Modeling hallucinations in large-scale pretrained networks”; Figure 6, S7, S8; Page 12, paragraph 3; Methods section “Generating hallucinations in hierarchical variational autoencoders.”

      Your model assumes domination by entirely bottom-up activity during the ‘wake’ phase, and domination entirely by top-down activity during ‘sleep,’ despite experimental evidence indicating that a mixture of top-down and bottom-up inputs influence neural activity during both stages in the brain. How do you explain this?

      Our use of the Wake-Sleep algorithm, in which top-down inputs (Sleep) or bottom-up inputs (Wake) dominate network activity is an over-simplification made within our model for computational and theoretical reasons. Models that receive a mixture of top-down and bottom-up inputs during ‘Wake’ activity do exist (in particular the closely related Boltzmann machine (Ackley et al., 1985)), but these models are considerably more computationally costly to train due to a need to run extensive recurrent network relaxation dynamics for each input stimulus. Further, these models do not generalize as cleanly to processing temporal inputs. For this reason, we focused on the Wake-Sleep algorithm, at the cost of some biological realism, though we note that our model should certainly be extended to support mixed apical-basal waking regimes. We have added a discussion of this in our ‘Model Limitations’ section.

      Relevant modifications: Page 12, paragraph 4.

      Your model proposes that 5-HT2a agonism enhances glutamatergic transmission, but this is not true in the hippocampus, which shows decreases in glutamate after psychedelic administration.

      We should note that our model suggests only compartment specific increases in glutamatergic transmission; as such, our model does not predict any particular directionality for measures of glutamatergic transmission that includes signaling at both apical and basal compartments in aggregate, as was measured in the provided study (Mason et al., 2020).

      You claim that your model is consistent with the Entropic Brain theory, but you report increases in variance, not entropy. In fact, it has been shown that variance decreases while entropy increases under psychedelic administration. How do you explain this discrepancy?

      Unfortunately, ‘entropy’ and ‘variance’ are heavily overloaded terms in the noninvasive imaging literature, and the particularities of the method employed can exert a strong influence on the reported effects. The reduction in variance reported by (Carhart-Harris et al., 2016) is a very particular measure: they are reporting the variance of resting state synchronous activity, averaged across a functional subnetwork that spans many voxels; as such, the reduction in variance in this case is a reduction in broad, synchronous activity. We do not have any resting state synchronous activity in our network due to the simplified nature of our model (particularly an absence of recurrent temporal dynamics), so we see no reduction in variance in our model due to these effects.

      Other studies estimate ‘entropy’ or network state disorder via three different methods that we have been able to identify. 1) (Carhart-Harris et al., 2014) uses a different measure of variance: in this case, they subtract out synchronous activity within functional subnetworks, and calculate variability across units in the network. This measure reports increases in variance (Fig. 6), and is the closest measure to the one we employ in this study. 2) (Lebedev et al., 2016) uses sample entropy, which is a measure of temporal sequence predictability. It is specifically designed to disregard highly predictable signals, and so one might imagine that it is a measure that is robust to shared synchronous activity (e.g. resting state oscillations). 3) (Mediano et al., 2024) uses Lempel-Ziv complexity, which is, similar to sample entropy, a measure of sequence diversity; in this case the signal is binarized before calculation, which makes this method considerably different from ours. All three of the preceding methods report increases in sequence diversity, in agreement with our quantification method. Our strongest explanation for why the variance calculation in (Carhart-Harris et al., 2016) produces a variance reduction is therefore due to a reduction in low-rank synchronous activity in subnetworks during resting state.

      As for whether the entropy increase is meaningful: we share Reviewer 1’s concern that increases in entropy could simply be due to a higher degree of cognitive engagement during resting state recordings, due to the presence of sensory hallucinations or due to an inability to fall asleep. This could explain why entropy increases are much more minimal relative to non-hallucinating conditions during audiovisual task performance (Siegel et al., 2024; Mediano et al., 2024). However, we can say that our model is consistent with the Entropic Brain Theory without including any form of ‘cognitive processing’: we observe increases in variability during resting state in our model, but we observe highly similar distributions of activity when averaging over a wide variety of sensory stimulus presentations (Fig. 5b-c). This is because variability in our model is not due to unstructured noise: it corresponds to an exploration of network states that would ordinarily be visited by some stimulus. Therefore, when averaging across a wide variety of stimuli, the distribution of network states under hallucinating or non-hallucinating conditions should be highly similar.

      One final point of clarification: here we are distinguishing Entropic Brain Theory from the REBUS model–the oneirogen hypothesis is consistent with the increase in entropy observed experimentally, but in our model this entropy increase is not due to increased influence of bottom-up inputs (it is due instead to an increase in top-down influence). Therefore, one could view the oneirogen hypothesis as consistent with EBT, but inconsistent with REBUS.

      Relevant modifications: Page 10, paragraph 1.

      You relate your plasticity rule to behavioral-timescale plasticity (BTSP) in the hippocampus, but plasticity has been shown to be reduced in the hippocampus after psychedelic administration. Could you elaborate on this connection?

      When we were establishing a connection between our ‘Wake-Sleep’ plasticity rule and BTSP learning, the intended connection was exclusively to the mathematical form of the plasticity rule, in which activity in the apical dendrites of pyramidal neurons functions as an instructive signal for plasticity in basal synapses (and vice versa): we will clarify this in the text. Similarly, we point out that such a plasticity rule tends to result in correlated tuning between apical and basal dendritic compartments, which has been observed in hippocampus and cortex: this is intended as a sanity check of our mapping of the Wake-Sleep algorithm to cortical microcircuitry, and has limited further bearing on the effects of psychedelics specifically.

      Reduction in plasticity in the hippocampus after psychedelic administration could be due to a complementary learning systems-type model, in which the hippocampus becomes partly decoupled from the cortex during REM sleep (Singh et al., 2022); were this to be the case, it would not be incompatible with our model, which is mostly focused on the cortex. Notably, potentiating 5HT-2a receptors in the ventral hippocampus does not induce the head-twitch response, though it does produce anxiolytic effects (Tiwari et al., 2024), indicating that the hallucinatory and anxiolytic effects of classical psychedelics may be partly decoupled. 

      Reviewer 2 Concerns:

      Could you provide visualizations of the ‘ripple’ phenomenon that you’re referring to?

      In our revised submission, ‘ripple’ phenomena are now visible in two places: Fig 2c-d, and Fig 6 (rows 2 and 3). Because the VDVAE models used to generate Figure 6 produce higher quality generated images, the ripples appearing in these plots are likely more prototypical, but it is not easy to evaluate the quality of these visualizations relative to subjective hallucination phenomena.

      Could you provide a more nuanced description of alternative roles for top-down feedback, beyond being used exclusively for learning as depicted in your model?

      For the sake of simplicity, we only treat top-down inputs in our model as a source of an instructive teaching signal, the originator of generative replay events during the Sleep phase, and as the mechanism of hallucination generation. However, as discussed in a response to a previous question, in the cortex pyramidal neurons receive and respond to a mixture of top-down and bottom-up processing.

      There are a variety of theories for what role top-down inputs could play in determining network activity. To name several, top-down input could function as: 1) a denoising/pattern completion signal (Kadkhodaie & Simoncelli, 2021), 2) a feedback control signal (Podlaski & Machens, 2020), 3) an attention signal (Lindsay, 2020), 4) ordinary inputs for dynamic recurrent processing that play no specialized role distinct from bottom-up or lateral inputs except to provide inputs from higher-order association areas or other sensory modalities (Kar et al., 2019; Tugsbayar et al., 2025). Though our model does not include these features, they are perfectly consistent with our approach.

      In particular, denoising/pattern completion signals in the predictive coding framework (closely related to the Wake-Sleep algorithm) also play a role as an instructive learning signal (Salvatori et al., 2021); and top-down control signals can play a similar role in some models (Gilra & Gerstner, 2017; Meulemans et al., 2021). Thus, options 1 and 2 are heavily overlapping with our approach, and are a natural consequence of many biologically plausible learning algorithms that minimize a variational free energy loss (Rao & Ballard, 1997; Ackley et al., 1985). Similarly, top-down attentional signals can exist alongside top-down learning signals, and some models have argued that such signals can be heavily overlapping or mutually interchangeable (Roelfsema & van Ooyen, 2005). Lastly, generic recurrent connectivity (from any source) can be incorporated into the Wake-Sleep algorithm (Dayan & Hinton, 1996), though we avoided doing this in the present study due to an absence of empirical architecture exploration in the literature and the computational complexity associated with training on time series data.

      To conclude, there are a variety of alternative functions proposed for top-down inputs onto pyramidal neurons in the cortex, and we view these additional features as mutually compatible with our approach; for simplicity we did not include them in our Wake-Sleep-trained model, but we believe that these features are unlikely to interfere with our testable predictions or empirical results. In fact, the pretrained VDVAE models that we worked with do include top-down influence during the Wake-stage inference process, and these models recapitulated our key results and testable predictions (Fig. S8).

      Relevant modifications: Fig. S8; Page 12, paragraph 4.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:  

      Reviewer #1 (Public review):  

      Summary:  

      The image analysis pipeline is tested in analysing microscopy imaging data of gastruloids of varying sizes, for which an optimised protocol for in toto image acquisition is established based on whole mount sample preparation using an optimal refractive index matched mounting media, opposing dual side imaging with two-photon microscopy for enhanced laser penetration, dual view registration, and weighted fusion for improved in toto sample data representation. For enhanced imaging speed in a two-photon microscope, parallel imaging was used, and the authors performed spectral unmixing analysis to avoid issues of signal cross-talk.  

      In the image analysis pipeline, different pre-treatments are done depending on the analysis to be performed (for nuclear segmentation - contrast enhancement and normalisation; for quantitative analysis of gene expression - corrections for optical artifacts inducing signal intensity variations). Stardist3D was used for the nuclear segmentation. The study analyses into properties of gastruloid nuclear density, patterns of cell division, morphology, deformation, and gene expression.  

      Strengths:  

      The methods developed are sound, well described, and well-validated, using a sample challenging for microscopy, gastruloids. Many of the established methods are very useful (e.g. registration, corrections, signal normalisation, lazy loading bioimage visualisation, spectral decomposition analysis), facilitate the development of quantitative research, and would be of interest to the wider scientific community.

      We thank the reviewer for this positive feedback.

      Weaknesses:  

      A recommendation should be added on when or under which conditions to use this pipeline. 

      We thank the reviewer for this valuable feedback, we added the text in the revised version, ines 418 to 474. “In general, the pipeline is applicable to any tissue, but it is particularly useful for large and dense 3D samples—such as organoids, embryos, explants, spheroids, or tumors—that are typically composed of multiple cell layers and have a thickness greater than 50 µm”.

      “The processing and analysis pipeline are compatible with any type of 3D imaging data (e.g. confocal, 2 photon, light-sheet, live or fixed)”.

      “Spectral unmixing to remove signal cross-talk of multiple fluorescent targets is typically more relevant in two-photon imaging due to the broader excitation spectra of fluorophores compared to single-photon imaging. In confocal or light-sheet microscopy, alternating excitation wavelengths often circumvents the need for unmixing. Spectral decomposition performs even better with true spectral detectors; however, these are usually not non-descanned detectors, which are more appropriate for deep tissue imaging. Our approach demonstrates that simultaneous cross-talk-free four-color two-photon imaging can be achieved in dense 3D specimen with four non-descanned detectors and co-excitation by just two laser lines. Depending on the dispersion in optically dense samples, depth-dependent apparent emission spectra need to be considered”.

      “Nuclei segmentation using our trained StarDist3D model is applicable to any system under two conditions: (1) the nuclei exhibit a star-convex shape, as required by the StarDist architecture, and (2) the image resolution is sufficient in XYZ to allow resampling. The exact sampling required is object- and system-dependent, but the goal is to achieve nearly isotropic objects with diameters of approximately 15 pixels while maintaining image quality. In practice, images containing objects that are natively close to or larger than 15 pixels in diameter should segment well after resampling. Conversely, images with objects that are significantly smaller along one or more dimensions will require careful inspection of the segmentation results”.

      “Normalization is broadly applicable to multicolor data when at least one channel is expected to be ubiquitously expressed within its domain. Wavelength-dependent correction requires experimental calibration using either an ubiquitous signal at each wavelength. Importantly, this calibration only needs to be performed once for a given set of experimental conditions (e.g., fluorophores, tissue type, mounting medium)”.

      “Multi-scale analysis of gene expression and morphometrics is applicable to any 3D multicolor image. This includes both the 3D visualization tools (Napari plugins) and the various analytical plots (e.g., correlation plots, radial analysis). Multi-scale analysis can be performed even with imperfect segmentation, as long as segmentation errors tend to cancel out when averaged locally at the relevant spatial scale. However, systematic errors—such as segmentation uncertainty along the Z-axis due to strong anisotropy—may accumulate and introduce bias in downstream analyses. Caution is advised when analyzing hollow structures (e.g., curved epithelial monolayers with large cavities), as the pipeline was developed primarily for 3D bulk tissues, and appropriate masking of cavities would be needed”.

      Reviewer #2 (Public review):  

      Summary:  

      This study presents an integrated experimental and computational pipeline for high-resolution, quantitative imaging and analysis of gastruloids. The experimental module employs dual-view two-photon spectral imaging combined with optimized clearing and mounting techniques to image whole-mount immunostained gastruloids. This approach enables the acquisition of comprehensive 3D images that capture both tissue-scale and single-cell level information.  

      The computational module encompasses both pre-processing of acquired images and downstream analysis, providing quantitative insights into the structural and molecular characteristics of gastruloids. The pre-processing pipeline, tailored for dual-view two-photon microscopy, includes spectral unmixing of fluorescence signals using depth-dependent spectral profiles, as well as image fusion via rigid 3D transformation based on content-based block-matching algorithms. Nuclei segmentation was performed using a custom-trained StarDist3D model, validated against 2D manual annotations, and achieving an F1 score of 85+/-3% at a 50% intersection-over-union (IoU) threshold. Another custom-trained StarDist3D model enabled accurate detection of proliferating cells and the generation of 3D spatial maps of nuclear density and proliferation probability. Moreover, the pipeline facilitates detailed morphometric analysis of cell density and nuclear deformation, revealing pronounced spatial heterogeneities during early gastruloid morphogenesis.  

      All computational tools developed in this study are released as open-source, Python-based software.  

      Strengths:  

      The authors applied two-photon microscopy to whole-mount deep imaging of gastruloids, achieving in toto visualization at single-cell resolution. By combining spectral imaging with an unmixing algorithm, they successfully separated four fluorescent signals, enabling spatial analysis of gene expression patterns.  

      The entire computational workflow, from image pre-processing to segmentation with a custom-trained StarDist3D model and subsequent quantitative analysis, is made available as open-source software. In addition, user-friendly interfaces are provided through the open-source, community-driven Napari platform, facilitating interactive exploration and analysis.

      We thank the reviewer for this positive feedback.

      Weaknesses:  

      The computational module appears promising. However, the analysis pipeline has not been validated on datasets beyond those generated by the authors, making it difficult to assess its general applicability.

      We agree that applying our analysis pipeline to published datasets—particularly those acquired with different imaging systems—would be valuable. However, only a few high-resolution datasets of large organoid samples are publicly available, and most of these either lack multiple fluorescence channels or represent 3D hollow structures. Our computational pipeline consists of several independent modules: spectral filtering, dual-view registration, local contrast enhancement, 3D nuclei segmentation, image normalization based on a ubiquitous marker, and multiscale analysis of gene expression and morphometrics. We added the following sentences to the Discussion, lines 418 to 474, and completed the discussion on applicability with a table showing the purpose, requirements, applicability and limitations of each step of the processing and analysis pipeline.

      “Spectral filtering has already been applied in other systems (e.g. [7] and [8]), but is here extended to account for imaging depth-dependent apparent emission spectra of the different fluorophores. In our pipeline, we provide code to run spectral filtering on multichannel images, integrated in Python. In order to apply the spectral filtering algorithm utilized here, spectral patterns of each fluorophore need to be calibrated as a function of imaging depth, which depend on the specific emission windows and detector settings of the microscope”.

      “Image normalization using a wavelength-dependent correction also requires calibration on a given imaging setup to measure the difference in signal decay among the different fluorophores species. To our knowledge, the calibration procedures for spectral-filtering and our image-normalization approach have not been performed previously in 3D samples, which is why validation on published datasets is not readily possible. Nevertheless, they are described in detail in the Methods section, and the code used—from the calibration measurements to the corrected images—is available open-source at the Zenodo link in the manuscript”.

      Dual-view registration, local contrast enhancement, and multiscale analysis of gene expression and morphometrics are not limited to organoid data or our specific imaging modalities. To evaluate our 3D nuclei segmentation model, we tested it on diverse systems, including gastruloids stained with the nuclear marker Draq5 from Moos et al. [1]; breast cancer spheroids; primary ductal adenocarcinoma organoids; human colon organoids and HCT116 monolayers from Ong et al. [2]; and zebrafish tissues imaged by confocal microscopy from Li et al [3]. These datasets were acquired using either light-sheet or confocal microscopy, with varying imaging parameters (e.g., objective lens, pixel size, staining method). The results are added in the manuscript, Fig. S9b.

      Besides, the nuclei segmentation component lacks benchmarking against existing methods.  

      We agree with the reviewer that a benchmark against existing segmentation methods would be very useful. We tried different pre-trained models:

      CellPose, which we tested in a previous paper ([4]) and which showed poor performances compared to our trained StarDist3D model.

      DeepStar3D ([2]) is only available in the software 3DCellScope. We could not benchmark the model on our data, because the free and accessible version of the software is limited to small datasets. An image of a single whole-mount gastruloid with one channel, having dimensions (347,467,477) was too large to be processed, see screenshot below. The segmentation model could not be extracted from the source code and tested externally because the trained DeepStar3D weights are encrypted.

      Author response image 1.

      Screenshot of the 3DCellScore software. We could not perform 3D nuclei segmentation of a whole-mount gastruloids because the image size was too large to be processed.

      AnyStar ([5]), which is a model trained from the StarDist3D architecture, was not performing well on our data because of the heterogeneous stainings. Basic pre-processing such as median and gaussian filtering did not improve the results and led to wrong segmentation of touching nuclei. AnyStar was demonstrated to segment well colon organoids in Ong et al, 2025 ([2]), but the nuclei were more homogeneously stained. Our Hoechst staining displays bright chromatin spots that are incorrectly labeled as individual nuclei.

      Cellos ([6]), another model trained from StarDist3D, was also not performing well. The objects used for training and to validate the results are sparse and not touching, so the predicted segmentation has a lot of false negatives even when lowering the probability threshold to detect more objects. Additionally, the network was trained with an anisotropy of (9,1,1), based on images with low z resolution, so it performed poorly on almost isotropic images. Adapting our images to the network’s anisotropy results in an imprecise segmentation that can not be used to measure 3D nuclei deformations.

      We tried both Cellos and AnyStar predictions on a gastruloid image from Fig. S2 of our main manuscript.  The results are added in the manuscript, Fig. S9b. Fig3 displays the results qualitatively compared to our trained model Stardist-tapenade.

      Author response image 2.

      Qualitative comparison of two published segmentation models versus our model. We show one slice from the XY plane for simplicity. Segmentations are displayed with their contours only. (Top left) Gastruloid stained with Hoechst, image extracted from Fig S2 of our manuscript. (Top right) Same image overlayed with the prediction from the Cellos model, showing many false negatives. (Bottom left) Same image overlayed with the prediction from our Stardist-tapenade model. (Bottom right) Same image overlayed with the prediction from the AnyStar model, false positives are indicated with a red arrow.

      CellPose-SAM, which is a recent model developed building on the CellPose framework. The pre-trained model performs well on gastruloids imaged using our pipeline, and performs better than StarDist3D at segmenting elongated objects such as deformed nuclei. The performances are qualitatively compared on Fig. S9a and S10.  We also demonstrate how using local contrast enhancement improves the results of CellPose-SAM (Fig. S10a), showing the versatility of the Tapenade pre-processing module. Tissue-scale, packing-related metrics from Cellpose–SAM labels qualitatively match those from stardist-tapenade as shown Fig.10c and d.

      Appraisal:  

      The authors set out to establish a quantitative imaging and analysis pipeline for gastruloids using dual-view two-photon microscopy, spectral unmixing, and a custom computational framework for 3D segmentation and gene expression analysis. This aim is largely achieved. The integration of experimental and computational modules enables high-resolution in toto imaging and robust quantitative analysis at the single-cell level. The data presented support the authors' conclusions regarding the ability to capture spatial patterns of gene expression and cellular morphology across developmental stages.  

      Impact and utility:  

      This work presents a compelling and broadly applicable methodological advance. The approach is particularly impactful for the developmental biology community, as it allows researchers to extract quantitative information from high-resolution images to better understand morphogenetic processes. The data are publicly available on Zenodo, and the software is released on GitHub, making them highly valuable resources for the community.  

      We thank the reviewer for these positive feedbacks.

      Reviewer #3 (Public review):

      Summary  

      The paper presents an imaging and analysis pipeline for whole-mount gastruloid imaging with two-photon microscopy. The presented pipeline includes spectral unmixing, registration, segmentation, and a wavelength-dependent intensity normalization step, followed by quantitative analysis of spatial gene expression patterns and nuclear morphometry on a tissue level. The utility of the approach is demonstrated by several experimental findings, such as establishing spatial correlations between local nuclear deformation and tissue density changes, as well as the radial distribution pattern of mesoderm markers. The pipeline is distributed as a Python package, notebooks, and multiple napari plugins.  

      Strengths  

      The paper is well-written with detailed methodological descriptions, which I think would make it a valuable reference for researchers performing similar volumetric tissue imaging experiments (gastruloids/organoids). The pipeline itself addresses many practical challenges, including resolution loss within tissue, registration of large volumes, nuclear segmentation, and intensity normalization. Especially the intensity decay measurements and wavelength-dependent intensity normalization approach using nuclear (Hoechst) signal as reference are very interesting and should be applicable to other imaging contexts. The morphometric analysis is equally well done, with the correlation between nuclear shape deformation and tissue density changes being an interesting finding. The paper is quite thorough in its technical description of the methods (which are a lot), and their experimental validation is appropriate. Finally, the provided code and napari plugins seem to be well done (I installed a selected list of the plugins and they ran without issues) and should be very helpful for the community.

      We thank the reviewer for his positive feedback and appreciation of our work.

      Weaknesses  

      I don't see any major weaknesses, and I would only have two issues that I think should be addressed in a revision:  

      (1) The demonstration notebooks lack accompanying sample datasets, preventing users from running them immediately and limiting the pipeline's accessibility. I would suggest to include (selective) demo data set that can be used to run the notebooks (e.g. for spectral unmixing) and or provide easily accessible demo input sample data for the napari plugins (I saw that there is some sample data for the processing plugin, so this maybe could already be used for the notebooks?).  

      We thank the reviewer for this relevant suggestion. The 7 notebooks were updated to automatically download sample tests. The different parts of the pipeline can now be run immediately:

      https://github.com/GuignardLab/tapenade/tree/chekcs_on_notebooks/src/tapenade/notebooks

      (2) The results for the morphometric analysis (Figure 4) seem to be only shown in lateral (xy) views without the corresponding axial (z) views. I would suggest adding this to the figure and showing the density/strain/angle distributions for those axial views as well.

      A morphometric analysis based on the axial views was added as Fig. S6a of the manuscript, complementary to the XY views.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):  

      In lines 64 and 65, it is mentioned that confocal and light-sheet microscopy remain limited to samples under 100μm in diameter. I would recommend revising this sentence. In the paper of Moos and colleagues (also cited in this manuscript; PMID: 38509326), gastruloid samples larger than 100μm are imaged in toto with an open-top dual-view and dual-illumination light-sheet microscope, and live cell behaviour is analysed. Another example, if considering also multi-angle systems, is the impressive work of McDole and colleagues (PMID: 30318151), in which one of the authors of this manuscript is a corresponding author. There, multi-angle light sheet microscopy is used for in toto imaging and reconstruction of post-implantation mouse development (samples much larger than 100μm). Some multi-sample imaging strategies have been developed for this type of imaging system, though not to the sample number extent allowed by the Viventis LS2 system or the Bruker TruLive3D imager, which have higher image quality limitations.

      We thank the reviewer for this remark. As reported in their paper, Moos et al. used dual-view light-sheet microscopy to image gastruloids, which are particularly dense and challenging tissues, with whole-mount samples of approximately 250 µm in diameter. Nevertheless, their image quality metric (DCT) shows a rapid twofold decrease within 50 µm depth (Extended Fig 5.h), whereas with two-photon microscopy, our image quality metric (FRC-QE) decreases by a factor of two over 150 µm in non-cleared samples (PBS) (see Fig. 2 c). While these two measurements (FRC-QE versus DCT) are not directly comparable, the observed difference reflects the superior depth performance of two-photon microscopy, owing in part to the use of non-descanned detectors. In our case, imaging was performed with Hoechst, a blue fluorophore suboptimal for deep imaging, whereas in the Moos dataset (Draq5, far-red), the configuration was more favorable for imaging in depth  which further supports our conclusion.

      In McDole et al, tissues reaching 250µm were imaged from 4 views, but do not reach cellular-scale resolution in deeper layers compatible with cell segmentation to our knowledge.

      We corrected the sentence ‘However, light-sheet and confocal imaging approaches remain limited to relatively small organoids typically under 100 micrometers in diameter ‘ by the following (line 64) :

      “While advances in light-sheet microscopy have extended imaging depth in organoids, maintaining high image quality throughout thick samples remains challenging. In practice, quantitative analyses are still largely restricted to organoids under roughly 100 µm in diameter”.

      It is worth mentioning that two-photon microscopes are much more widely available than light sheet microscopes, and light sheet systems with 2-photon excitation are even less accessible, which makes the described workflow of Gros and colleagues have a wide community interest.  

      We thank the reviewer for this remark, and added this suggestion line 74:

      “Finally, two-photon microscopes are typically more accessible than light-sheet systems and allow for straightforward sample mounting, as they rely on procedures comparable to standard confocal imaging”.

      Reviewer #2 (Recommendations for the authors):  

      Suggestions:  

      A comparison with established pre-trained models for 3D organoid image segmentation (e.g., Cellos[1], AnyStar[2], and DeepStar3D[3], all based on StarDist3D) would help highlight the advantages of the authors' custom StarDist3D model, which has been specifically optimized for two-photon microscopy images.  

      (1)  Cellos: https://doi.org/10.1038/s41467-023-44162-6

      (2)  AnyStar: https://doi.org/10.1109/WACV57701.2024.00742

      (3)  DeepStar3D: https://doi.org/10.1038/s41592-025-02685-4

      We agree with the reviewer that a benchmark against existing segmentation methods is very useful. This is addressed in the revised version, as detailed above (Figure 3).

      Recommendations:  

      Please clarify the following point. In line 195, the authors state, "This allowed us to detect all mitotic nuclei in whole-mount samples for any stage and size." Does this mean that the custom-trained StarDist3D model can detect 100% of mitotic nuclei? It was not clear from the manuscript, figures, or videos how this was validated. Given the reported performance scores of the StarDist3D model for detecting all nuclei, claiming 100% detection of mitotic nuclei seems surprisingly high.

      We thank the reviewer for this comment. As it was detailed in the methods section, the detection score reaches 82%, and only the complete pipeline (detection+minimal manual curation) allows us to detect all mitotic nuclei. To make it clearer, the following precisions were added in the Results section:

      ”To detect division events, we stained gastruloids with phosphohistone H3 (ph3) and trained a separate custom Stardist3D model using 3D annotations of nuclei expressing ph3 (see Methods III H). This model together allowed us to detect nearly all mitotic nuclei in whole-mount samples for any stage and size (Fig.3f and Suppl.Movie 4), and we used minimal manual curation to correct remaining errors.”

      Minor corrections:  

      It appears that Figures 4-6 are missing from the submitted version, but they can be found in the manuscript available on bioRxiv.

      We thank the reviewer for this remark, this was corrected immediately to add Figures 4 to 6.

      In line 185, is the intended phrase "by comparing the 2D predictions and the 2D sliced annotated segments..."? 

      To gain some clarity, we replaced the initial sentence:

      “The f1 score obtained by comparing the 3D prediction and the 3D ground-truth is well approximated by the f1 score obtained by comparing the 2D annotations and the 2D sliced annotated segments, with at most a 5% difference between the two scores.” by

      “The f1 score obtained in 3D (3D prediction compared with the 3D ground-truth) is well approximated by the f1 score obtained in 2D (2D predictions compared with the 2D sliced annotated segments). The difference between the 2 scores was at most 5%.”

      Reviewer #3 (Recommendations for the authors):

      (1) How is the "local neighborhood volume" defined, and how was it computed?

      The reviewer is referring to this paragraph (the term is underscored) :

      “To probe quantities related to the tissue structure at multiple scales, we smooth their signal with a Gaussian kernel of width σ, with σ defined as the spatial scale of interest. From the segmented nuclei instances, we compute 3D fields of cell density (number of cells per unit volume), nuclear volume fraction (ratio of nuclear volume to local neighborhood volume), and nuclear volume at multiple scales.”

      To improve clarity, the phrasing has been revised: the term local neighborhood volume has been replaced by local averaging volume, and a reference to the Methods section has been added.

      From the segmented nuclei instances, we compute 3D fields of cell density (number of cells per unit volume), nuclear volume fraction (ratio of space occupied by nuclear volume within the local averaging volume, as defined in the Methods III I), and nuclear volume at multiple scales.

      (2) In the definition of inertia tensor (18), isn't the inner part normally defined in the reversed way (delta_i,j - ...)?

      We thank the reviewer for noticing this error, which we fixed in the manuscript.

      (3) For intensity normalization, the paper uses the Hoechst signal density as a proxy for a ubiquitous nuclei signal. I would assume that this is problematic, for eg, dividing cells (which would overestimate it). Would using the average Hoechst signal per nucleus mask (as segmentation is available) be a better proxy?

      We agree that this idea is appealing if one assumes a clear relationship between nuclear volume and Hoechst intensity. However, since cell and nuclear volumes vary substantially with differentiation state (see Fig. 4), such a normalization approach would introduce additional biases at large spatial scales. We believe that the most robust improvement would instead consist in masking dividing cells during the normalization procedure, as these events could be detected and excluded from the computation.

      Nonetheless, we believe the method proposed by the reviewer could prove relevant for other types of data, so we will implement this recommendation in the code available in the Tapenade package.

      (4) Figures 4-6 were part of the Supplementary Material, but should be included in the main text?

      We thank the reviewer for this remark, this was corrected immediately to add Figures 4-6.

      We also noticed a missing reference to Fig. S3 in the main text, so we added lines 302 to 307 to comment on the wavelength-dependency of the normalization method. We improved the description of Fig.6, which lacked clarity (line 316 to 321, line 327).

      (1) Moos, F., Suppinger, S., de Medeiros, G., Oost, K.C., Boni, A., Rémy, C., Weevers, S.L., Tsiairis, C., Strnad, P. and Liberali, P., 2024. Open-top multisample dual-view light-sheet microscope for live imaging of large multicellular systems. Nature Methods, 21(5), pp.798-803.

      (2) Ong, H. T.; Karatas, E.; Poquillon, T.; Grenci, G.; Furlan, A.; Dilasser, F.; Mohamad Raffi, S. B.; Blanc, D.; Drimaracci, E.; Mikec, D.; Galisot, G.; Johnson, B. A.; Liu, A. Z.; Thiel, C.; Ullrich, O.; OrgaRES Consortium; Racine, V.; Beghin, A. (2025). Digitalized organoids: integrated pipeline for high-speed 3D analysis of organoid structures using multilevel segmentation and cellular topology.  Nature Methods, 22(6), pp.1343-1354

      (3) Li, L., Wu, L., Chen, A., Delp, E.J. and Umulis, D.M., 2023. 3D nuclei segmentation for multi-cellular quantification of zebrafish embryos using NISNet3D. Electronic Imaging, 35, pp.1-9.

      (4) Vanaret, J., Dupuis, V., Lenne, P. F., Richard, F., Tlili, S., & Roudot, P. (2023). A detector-independent quality score for cell segmentation without ground truth in 3D live fluorescence microscopy. IEEE Journal of Selected Topics in Quantum Electronics, 29(4:Biophotonics), 1-12.

      (5) Dey, N., Abulnaga, M., Billot, B., Turk, E. A., Grant, E., Dalca, A. V., & Golland, P. (2024). AnyStar: Domain randomized universal star-convex 3D instance segmentation. In Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (pp. 7593-7603).

      (6) Mukashyaka, P., Kumar, P., Mellert, D. J., Nicholas, S., Noorbakhsh, J., Brugiolo, M., ... & Chuang, J. H. (2023). High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos. Nature Communications, 14(1), 8406.

      (7) Rakhymzhan, A., Leben, R., Zimmermann, H., Günther, R., Mex, P., Reismann, D., ... & Niesner, R. A. (2017). Synergistic strategy for multicolor two-photon microscopy: application to the analysis of germinal center reactions in vivo. Scientific reports, 7(1), 7101.

      (8) Dunsing, V., Petrich, A., & Chiantia, S. (2021). Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection. Elife, 10, e69687.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews: 

      Reviewer #1 (Public review):

      We thank Reviewer #1 for its thoughtful and constructive feedback. We found the suggestions particularly helpful in refining the conceptual framework and clarifying key aspects of our interpretations.

      Summary:

      This paper investigates the potential link between amygdala volume and social tolerance in multiple macaque species. Through a comparative lens, the authors considered tolerance grade, species, age, sex, and other factors that may contribute to differing brain volumes. They found that amygdala, but not hippocampal, volume differed across tolerance grades, such that hightolerance species showed larger amygdala than low-tolerance species of macaques. They also found that less tolerant species exhibited increases in amygdala volume with age, while more tolerant species showed the opposite. Given their wide range of species with varied biological and ecological factors, the authors' findings provide new evidence for changes in amygdala volume in relation to social tolerance grades. Contributions from these findings will greatly benefit future efforts in the field to characterize brain regions critical for social and emotional processing across species.

      Strengths:

      (1) This study demonstrates a concerted and impressive effort to comparatively examine neuroanatomical contributions to sociality in monkeys. The authors impressively collected samples from 12 macaque species with multiple datapoints across species age, sex, and ecological factors. Species from all four social tolerance grades were present. Further, the age range of the animals is noteworthy, particularly the inclusion of individuals over 20 years old - an age that is rare in the wild but more common in captive settings. 

      (2) This work is the first to report neuroanatomical correlates of social tolerance grade in macaques in one coherent study. Given the prevalence of macaques as a model of social neuroscience, considerations of how socio-cognitive demands are impacted by the amygdala are highly important. The authors' findings will certainly inform future studies on this topic.

      (3) The methodology and supplemental figures for acquiring brain MRI images are well detailed. Clear information on these parameters is crucial for future comparative interpretations of sociality and brain volume, and the authors do an excellent job of describing this process in full.

      Weaknesses:

      (1) The nature vs. nurture distinction is an important one, but it may be difficult to draw conclusions about "nature" in this case, given that only two data points (from grades 3 and 4) come from animals under one year of age (Method Figure 1D). Most brains were collected after substantial social exposure-typically post age 1 or 1.5-so the data may better reflect developmental changes due to early life experience rather than innate wiring. It might be helpful to frame the findings more clearly in terms of how early experiences shape development over time, rather than as a nature vs. nurture dichotomy.

      We agree with the reviewer that presenting our findings through a strict nature vs. nurture dichotomy was potentially misleading. We have revised the introduction and the discussion (e.g. lines 85-95 and 363-365) to clarify that we examined how neurodevelopmental trajectories differ across social grades with the caveat of related to the absence of very young individuals in our samples.  We now explicitly mention that our results may reflect both early species-typical biases and experience-dependent maturation.

      We positioned our study on social tolerance in a comparative neuroscience framework and introduced a tentative working model that articulates behavioral traits, cognitive dimensions, and their potential subcortical neural substrates

      Drawing upon 18 behavioral traits identified in Thierry’s comparative analyses (Thierry, 2021, 2007), we organize these traits into three core dimensions: socio-cognitive demands, behavioral inhibition, and the predictability of the social environment (Table 1). This conceptualization does not aim to redefine social tolerance itself, but rather to provide a structured basis for testing neuroanatomical hypotheses related to social style variability. It echoes recent efforts to bridge behavioral ecology and cognitive neuroscience by linking specific mental abilities – such as executive functions or metacognition – with distinct prefrontal regions shaped by social and ecological pressures (Bouret et al., 2024).

      “Cross-fostering experiments (De Waal and Johanowicz, 1993), along with our own results, suggest that social tolerance grades reflect both early, possibly innate predispositions and later environmental shaping”.

      (2) It would be valuable to clarify how the older individuals, especially those 20+ years old, may have influenced the observed age-related correlations (e.g., positive in grades 1-2, negative in grades 3-4). Since primates show well-documented signs of aging, some discussion of the potential contribution of advanced age to the results could strengthen the interpretation.

      We thank the reviewer for highlighting this important point. In our dataset, younger and older subjects are underrepresented, but they are distributed across all subgroups. Therefore, we do not think that it could drive the interaction effect we are reporting. In our sample, amygdala volume tended to increase with age in intolerant species and decrease in tolerant species. We included a new analysis (Figure 4) that allows providing a clearer assessment of when social grades 1 vs 4 differed in terms of amygdala and hippocampus volume. While our model accounts for age continuously, we agree that age-related variation deserves cautious interpretation and require longitudinal designs in future studies.

      We also added the following statements in the discussion (lines 386-391)

      “Due to a limited sample size of our study, this crossing trend, already accounted for by our continuous age model, should be further investigated. These results call for cautious interpretation of age-related variation and further emphasize the importance of longitudinal studies integrating both behavioral, cognitive and anatomical data in non-human primates, which would help to better understand the link between social environment and brain development (Song et al., 2021)”.

      (3) The authors categorize the behavioral traits previously described in Thierry (2021) into 3 selfdefined cognitive requirements, however, they do not discuss under what conditions specific traits were assigned to categories or justify why these cognitive requirements were chosen. It is not fully clear from Thierry (2021) alone how each trait would align with the authors' categories. Given that these traits/categories are drawn on for their neuroanatomical hypotheses, it is important that the authors clarify this. It would be helpful to include a table with all behavioral traits with their respective categories, and explain their reasoning for selecting each cognitive requirement category.

      Thank you for this important suggestion. We have extensively revised the introduction to explain how we derived from the scientific literature the three cognitive dimensions—socio-cognitive demands, behavioral inhibition, and predictability of the social environment—. We now provide a complete overview of the 18 behavioral traits described in Thierry’s framework and their cognitive classification in a dedicated table , along with hypothesized neural correlates. We have also mentioned traits that were not classified in our framework along with short justification of this classification. We believe this addition significantly improves the transparency and intelligibility of our conceptual approach.

      “The concept of social tolerance, central to this comparative approach, has sometimes been used in a vague or unidimensional way. As Bernard Thierry (2021) pointed out, the notion was initially constructed around variations in agonistic relationships – dominance, aggressiveness, appeasement or reconciliation behaviors – before being expanded to include affiliative behaviors, allomaternal care or male–male interactions (Thierry, 2021). These traits do not necessarily align along a single hierarchical axis but rather reflect a multidimensional complexity of social style, in which each trait may have co-evolved with others (Thierry, 2021, 2000; Thierry et al., 2004). Moreover, the lack of a standardized scientific definition has sometimes led to labeling species as “tolerant” or “intolerant” without explicit criteria (Gumert and Ho, 2008; Patzelt et al., 2014). These behavioral differences are characterized by different styles of dominance (Balasubramaniam et al., 2012), severity of agonistic interactions (Duboscq et al., 2014), nepotism (Berman and Thierry, 2010; Duboscq et al., 2013; Sueur et al., 2011) and submission signals (De Waal and Luttrell, 1985; Rincon et al., 2023), among the 18 covariant behavioral traits described in Thierry's classification of social tolerance (Thierry, 2021, 2017, 2000)”.

      “To ground the investigation of social tolerance in a comparative neuroanatomical framework, we introduce a tentative working model that articulates behavioral traits, cognitive dimensions, and their potential subcortical neural substrates. Drawing upon 18 behavioral traits identified in Thierry’s comparative analyses (Thierry, 2021, 2007), we organized these traits into three core dimensions: socio-cognitive demands, behavioral inhibition, and the predictability of the social environment (Table 1). This conceptualization does not aim to redefine social tolerance itself, but rather to provide a structured basis for testing neuroanatomical hypotheses related to social style variability. It echoes recent efforts to bridge behavioral ecology and cognitive neuroscience by linking specific mental abilities – such as executive functions or metacognition – with distinct prefrontal regions shaped by social and ecological pressures (Bouret et al., 2024; Testard 2022)”.

      (4) One of the main distinctions the authors make between high social tolerance species and low tolerance species is the level of complex socio-cognitive demands, with more tolerant species experiencing the highest demands. However, socio-cognitive demands can also be very complex for less tolerant species because they need to strategically balance behaviors in the presence of others. The relationships between socio-cognitive demands and social tolerance grades should be viewed in a more nuanced and context-specific manner. 

      We fully agree and we did not mean that intolerant species lives in a ‘simple’ social environment but that the ones of more tolerant species is markedly more demanding. Evidence supporting this statement include their more efficient social networks (Sueur et al., 2011) and more complex communicative skills (e.g. tolerant macaques displayed higher levels of vocal diversity and flexibility than intolerant macaques in social situation with high uncertainty (Rebout et al., 2020).

      In the revised version (lines 106-122), we now highlight that socio-cognitive challenges arise across the tolerance spectrum, including in less tolerant species where strategic navigation of rigid hierarchies and risk-prone interactions is required. We hope that this addition offers a more balanced and nuanced framing of socio-cognitive demands across macaque societies

      “The first category, socio-cognitive demands, refers to the cognitive resources needed to process, monitor, and flexibly adapt to complex social environments. Linking those parameters to neurological data is at the core of the social brain theory to explain the expansion of the neocortex in primates (Dunbar). Macaques social systems require advanced abilities in social memory, perspective-taking, and partner evaluation (Freeberg et al., 2012). This is particularly true in tolerant species, where the increased frequency and diversity of interactions may amplify the demands on cognitive tracking and flexibility. Tolerant macaque species typically live in larger groups with high interaction frequencies, low nepotism, and a wider range of affiliative and cooperative behaviors, including reconciliation, coalition-building, and signal flexibility (REF). Tolerant macaque species also exhibit a more diverse and flexible vocal and facial repertoire than intolerants ones which may help reduce ambiguity and facilitate coordination in dense social networks (Rincon et al., 2023; Scopa and Palagi, 2016; Rebout 2020). Experimental studies further show that macaques can use facial expressions to anticipate the likely outcomes of social interactions, suggesting a predictive function of facial signals in managing uncertainty (Micheletta et al., 2012; Waller et al., 2016). Even within less tolerant species, like M. mulatta, individual variation in facial expressivity has been linked to increased centrality in social networks and greater group cohesion, pointing to the adaptive value of expressive signaling across social styles (Whitehouse et al., 2024)”.

      (5) While the limitations section touches on species-related considerations, the issue of individual variability within species remains important. Given that amygdala volume can be influenced by factors such as social rank and broader life experience, it might be useful to further emphasize that these factors could introduce meaningful variation across individuals. This doesn't detract from the current findings but highlights the importance of considering life history and context when interpreting subcortical volumes-particularly in future studies.

      We have now emphasized this point in the limitations section (lines 441-456). While our current dataset does not allow us to fully control for individual-level variables across all collection centers, we recognize that factors such as rank, social exposure, and individual life history may influence subcortical volumes

      “Although we explained some interspecies variability, adding subjects to our database will increase statistical power and will help addressing potential confounding factors such as age or sex in future studies. One will benefit from additional information about each subject. While considered in our modelling, the social living and husbandry conditions of the individuals in our dataset remain poorly documented. The living environment has been considered, and the size of social groups for certain individuals, particularly for individuals from the CdP, have been recorded. However, these social characteristics have not been determined for all individuals in the dataset. As previously stated, the social environment has a significant impact on the volumetry of certain regions. Furthermore, there is a lack of data regarding the hierarchy of the subjects under study and the stress they experience in accordance with their hierarchical rank and predictability of social outcomes position (McCowan et al., 2022)”. 

      Reviewer #2 (Public review):

      We thank Reviewer #2 for its thoughtful remarks and for acknowledging the value of our comparative approach despite its inherent constraints.

      Summary:

      This comparative study of macaque species and the type of social interaction is both ambitious and inevitably comes with a lot of caveats. The overall conclusion is that more intolerant species have a larger amygdala. There are also opposing development profiles regarding amygdala volume depending on whether it is a tolerant or intolerant species.

      To achieve any sort of power, they have combined data from 4 centres, which have all used different scanning methods, and there are some resolution differences. The authors have also had to group species into 4 classifications - again to assist with any generalisations and power. They have focused on the volumes of two structures, the amygdala and the hippocampus, which seems appropriate. Neither structure is homogeneous and so it may well be that a targeted focus on specific nuclei or subfields would help (the authors may well do this next) - but as the variables would only increase further along with the number of potential comparisons, alongside small group numbers, it seems only prudent to treat these findings are preliminary. That said, it is highly unlikely that large numbers of macaque brains will become available in the near future.

      This introduction is by way of saying that the study achieves what it sets out to do, but there are many reasons to see this study as preliminary. The main message seems to be twofold: (1) that more intolerant species have relatively larger amygdalae, and (2) that with development, there is an opposite pattern of volume change (increasing with age in intolerant species and decreasing with age in tolerant species). Finding 1 is the opposite of that predicted in Table 1 - this is fine, but it should be made clearer in the Discussion that this is the case, otherwise the reader may feel confused. As I read it, the authors have switched their prediction in the Discussion, which feels uncomfortable. 

      We thank the reviewer for this important observation. In the original version, Table 1 presented simplified direct predictions linking social tolerance grades to amygdala and hippocampus volumes. We recognize that this formulation may have created confusion In the revised manuscript, we have thoroughly restructured the table and its accompanying rationale. Table 1 now better reflects our conceptual framework grounded in three cognitive dimensions—sociocognitive demands, behavioral inhibition, and social predictability—each linked to behavioral traits and associated neural hypotheses based on published literature. This updated framework, detailed in lines 144-169 of the introduction, provides a more nuanced basis for interpreting our results and avoids the inconsistencies previously noted. The Discussion was also revised accordingly (lines 329-255) to clarify where our findings diverge from the original predictions and to explore alternative explanations based on social complexity. Rather than directly predicting amygdala size from social tolerance grades, we propose that variation in volume emerges from differing combinations of cognitive pressures across species.

      It is inevitable that the data in a study of this complexity are all too prone to post hoc considerations, to which the authors indulge. In the case of Grade 1 species, the individuals have a lot to learn, especially if they are not top of the hierarchy, but at the same time, there are fewer individuals in the troop, making predictions very tricky. As noted above, I am concerned by the seemingly opposite predictions in Table 1 and those in the Discussion regarding tolerance and amygdala volume. (It may be that the predictions in Table 1 are the opposite of how I read them, in which case the Table and preceding text need to align.)

      In order to facilitate the interpretation of our Bayesian modelling, we have selected a more focused ROI in our automatic segmentation procedure of the Hippocampus (from Hippocampal Formation to Hippocampus) and have added to the new analysis (Figure 4) that helps to properly test whether the hippocampus significantly differs between species from social grade 1 vs 4. The present analysis found that this is the case in adult monkeys. This is therefore consistent with our hypothesis that amygdala volumes are principally explained by heightened sociocognitive demands in more tolerant species.

      We also acknowledge the reviewer’s concerns about the limited generalizability due to our sample. The challenges of comparative neuroimaging in non-human primates—especially when using post-mortem datasets—are substantial. Given the ethical constraints and the rarity of available specimens, increasing the number of individuals or species is not feasible in the short term. However, we have made all data and code publicly available and clearly stated the limitations of our sample in the manuscript. Despite these constraints, we believe our dataset offers an unprecedented comparative perspective, particularly due to the inclusion of rare and tolerant species such as M. tonkeana, M. nigra, and M. thibetana, which have never been included in structural MRI studies before. We hope this effort will serve as a foundation for future collaborative initiatives in primate comparative neuroscience.

      Reviewer #3 (Public review):

      We thank Reviewer #3 for their thoughtful and detailed review. Their comments helped us refine both the conceptual and interpretative aspects of the manuscript. We respond point by point below.

      Summary:

      In this study, the authors were looking at neurocorrelates of behavioural differences within the genus Macaca. To do so, they engaged in real-world dissection of dead animals (unconnected to the present study) coming from a range of different institutions. They subsequently compare different brain areas, here the amygdala and the hippocampus, across species. Crucially, these species have been sorted according to different levels of social tolerance grades (from 1 to 4). 12 species are represented across 42 individuals. The sampling process has weaknesses ("only half" of the species contained by the genus, and Macaca mulatta, the rhesus macaque, representing 13 of the total number of individuals), but also strengths (the species are decently well represented across the 4 grades) for the given purpose and for the amount of work required here. I will not judge the dissection process as I am not a neuroanatomist, and I will assume that the different interventions do not alter volume in any significant ways / or that the different conditions in which the bodies were kept led to the documented differences across species. 

      25 brains were extracted by the authors themselves who are highly with this procedure. Overall, we believe that dissection protocols did not alter the total brain volume. Despite our expertise, we experienced some difficulties to not damage the cerebellum. Therefore, this region was not included in our analysis. We also noted that this brain region was also damaged or absent from the Prime-DE dataset.

      Several protocols were used to prepare and store tissue. It could have impacted the total brain volume.

      We agree that differences in tissue preparation and storage could potentially affect total brain volume. Therefore, we explicitly included the main sample preparation variable — whether brains had been previously frozen — as a covariate in our model. This factor did not explain our results. Moreover, Figures 1D and 1I display the frozen status and its correlation with the amygdala and hippocampus ratios, respectively. Figure 2 shows the parameters of the model and the posterior distributions for the frozen status and total brain volume effects.

      There are two main results of the study. First, in line with their predictions, the authors find that more tolerant macaque species have larger amygdala, compared to the hippocampus, which remains undifferentiated across species. Second, they also identify developmental effects, although with different trends: in tolerant species, the amygdala relative volume decreases across the lifespan, while in intolerant species, the contrary occurs. The results look quite strong, although the authors could bring up some more clarity in their replies regarding the data they are working with. From one figure to the other, we switch from model-calculated ratio to modelpredicted volume. Note that if one was to sample a brain at age 20 in all the grades according to the model-predicted volumes, it would not seem that the difference for amygdala would differ much across grades, mostly driven with Grade 1 being smaller (in line with the main result), but then with Grade 2 bigger than Grade 3, and then Grade 4 bigger once again, but not that different from Grade 2.

      Overall, despite this, I think the results are pretty strong, the correlations are not to be contested, but I also wonder about their real meaning and implications. This can be seen under 3 possible aspects:

      (1)  Classification of the social grade

      While it may be familiar to readers of Thierry and collaborators, or to researchers of the macaque world, there is no list included of the 18 behavioral traits used to define the three main cognitive requirements (socio-cognitive demands, predictability of the environment, inhibitory control). It would be important to know which of the different traits correspond to what, whether they overlap, and crucially, how they are realized in the 12 study species, as there could be drastic differences from one species to the next. For now, we can only see from Table S1 where the species align to, but it would be a good addition to have them individually matched to, if not the 18 behavioral traits, at least the 3 different broad categories of cognitive requirements.

      We fully agree with this observation. In the revised version of the manuscript, we now include a detailed conceptual table listing all 18 behavioral traits from Thierry’s framework. For each trait, we provide its underlying social implications, its associated cognitive dimension (when applicable), and the hypothesized neural correlate. 

      While some traits may could have been arguably classified in several cognitive dimensions (e.g. reconciliation rate), we preferred to assign each to a unique dimension for clarity. Additionally, the introduction (lines 95-169 + Table1) now explains how each trait was evaluated based on existing literature and assigned to one of the three proposed cognitive categories: socio-cognitive demands, behavioral inhibition, or social unpredictability. This structure offers a clearer and more transparent basis for the neuroanatomical hypotheses tested in the study.

      “Navigating social life in primate societies requires substantial cognitive resources: individuals must not only track multiple relationships, but also regulate their own behavior, anticipate others’ reactions, and adapt flexibly to changing social contexts. Taken advantage of databases of magnetic resonance imaging (MRI) structural scans, we conducted the first comparative study integrating neuroanatomical data and social behavioral data from closely related primate species of the same genus to address the following questions: To what extent can differences in volumes of subcortical brain structures be correlated with varying degrees of social tolerance? Additionally, we explored whether these dispositions reflect primarily innate features, shaped by evolutionary processes, or acquired through socialization within more or less tolerant social environments”.

      “The first category, socio-cognitive demands, refers to the cognitive resources needed to process, monitor, and flexibly adapt to complex social environments. Linking those parameters to neurological data is at the core of the social brain theory to explain the expansion of the neocortex in primates (Dunbar). Macaques social systems require advanced abilities in social memory, perspective-taking, and partner evaluation (Freeberg et al., 2012). This is particularly true in tolerant species, where the increased frequency and diversity of interactions may amplify the demands on cognitive tracking and flexibility. Tolerant macaque species typically live in larger groups with high interaction frequencies, low nepotism, and a wider range of affiliative and cooperative behaviors, including reconciliation, coalition-building, and signal flexibility (REF). Tolerant macaque species also exhibit a more diverse and flexible vocal and facial repertoire than intolerants ones which may help reduce ambiguity and facilitate coordination in dense social networks (Rincon et al., 2023; Scopa and Palagi, 2016; Rebout 2020). Experimental studies further show that macaques can use facial expressions to anticipate the likely outcomes of social interactions, suggesting a predictive function of facial signals in managing uncertainty (Micheletta et al., 2012; Waller et al., 2016). Even within less tolerant species, like M. mulatta, individual variation in facial expressivity has been linked to increased centrality in social networks and greater group cohesion, pointing to the adaptive value of expressive signaling across social styles (Whitehouse et al., 2024)”.

      “The second category, inhibitory control, includes traits that involve regulating impulsivity, aggression, or inappropriate responses during social interactions. Tolerant macaques have been shown to perform better in tasks requiring behavioral inhibition and also express lower aggression and emotional reactivity in both experimental and natural contexts (Joly et al., 2017; Loyant et al., 2023). These features point to stronger self-regulation capacities in species with egalitarian or less rigid hierarchies. More broadly, inhibition – especially in its strategic form (self-control) – has been proposed to play a key role in the cohesion of stable social groups. Comparative analyses across mammals suggest that this capacity has evolved primarily in anthropoid primates, where social bonds require individuals to suppress immediate impulses in favour of longer-term group stability (Dunbar and Shultz, 2025). This view echoes the conjecture of Passingham and Wise (2012), who proposed that the emergence of prefrontal area BA10 in anthropoids enabled the kind of behavioural flexibility needed to navigate complex social environments (Passingham et al., 2012)”.

      “The third category, social environment predictability, reflects how structured and foreseeable social interactions are within a given society. In tolerant species, social interactions are more fluid and less kin-biased, leading to greater contextual variation and role flexibility, which likely imply a sustained level of social awareness. In fact, as suggested by recent research, such social uncertainty and prolonged incentives are reflected by stress-related physiology : tolerant macaques such as M. tonkeana display higher basal cortisol levels, which may be indicative of a chronic mobilization of attentional and regulatory resources to navigate less predictable social environments (Sadoughi et al., 2021)”.

      “Each behavioral trait was individually evaluated based on existing empirical literature regarding the types of cognitive operations it likely involves. When a primary cognitive dimension could be identified, the trait was assigned accordingly. However, some behaviors – such as maternal protection, allomaternal care, or delayed male dispersal – do not map neatly onto a single cognitive process. These traits likely emerge from complex configurations of affective and socialmotivational systems, and may be better understood through frameworks such as attachment theory (Suomi, 2008), which emphasizes the integration of social bonding, emotional regulation, and contextual plasticity. While these dimensions fall beyond the scope of the present framework, they offer promising directions for future research, particularly in relation to the hypothalamic and limbic substrates of social and reproductive behavior”.

      “Rather than forcing these traits into potentially misleading categories, we chose to leave them unclassified within our current cognitive framework. This decision reflects both a commitment to conceptual clarity and the recognition that some behaviors emerge from a convergence of cognitive demands that cannot be neatly isolated. This tripartite framework, leaving aside reproductive-related traits, provides a structured lens through which to link behavioral diversity to specific cognitive processes and generate neuroanatomical predictions”.

      (2) Issue of nature vs nurture

      Another way to look at the debate between nature vs nurture is to look at phylogeny. For now, there is no phylogenetic tree that shows where the different grades are realized. For example, it would be illuminating to know whether more related species, independently of grades, have similar amygdala or hippocampus sizes. Then the question will go to the details, and whether the grades are realized in particular phylogenetic subdivisions. This would go in line with the general point of the authors that there could be general species differences.

      As pointed out by Thierry and collaborators, the social tolerance concept is already grounded in a phylogenetic framework as social tolerance matches the phylogenetical tree of these macaque species, suggesting a biological ground of these behavioral observations. Given the modest sample size and uneven species representation, we opted not to adopt tools such as Phylogenetic Generalized Least Squares (PGLS) in our analysis. Our primary aim in this study was to explore neuroanatomical variation as a function of social traits, not to perform a phylogenetic comparative analysis per see. That said, we now explicitly acknowledge this limitation in the Discussion and indicate that future work using larger datasets and phylogenetic methods will be essential to disentangle social effects from evolutionary relatedness. We hope that making our dataset openly available will facilitate such futures analyses.

      With respect to nurture, it is likely more complicated: one needs to take into account the idiosyncrasies of the life of the individual. For example, some of the cited literature in humans or macaques suggests that the bigger the social network, the bigger the brain structure considered. Right, but this finding is at the individual level with a documented life history. Do we have any of this information for any of the individuals considered (this is likely out of the scope of this paper to look at this, especially for individuals that did not originate from CdP)?

      We appreciate this insightful observation. Indeed, findings from studies in humans and nonhuman primates showing associations between brain structure and social network size typically rely on detailed life history and behavioral data at the individual level. Unfortunately, such finegrained information was not consistently available across our entire sample. While some individuals from the Centre de Primatologie (CdP) were housed in known group compositions and social settings, we did not have access to longitudinal social data—such as rank, grooming rates, or network centrality—that would allow for robust individual-level analyses. We now acknowledge this limitation more clearly in the Discussion (lines 436-443), and we fully agree that future work combining neuroimaging with systematic behavioral monitoring will be necessary to explore how species-level effects interact with individual social experience.

      (3) Issue of the discussion of the amygdala's function

      The entire discussion/goal of the paper, states that the amygdala is connected to social life. Yet, before being a "social center", the amygdala has been connected to the emotional life of humans and non-humans alike. The authors state L333/34 that "These findings challenge conventional expectations of the amygdala's primary involvement in emotional processes and highlight the complexity of the amygdala's role in social cognition". First, there is no dichotomy between social cognition and emotion. Emotion is part of social cognition (unless we and macaques are robots). Second, there is nowhere in the paper a demonstration that the differences highlighted here are connected to social cognition differences per se. For example, the authors have not tested, say, if grade 4 species are more afraid of snakes than grade 1 species. If so, one could predict they would also have a bigger amygdala, and they would probably also find it in the model. My point is not that the authors should try to correlate any kind of potential aspect that has been connected to the amygdala in the literature with their data (see for example the nice review by DomínguezBorràs and Vuilleumier, https://doi.org/10.1016/B978-0-12-823493-8.00015-8), but they should refrain from saying they have challenged a particular aspect if they have not even tested it. I would rather engage the authors to try and discuss the amygdala as a multipurpose center, that includes social cognition and emotion.

      We thank the reviewer for this important and nuanced point. We have revised the manuscript to adopt a more cautious and integrative tone regarding the function of the amygdala. In the revised Discussion (lines 341-355), we now explicitly state that the amygdala is involved in a broad range of processes—emotional, social, and affective—and that these domains are deeply intertwined. Rather than proposing a strict dissociation, we now suggest that the amygdala supports integrated socio-emotional functions that are mobilized differently across social tolerance styles. We also cite recent relevant literature (e.g., Domínguez-Borràs & Vuilleumier, 2021) to support this view and have removed any claim suggesting we challenge the emotional function of the amygdala per se. Our aim is to contribute to a richer understanding of how affective and social processes co-construct structural variation in this region.

      Strengths:

      Methods & breadth of species tested.

      Weaknesses:

      Interpretation, which can be described as 'oriented' and should rather offer additional views.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Private Comments:

      (1) Table 1 should be formatted for clarity i.e., bolded table headers, text realignment, and spacing. It was not clear at first glance how information was organized. It may also be helpful to place behavioral traits as the first column, seeing that these traits feed into the author's defined cognitive requirements.

      We have reformatted Table 1 to improve clarity and readability. Behavioral traits now appear in the first column, followed by cognitive dimensions and hypothesized neural correlates. Column headers have been bolded and alignment has been standardized.

      (2) Figures could include more detail to help with interpretations. For example, Figure 3 should define values included on the x-axis in the figure caption, and Figure 4 should explain the use of line, light color, and dark color. Figure 1 does not have a y-axis title.

      The figures have been revised and legends completed to ensure more clarity.

      (3) Please proofread for typos throughout.

      The manuscript has been carefully proofread, and all typographical and grammatical errors have been corrected. These changes are visible in the tracked version.

      Reviewer #2 (Recommendations for the authors):

      Specific comments:

      (1) Given all of the variability would it not be a good idea to just compare (eg in the supplemental) the macaque data from just the Strasbourg centre for m mulatta and m toneanna. I appreciate the ns will be lower, but other matters are more standardized.

      We fully understand the reviewer’s suggestion to restrict the comparison to data collected at a single site in order to minimize inter-site variability. However, as noted, such an analysis would come at the cost of statistical power, as the number of individuals per species within a single center is small. For example, while M. tonkeana is well represented at the Strasbourg centre, only one individual of M. mulatta is available from the same site. Thus, a restricted comparison would severely limit the interpretability of results, particularly for age-related trajectories. To address variability, we included acquisition site and brain preservation method as covariates or predictors where appropriate, and we have been cautious in our interpretations. We also now emphasize in the Methods and Discussion the value of future datasets with more standardized acquisition protocols across species and centers. We hope that by openly sharing our data and workflow, we can contribute to this broader goal.

      (2) I have various minor edits:

      (a) L 25 abstract - Specify what is meant by 'opposite trend'; the reader cannot infer what this is.

      Modified in line 25-28: “Unexpectedly, tolerant species exhibited a decrease in relative amygdala volume across the lifespan, contrasting with the age-related increase observed in intolerant species—a developmental pattern previously undescribed in primates.”

      (b) L67 - The reference 'Manyprimates' needs fixing as it does in the references section.

      After double checking, Manyprimates studies are international collaborative efforts that are supposed to be cite this way (https://manyprimates.github.io/#pubs).

      (c) L74 - Taking not Taken.

      This typo has been corrected.

      (d) L129 - It says 'total volume', but this is corrected total volume?

      We have clarified in the figures legends that the “total brain volume” used in our analyses excludes the cerebellum and the myelencephalon, as specified in our image preprocessing protocol. This ensures consistency across individuals and institutions.

      (e) L138 - Suddenly mentions 'frozen condition' without any prior explanation - this needs explaining in the legend - also L144.

      We have added an explanation of the ‘frozen condition’ variable in in the relevant figure legend.

      (f) L166 - Results - it would be helpful to remind readers what Grade 1 signifies, ie intolerant species.

      We now include a brief reminder in the Results section that Grade 1 corresponds to socially intolerant species, to help readers unfamiliar with the classification (Lines 240-251).

      (g)Figure 4 - Provide the ns for each of the 4 grades to help appreciate the meaningfulness of the curves, etc.

      The number of subjects has been added to the Figure and a novel analysis helps in the revised ms help to appreciate the meaningfulness of some of these curves.

      (h) L235 - 'we had assumed that species of high social tolerance grade would have presented a smaller amygdala in size compared to grade 1'. But surely this is the exact opposite of what is predicted in Table 1 - ie, the authors did not predict this as I read the paper (Unless Table l is misleading/ambiguous and needs clarification).

      As discussed in our response to Reviewer #2 and #3, we have restructured both Table 1 and the Discussion to ensure consistency. We now explicitly state that the findings diverge from our initial inhibitory-control-based prediction and propose alternative interpretations based on sociocognitive demands.

      (i) L270 - 'This observation' which?? Specify.

      We have replaced ‘this observation’ with a precise reference to the observed developmental decrease in amygdala volume in tolerant species.

      (j) L327 - 'groundbreaking' is just hype given that there are so many caveats - I personally do not like the word - novel is good enough.

      We have replaced the word ‘groundbreaking’ with ‘novel’ to adopt a more measured and appropriate tone in the discussion.

      (3) I might add that I am happy with the ethics regarding this study. 

      Thanks, we are also happy that we were able to study macaque brains from different species using opportunistic samplings along with already available data. We are collectively making progress on this!

      (4) Finally, I should commend the authors on all the additional information that they provide re gender/age/species. Given that there are 2xs are many females as males, it would be good to know if this affects the findings. I am not a primatologist, so I don't know, for example, if the females in Grade 1 monkeys are just as intolerant as the males?

      We thank the reviewer for this thoughtful comment. We now explicitly mention the female-biased sex ratio in the Methods section and report in the Results (Figure 2, Figure 3) that sex was included as a covariate in our Bayesian models. While a small effect of sex was found for hippocampal volume, no effect was observed for the amygdala. Given the strong imbalance in our dataset (2:1 female-to-male ratio), we refrained from drawing any conclusion about sex-specific patterns, as these would require larger and more balanced samples. Although we did not test for sex-by-grade interactions, we agree that this question—especially regarding whether females and males express social style differences similarly across grades—represents an important direction for future comparative work.

      Reviewer #3 (Recommendations for the authors):

      I found the article well-written, and very easy to follow, so I have little ways to propose improvements to the article to the authors, besides addressing the various major points when it comes to interpretation of the data.

      One list I found myself wanting was in fact the list of the social tolerance grades, and the process by which they got selected into 3 main bags of socio-cognitive skills. Then it would become interesting to see how each of the 12 species compares within both the 18 grades (maybe once again out of the scope of this paper, there are likely reviews out there that already do that, but then the authors should explicitly mention so in the paper: X, 19XX have compared 15 out of 18 traits in YY number of macaque species); and within the 3 major subcognitive requirements delineated by the authors, maybe as an annex?

      We thank the reviewer for this thoughtful suggestion. In the revised manuscript, we now include a detailed table (Table 1) that lists the 18 behavioral traits derived from Thierry’s framework, along with their associated cognitive dimension and hypothesized neuroanatomical correlate. While we did not create a matrix mapping each of the 12 species across all 18 traits due to space and data availability constraints, we agree this is an important direction that should be tackled by primatologist. We now include a sentence (line 87-90) in the manuscript to guide readers to previous comparative reviews (e.g., Thierry, 2000; Thierry et al., 2004, 2021) that document the expression of these traits across macaque species. We also clarify that our three cognitive categories are conceptual tools intended to structure neuroanatomical predictions, and not formal clusters derived from quantitative analyses.

      In the annex, it would also be good to have a general summarizing excel/R file for the raw data, with important information like age, sex, and the relevant calculated volumes for each individual. The folders available following the links do not make it an easy task for a reader to find the raw data in one place.

      We fully agree with the reviewer on the importance of data accessibility. We have now uploaded an additional supplementary file in .csv format on our OSF repository, which includes individuallevel metadata for all 42 macaques: species, sex, age, social grade, total brain volume, amygdala volume, and hippocampus volume. The link to this file is now explicitly mentioned in the Data Availability section. We hope this will facilitate comparisons with other datasets and improve usability for the community. In addition, we provide in a supplementary table the raw data that were used for our Bayesian modelling (see below).

      The availability of the raw data would also clear up one issue, which I believe results from the modelling process: it looks odd on Figure 2, that volume ratios, defined as the given brain area volume divided by the total brain volume, give values above 1 (especially for the hippocampus). As such, the authors should either modify the legend or the figure. In general, it would be nicer to have the "real values" somewhere easily accessible, so that they can be compared more broadly with: 1) other macaques species to address questions relevant to the species; 2) other primates to address other questions that are surely going to arise from this very interesting work!

      We thank the reviewer for pointing this out. The ratio values in Figure 1 correspond to the proportion of the regional volume (amygdala or hippocampus) relative to the total brain volume, excluding the cerebellum and myelencephalon. As such, values above 0.01 (i.e., above 1% of the brain volume) are expected for these structures and do not indicate an error. We have updated the figure legend to clarify this point explicitly. In addition, we have now made a cleaned .csv file available via OSF, containing all raw volumetric data and metadata in a format that facilitates cross-species or cross-study comparisons. This replaces the previous folder-based structure, which may have been less accessible.

      Typos:

      L233: delete 'in'

      L430: insert space in 'NMT template(Jung et al., 2021).'

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Recommendations for the authors):

      (1) My primary concern is that in some of the studies, there are not enough data points to be totally convincing. This is particularly apparent in the low z-force condition of Figure 1C.

      We agree that adequate sampling is essential for drawing robust conclusions. To address this concern, we performed a post hoc sensitivity analysis to assess the statistical power of our dataset. Given our sample sizes (N = 85 and 45) and observed variability, the experiment had 80% power (α = 0.05) to detect a difference in stall force of approximately 0.36 pN (Cohen’s d ≈ 0.38). The actual difference observed between conditions was 0.25 pN (d ≈ 0.26), which lies below the minimum detectable effect size. Thus, the non-significant result (p = 0.16) likely reflects that any true difference, if present, is smaller than the experimental sensitivity, rather than a lack of sufficient sampling.

      Importantly, both measured stall forces fall within the reported range for kinesin-1 in the literature, supporting that the dataset is representative and the measurements are reliable.

      (2) I'm also concerned about Figure 2B. Does each data point in the three graphs represent only a single event? If so, this should probably be repeated several more times to ensure that the data are robust.

      Each data point shown corresponds to the average of many processive runs, ranging from 32 to 167. This has been updated in the figure caption accordingly.

      (3) Figure 3. I'm surprised that the authors could not obtain a higher occupancy of the multivalent DNA tether with kinesin motors. They were adding up to a 30X higher concentration of kinesin, but still did not achieve stoichiometric labeling. The reasons for this should be discussed. This makes interpretation of the mechanical data much tougher. For instance, only 6-7% of the beads would be driven by three kinesins. Unless the movement of hundreds of beads were studied, I think it would be difficult to draw any meaningful insight, since most of the events would be reflective of beads with only one or sometimes two kinesins bound. I think more discussion is required to describe how these data were treated.

      The mass-photometry data in Figure 3B were acquired in the presence of a 3-fold molar excess of kinesin (Supplemental Figure 4) relative to the DNA chassis. In comparison, optical trapping studies were performed at a 10-20-fold molar excess of kinesin, resulting in a substantially higher percentage of chassis with multiple motors. The reason why we had to perform mass photometry measurements at lower molar excess than the optical trap is that at higher kinesin concentrations, the “kinesin-only” peak dominated and obscured 2- or 3-kinesin-bound species, preventing reliable fitting of the mass photometry data. 

      We have now used the mass photometry measurements to extrapolate occupancies under trapping conditions. We estimate 76-93% of 2-motor chassis are bound to two kinesins and ~70% of 3-motor chassis are bound to three kinesins under our trapping conditions. Moreover, the mean forces in Figures 3C–D exceed those expected for a single kinesin, consistent with occupancy substantially greater than one motor per chassis.

      We wrote: “To estimate the percentage of chassis with two and three motors bound, we performed mass photometry measurements at a 3-fold molar excess of kinesin to the chassis, as higher ratios would obscure the distinction of complexes from the kinesin-only population. Assuming there is no cooperativity among the binding sites, we modeled motor occupancy using a Binomial distribution (Figure 3_figure supplement 2). We observed 17-29% of particles corresponded to the two-motor species on the 2-motor chassis in mass photometry, indicating that 45-78% of the 2-motor chassis was bound to two kinesins. Similarly, 15% and 40% of the 3motor chassis were bound to two and three kinesins, respectively.  

      In optical trapping assays, we used 10-fold and 20-fold molar excess of kinesin for 2-motor and 3-motor chassis, respectively, to substantially increase the percentage of the chassis carried by multiple kinesins. Under these conditions, we estimate 76-93% of the 2-motor chassis were bound to two kinesins, and 30% and 70% of 3-motor chassis were bound to two and three kinesins, respectively.”

      “Multi-motor trapping assays were performed similarly using 10x and 20x kinesin for 2- and 3motor chassis, respectively. To estimate the percentage of chassis with multiple motors, we used the probability of kinesin binding to a site on a chassis from mass photometry in 3x excess condition to compute an effective dissociation constant where r is the molar ratio of kinesin to chassis. Single-site occupancy at higher molar excesses of kinesin was calculated using this parameter. ”

      We also added Figure 3_figure supplement 2 to explain our Binomial model.

      (4) Page 5, 1st paragraph. Here, the authors are comparing time constants from stall experiments to data obtained with dynein from Ezber et al. This study used the traditional "one bead" trapping approach with dynein bound directly to the bead under conditions where it would experience high z-forces. Thus, the comparison between the behavior of kinesin at low z-forces is not necessarily appropriate. Has anyone studied dynein's mechanics under low z-force regimes?

      We thank the reviewer for catching a citation error. The text has been corrected to reference Elshenawy et al. 2020, which reported stall time constants for mammalian dynein. 

      To our knowledge, dynein’s mechanics under explicitly low z-force conditions have not yet been reported; however, given the more robust stalling behavior of dynein and greater collective force generation, the cited paper was chosen to compare low z-force kinesin to a motor that appears comparatively unencumbered by z-forces. Our study adds to growing evidence that high z-forces disproportionately limit kinesin performance. 

      For clarification, we modified that sentence as follows: “These time constants are comparable to those reported for minus-end-directed dynein under high z-forces”.

      Reviewer #2 (Recommendations for the authors):

      (1) P3 pp2, a DNA tensiometer cannot control the force, but it can measure it; get the distance between the two ends of the tensiometer, and apply WLC.

      The text has been updated to more accurately reflect the differences between optical trapping and kinesin motility against a DNA tensiometer with a fixed lattice position.

      (2) Fig. 2b, SEM is a poor estimate or error for exponentially distributed run lengths. Other methods, like bootstrapping an exponential distribution fit, may provide a more realistic estimate.

      Run lengths were plotted as an inverse cumulative distribution function and fitted to a single exponential decay (Supplementary Figure S3). The plotted value represents the fitted decay constant (characteristic run length) ± SE (standard error of the fit), not the arithmetic mean ± SEM. Velocity values are reported as mean ± SEM. Detachment rate was computed as velocity divided by run length, except at 6 and 10 pN hindering loads, where minimal forward displacement necessitated fitting run-time decays directly. In those cases, the plotted detachment rate equals the inverse of the fitted time constant. The figure caption has been updated accordingly.

      (3) Kinesin-1 is covalently bound to a DNA oligo, which then attaches to the DNA chassis by hybridization. This oligo is 21 nt with a relatively low GC%. At what force does this oligo unhybridize? Can the authors verify that their stall force measurements are not cut short by the oligo detaching from the chassis?

      The 21-nt attachment oligo (38 % GC) is predicted to have ΔG<sub>37C</sub> ≈-25 kcal/mole or approximately 42 kT. If we assume this is the approximate amount of work required to unhybridize the oligo, we would expect the rupture force to be >15 pN. This significantly exceeds the stall force of a single kinesin. Since the stalling events rarely exceed a few seconds, it is unlikely that our oligos quickly detach from the chassis under such low forces.  

      Furthermore, optical trapping experiments are tuned such that no more than 30% of beads display motion within several minutes after they are brought near microtubules. After stalling events, the motor dissociates from the MT, and the bead snaps back to the trap center. Most beads robustly reengage with the microtubule, typically within 10 s, suggesting that the same motor chassis reengages with the microtubule after microtubule detachment. Successive runs of the same bead typically have similar stall forces, suggesting that the motors do not disengage from the chassis under resistive forces exerted by the trap.

      (4) Figure 1, a justification or explanation should be provided for why events lower than 1.5 pN were excluded. It appears arbitrary.

      Single-motor stall-force measurements used a trap stiffness of 0.08–0.10 pN/nm. At this stiffness, a 1.5 pN force corresponds to 15–19 nm bead displacement, roughly two kinesin steps, and events below this threshold could not be reliably distinguished from Brownian noise. For this reason, forces < 1.5 pN were excluded.

      In Methods, we wrote “Only peak forces above 1.5 pN (corresponding to a 15-19 nm bead displacement) were analyzed to clearly distinguish runs from the tracking noise.”

      (5) Figure 2b, is the difference in velocity statistically significant?

      The difference in velocity is statistically significant for most conditions. We did not compare velocities for -10 and -6 pN as these conditions resulted in little forward displacement. However, the p-values for all of the other conditions are -4 pN: 0.0026, -2 pN: 0.0001, -1 pN: 0.0446, +0.5 pN: 0.3148, +2 pN: 0.0001, +3 pN: 0.1191, +4 pN: 0.0004.

      (6) The number of measurements for each experimental datapoint in the corresponding figure caption should be provided. SEM is used without, but N is not reported in the caption.

      Figure captions have now been updated to report the number of trajectories (N) for each data point.

      Reviewer #3 (Recommendations for the authors):  

      (1) The method of DNA-tethered motor trapping to enable low z-force is not entirely novel, but adapted from Urbanska (2021) for use in conventional optical trapping laboratories without reliance on microfluidics. However, I appreciate that they have fully established it here to share with the community. The authors could strengthen their methods section by being transparent about protein weight, protein labelling, and DNA ladders shown in the supplementary information. What organism is the protein from? Presumably human, but this should be specified in the methods. While the figures show beautiful data and exemplary traces, the total number of molecules analysed or events is not consistently reported. Overall, certain methodological details should be made sufficient for reproducibility.

      We appreciate the reviewer’s attention to methodological clarity. The constructs used are indeed human kinesin-1, KIF5B. The Methods now specify protein origin, molecular weights, and labeling details, and all figure captions report the number of trajectories analyzed to ensure reproducibility.

      (2) The major limitation the study presents is overarching generalisability, starting with the title. I recommend that the title be specific to kinesin-1. 

      The title has been revised to specify kinesin-1. 

      The study uses two constructs: a truncated K560 for conventional high-force assays, and full-length Kif5b for the low z-force method. However, for the multi-motor assay, the authors use K560 with the rationale of preventing autoinhibition due to binding with DNA, but that would also have limited characterisation in the single-molecule assay. Overall, the data generated are clear, high-quality, and exciting in the low z-force conditions. But why have they not compared or validated their findings with the truncated construct K560? This is especially important in the force-feedback experiments and in comparison with Andreasson et al. and Carter et al., who use Drosophila kinesin-1. Could kinesin-1 across organisms exhibit different force-detachment kinetics? It is quite possible. 

      Construct choice was guided by physiological relevance and considerations of autoinhibition: K560 was used for high z-force single-motor assays. The results of these assays are consistent with conventional bead assays performed by Andreasson et al. and Carter et al. using kinesin from a different organism. Therefore, we do not believe there are major differences between force properties of Drosophila and human kinesin-1.

      For low z-force assays, we used full-length KIF5B, which has nearly identical velocity and stall force to K560 in standard bead assays. We used this construct for low z force assays because it has a longer and more flexible stalk than K560 and better represents the force behavior of kinesin under physiological conditions. We then used constitutively-active K560 motors for multi-motor experiments to avoid potential complications from autoinhibition of full-length kinesin.

      Similarly, the authors test backward slipping of Kif5b and K560 and measure dwell times in multi-motor assays. Why not detail the backward slippage kinetics of Kif5b and any step-size impact under low z-forces? For instance, with the traces they already have, the authors could determine slip times, distances, and frequency in horizontal force experiments. Overall, the manuscript could be strengthened by analysing both constructs more fully.

      Slip or backstep analyses were not performed on single-motor data because such events were rare; kinesin typically detached rather than slipped. In contrast, multi-motor assays exhibited frequent slip events corresponding to the detachment of individual motors, which were analyzed in detail.

      We wrote “In comparison, slipping events were rarely observed in beads driven by a single motor, suggesting that kinesin typically detaches rather than slipping back on the microtubule under hindering loads.”

      Appraisal and impact:

      This study contributes to important and debated evidence on kinesin-1 force-detachment kinetics. The authors conclude that kinesin-1 exhibits a slip-bond interaction with the microtubule under increasing forces, while other recent studies (Noell et al. and Kuo et al.), which also use low z-force setups, conclude catch-bond behaviour under hindering loads. I find the results not fully aligned with their interpretation. The first comparison of low zforces in their setup with Noell et al. (2024), based on stall times, does not hold, because it is an apples-to-oranges comparison. Their data show a stall time constant of 2.52 s, which is comparable to the 3 s reported by Noell et al., but the comparison is made with a weighted average of 1.49 s. The authors do report that detachment rates are lower in low z-force conditions under unloaded scenarios. So, to completely rule out catch-bond-like behaviour is unfair. That said, their data quality is good and does show that higher hindering forces lead to higher detachment rates. However, on closer inspection, the range of 0-5 pN shows either a decrease or no change in detachment rate, which suggests that under a hindering force threshold, catch-bond-like or ideal-bond-like behaviour is possible, followed by slipbond behaviour, which is amazing resolution. Under assisting loads, the slip-bond character is consistent, as expected. Overall, the study contributes to an important discussion in the biophysical community and is needed, but requires cautious framing, particularly without evidence of motor trapping in a high microtubule-affinity state rather than genuine bond strengthening.

      We are not completely ruling out the catch bond behavior in our manuscript. As the reviewer pointed out, our results are consistent with the asymmetric slip bond model, whereas DNA tensiometer assays are more consistent with the catch bond behavior. The advantage of our approach is the capability to directly control the magnitude and direction of load exerted on the motor in the horizontal axis and measure the rate at which the motor detaches from the microtubule as it walks under constant load. In comparison, DNA tensiometer assays cannot control the force, but measure the time it takes the motor to fall off from the microtubule after a brief stall. The extension of the DNA tether is used to estimate the force exerted on the motor during a stall in those assays. The slight disadvantage of our method is the presence of low zforces, whereas DNA tensiometer assays are expected to have little to no z-force. We wrote that the discrepancy between our results can be attributed to the presence of low z forces in our DNA tethered trapping assembly, which may result in a higher-than-normal detachment rate under high hindering loads, thereby resulting in less asymmetry in the force detachment kinetics. We also added that this discrepancy can be addressed by future studies that directly control and measure horizontal force and measure the motor detachment rate in the absence of z forces. Optical trapping assays with small nanoparticles (Sudhakar et al. Science 2021) may be well suited to conclusively reveal the bond characteristics of kinesin under hindering loads.

      Reviewing Editor Comments:

      The reviewers are in agreement with the importance of the findings and the quality of the results. The use of the DNA tether reduces the z-force on the motor and provides biologically relevant insight into the behavior of the motor under load. The reviewers' suggestions are constructive and focus on bolstering some of the data points and clarifying some of the methodological approaches. My major suggestion would be to clarify the rationale for concluding that kinesin-1 exhibits slip-bond behavior with increasing force in light of the work of Noell (10.1101/2024.12.03.626575) and Kuo et al (2022 10.1038/s41467022-31069-x), both of which take advantage of DNA tethers.

      Please see our response to the previous comment. In the revised manuscript, we first clarified that our results are in agreement with previous theoretical (Khataee & Howard, 2019) and experimental studies (Kuo et al., 2022; Noell et al., 2024; Pyrpassopoulos et al., 2020) that kinesin exhibits slower detachment under hindering load. This asymmetry became clear when the z-force was reduced or eliminated. 

      We clarified the differences between our results and DNA tensiometer assays and provided a potential explanation for these discrepancies. We also proposed that future studies might be required to fully distinguish between asymmetric slip, ideal, or catch bonding of kinesin under hindering loads.

      We wrote:

      “Our results agree with the theoretical prediction that kinesin exhibits higher asymmetry in force-detachment kinetics without z-forces (Khataee & Howard, 2019), and are consistent with optical trapping and DNA tensiometer assays that reported more persistent stalling of kinesin in the absence of z-forces (Kuo et al., 2022; Noell et al., 2024; Pyrpassopoulos et al., 2020).

      Force-detachment kinetics of protein-protein interactions have been modeled as either a slip, ideal, or catch bond, which exhibit an increase, no change, or a decrease in detachment rate, respectively, under increasing force (Thomas et al., 2008). Slip bonds are most commonly observed in biomolecules, but studies on cell adhesion proteins reported a catch bond behavior (Marshall et al., 2003). Although previous trapping studies of kinesin reported a slip bond behavior (Andreasson et al., 2015; Carter & Cross, 2005), recent DNA tensiometer studies that eliminated the z-force showed that the detachment rate of the motor under hindering forces is lower than that of an unloaded motor walking on the microtubule (Kuo et al., 2022; Noell et al., 2024), consistent with the catch bond behavior. Unlike these reports, we observed that the stall duration of kinesin is shorter than the motor run time under unloaded conditions, and the detachment rate of kinesin increases with the magnitude of the hindering force. Therefore, our results are more consistent with the asymmetric slip bond behavior. The difference between our results and the DNA tensiometer assays (Kuo et al., 2022; Noell et al., 2024) can be attributed to the presence of low z-forces in our DNA-tethered optical trapping assays, which may increase the detachment rate under high hindering forces. Future studies that could directly control hindering forces and measure the motor detachment rate in the absence of z-forces would be required to conclusively reveal the bond characteristics of kinesin under hindering loads.”

    1. Author response:

      The following is the authors’ response to the original reviews

      eLife Assessment

      This paper undertakes an important investigation to determine whether movement slowing in microgravity is due to a strategic conservative approach or rather due to an underestimation of the mass of the arm. While the experimental dataset is unique and the coupled experimental and computational analyses comprehensive, the authors present incomplete results to support the claim that movement slowing is due to mass underestimation. Further analysis is needed to rule out alternative explanations.

      We thank the editor and reviewers for the thoughtful and constructive comments, which helped us substantially improve the manuscript. In this revised version, we have made the following key changes:

      - Directly presented the differential effect of microgravity in different movement directions, showing its quantitative match with model predictions.

      - Showed that changing cost function with the idea of conservative strategy is not a viable alternative.

      - Showed our model predictions remain largely the same after adding Coriolis and centripetal torques.

      - Discussed alternative explanations including neuromuscular deconditioning, friction, body stability, etc.

      - Detailed the model description and moved it to the main text, as suggested.

      Our point-to-point response is numbered to facilitate cross-referencing.

      We believe the revisions and the responses adequately addresses the reviewers’ concerns, and new analysis results strengthened our conclusion that mass underestimation is the major contributor to movement slowing in microgravity.

      Reviewer #1 (Public review):

      Summary:

      This article investigates the origin of movement slowdown in weightlessness by testing two possible hypotheses: the first is based on a strategic and conservative slowdown, presented as a scaling of the motion kinematics without altering its profile, while the second is based on the hypothesis of a misestimation of effective mass by the brain due to an alteration of gravity-dependent sensory inputs, which alters the kinematics following a controller parameterization error.

      Strengths:

      The article convincingly demonstrates that trajectories are affected in 0g conditions, as in previous work. It is interesting, and the results appear robust. However, I have two major reservations about the current version of the manuscript that prevent me from endorsing the conclusion in its current form.

      Weaknesses:

      (1) First, the hypothesis of a strategic and conservative slow down implicitly assumes a similar cost function, which cannot be guaranteed, tested, or verified. For example, previous work has suggested that changing the ratio between the state and control weight matrices produced an alteration in movement kinematics similar to that presented here, without changing the estimated mass parameter (Crevecoeur et al., 2010, J Neurophysiol, 104 (3), 1301-1313). Thus, the hypothesis of conservative slowing cannot be rejected. Such a strategy could vary with effective mass (thus showing a statistical effect), but the possibility that the data reflect a combination of both mechanisms (strategic slowing and mass misestimation) remains open.

      Response (1): Thank you for raising this point. The basic premise of this concern is that changing the cost function for implementing strategic slowing can reproduce our empirical findings, thus the alternative hypothesis that we aimed to refute in the paper remain possible. At least, it could co-exist with our hypothesis of mass underestimation. In the revision, we show that changing the cost function only, as suggested here, cannot produce the behavioral patterns observed in microgravity.

      As suggested, we modified the relative weighting of the state and control cost matrices (i.e., Q and R in the cost function Eq 15) without considering mass underestimation. While this cost function scaling can decrease peak velocity – a hallmark of strategic slowing – it also inevitably leads to later peak timings. This is opposite to our robust findings: the taikonauts consistently “advanced” their peak velocity and peak acceleration in time. Note, these model simulation patterns have also been shown in Crevecoeur et al. (2010), the paper mentioned by the reviewer (see their Figure 7B).

      We systematically changed the ratio between the state and control weight matrices in the simulation, as suggested. We divided Q and multiplied R by the same factor α, the cost function scaling parameter α as defined in Crevecoeur et al. (2010). This adjustment models a shift in movement strategy in microgravity, and we tested a wide range of α to examine reasonable parameter space. Simulation results for α = 3 and α = 0.3 are shown in Figure 1—figure supplement 2 and Figure 1—figure supplement 3 respectively. As expected, with α = 3 (higher control effort penalty), peak velocities and accelerations are reduced, but their timing is delayed. Conversely, with α = 0.3, both peak amplitude and timing increase. Hence, changing the cost function to implement a conservative strategy cannot produce the kinematic pattern observed in microgravity, which is a combination of movement slowing and peak timing advance.

      Therefore, we conclude that a change in optimal control strategy alone is insufficient to explain our empirical findings. Logically speaking, we cannot refute the possibility of strategic slowing, which can still exist on top of the mass underestimation we proposed here. However, our data does not support its role in explaining the slowing of goal-directed hand reaching in microgravity. We have added these analyses to the Supplementary Materials and expanded the Discussion to address this point.

      (2) The main strength of the article is the presence of directional effects expected under the hypothesis of mass estimation error. However, the article lacks a clear demonstration of such an effect: indeed, although there appears to be a significant effect of direction, I was not sure that this effect matched the model's predictions. A directional effect is not sufficient because the model makes clear quantitative predictions about how this effect should vary across directions. In the absence of a quantitative match between the model and the data, the authors' claims regarding the role of misestimating the effective mass remain unsupported.

      Response (2): First, we have to clarify that our study does not aim to quantitatively fit observed hand trajectory. The two-link arm model simulates an ideal case of moving a point mass (effective mass) on a horizontal plane without friction (Todorov, 2004; 2005). In contrast, in the experiment, participants moved their hand on a tabletop without vertical arm support, so the movement was not strictly planar and was affected by friction. Thus, this kind of model can only illustrate qualitative differences between conditions, as in the majorities of similar modeling studies (e.g., Shadmehr et al., 2016). In our study, qualitative simulation means the model is intended to reproduce the directional differences between conditions—not exact numeric values—in key kinematic measures. Specifically, it should capture how the peak velocity and acceleration amplitudes and their timings differ between normal gravity and microgravity (particularly under the mass-underestimation assumption).

      Second, the reviewer rightfully pointed out that the directional effect is essential for our theorization of the importance of mass underestimation. However, the directional effect has two aspects, which were not clearly presented in our original manuscript. We now clarify both here and in the revision. The first aspect is that key kinematic variables (peak velocity/acceleration and their timing) are affected by movement direction, even before any potential microgravity effect. This is shown by the ranking order of directions for these variables (Figure 1C-H). The direction-dependent ranking, confirmed by pre-flight data, indicates that effective mass is a determining factor for reaching kinematics, which motivated us to study its role in eliciting movement slowing in space. This was what our original manuscript emphasized and clearly presented.

      The second aspect is that the hypothetical mass underestimation might also differentially affect movements in different directions. This was not clearly presented in the original manuscript. However, we would not expect a quantitative match between model predictions and empirical data, for the reasons mentioned above. We now show this directional ranking in microgravity-elicited kinematic changes in both model simulations and empirical data. The overall trend is that the microgravity effect indeed differs between directions, and the model predictions and the data showed a reasonable qualitative match (Author response image 1 below).

      Shown in Author response image 1, we found that for amplitude changes (Δ peak speed, Δ peak acceleration) both the model and the mean of empirical data show the same directional ordering (45° > 90° > 135°) in pre-in and post-in comparisons. For timing (Δ peak-speed time, Δ peak-acceleration time), which we consider the most diagnostic, the same directional ranking was observed. We only found one deviation, i.e., the predicted sign (earlier peaks) was confirmed at 90° and 135°, but not at 45°. As discussed in Response (6), the absence of timing advance at 45° may reflect limitations of our simplified model, which did not consider that the 45° direction is essentially a single-joint reach. Taken together, the directional pattern is largely consistent with the model predictions based on mass underestimation. The model successfully reproduces the directional ordering of amplitude measures -- peak velocity and peak acceleration. It also captures the sign of the timing changes in two out of the three directions. We added these new analysis results in the revision and expanded Discussion accordingly.

      The details of our analysis on directional effects: We compared the model predictions (Author response image 1, left) with the experimental data (Author response image 1, right) across the three tested directions (45°, 90°, 135°). In the experimental data panels, both Δ(pre-in) (solid bars) and Δ(post-in) (semi-transparent bars) with standard error are shown. The directional trends are remarkably similar between model prediction and actual data. The post-in comparison is less aligned with model prediction; we postulate that the incomplete after-flight recovery (i.e., post data had not returned to pre-flight baselines) might obscure the microgravity effect. Incomplete recovery has also been shown in our original manuscript: peak speed and peak acceleration did not fully recover in post-flight sessions when compared to pre-flight sessions. To further quantify the correspondence between model and data, we performed repeated-measures correlation (rm-corr) analyses. We found significant within-subject correlations for three of the four metrics. For pre–in, Δ peak speed time (r<sub>rm</sub> = 0.627, t(23) = 3.858, p < 0.001), Δ peak acceleration time (r<sub>rm</sub> = 0.591, t(23) = 3.513, p = 0.002), and Δ peak acceleration (r<sub>rm</sub> = 0.573, t(23) = 3.351, p = 0.003) were significant, whereas Δ peak speed was not (r<sub>rm</sub> = 0.334, t(23) = 1.696, p = 0.103). These results thus show that the directional effect, as predicted our model, is observed both before spaceflight and in spaceflight (the pre-in comparison).

      Author response image 1.

      Directional comparison between model predictions and experimental data across the three reach directions (45°, 90°, 135°). Left: model outputs. Right: experimental data shown as Δ relative to the in-flight session; solid bars = Δ(in − pre) and semi-transparent bars = Δ(in − post). Colors encode direction consistently across panels (e.g., 45° = darker hue, 90° = medium, 135° = lighter/orange). Panels (clockwise from top-left): Δ peak speed (cm/s), Δ peak speed time (ms), Δ peak acceleration time (ms), and Δ peak acceleration (cm/s²). Bars are group means; error bars denote standard error across participants.

      Citations:

      Todorov, E. (2004). Optimality principles in sensorimotor control. Nature Neuroscience, 7(9), 907.

      Todorov, E. (2005). Stochastic optimal control and estimation methods adapted to the noise characteristics of the sensorimotor system. Neural Computation, 17(5), 1084–1108.

      Shadmehr, R., Huang, H. J., & Ahmed, A. A. (2016). A Representation of Effort in Decision-Making and Motor Control. Current Biology: CB, 26(14), 1929–1934.

      In general, both the hypotheses of slowing motion (out of caution) and misestimating mass have been put forward in the past, and the added value of this article lies in demonstrating that the effect depended on direction. However, (1) a conservative strategy with a different cost function can also explain the data, and (2) the quantitative match between the directional effect and the model's predictions has not been established.

      We agree that both hypotheses have been put forward before, however they are competing hypotheses that have not been resolved. Furthermore, the mass underestimation hypothesis is a conjecture without any solid evidence; previous reports on mass underestimation of object cannot directly translate to underestimation of body. As detailed in our responses above, we have shown that a conservative strategy implemented via a different cost function cannot reproduce the key findings in our dataset, thereby supporting the alternative hypothesis of mass underestimation. Moreover, we found qualitative agreement between the model predictions and the experimental data in terms of directional effects, which further strengthens our interpretation.

      Specific points:

      (1) I noted a lack of presentation of raw kinematic traces, which would be necessary to convince me that the directional effect was related to effective mass as stated.

      Response (3): We are happy to include exemplary speed and acceleration trajectories. Kinematic profiles from one example participant are shown in Figure 2—figure supplement 6.

      (2) The presentation and justification of the model require substantial improvement; the reason for their presence in the supplementary material is unclear, as there is space to present the modelling work in detail in the main text. Regarding the model, some choices require justification: for example, why did the authors ignore the nonlinear Coriolis and centripetal terms?

      Response (4): Great suggestion. In the revision, we have moved the model into the main text and added further justification for using this simple model.

      We initially omitted the nonlinear Coriolis and centripetal terms in order to start with a minimal model. Importantly, excluding these terms does not affect the model’s main conclusions. In the revision we added simulations that explicitly include these terms. The full explanation and simulations are provided in the Supplementary Notes 2 (this time we have to put it into the Supplementary to reduce the texts devoted to the model). More explanations can also be found in our response to Reviewer 2 (response (6)). The results indicate that, although these velocity-dependent forces show some directional anisotropy, their contribution is substantially smaller relative to that of the included inertial component; specifically, they have only a negligible impact on the predicted peak amplitudes and peak times.

      (3) The increase in the proportion of trials with subcomponents is interesting, but the explanatory power of this observation is limited, as the initial percentage was already quite high (from 60-70% during the initial study to 70-85% in flight). This suggests that the potential effect of effective mass only explains a small increase in a trend already present in the initial study. A more critical assessment of this result is warranted.

      Response (5): Thank you for your thoughtful comment. You are correct that the increase in the percentage of trials with submovements is modest, but a more critical change was observed in the timing between submovement peaks—specifically, the inter-peak interval (IPI). These intervals became longer during flight. Taken together with the percentage increase, the submovement changes significantly predicted the increase in movement duration, as shown by our linear mixed-effects model, which indicated that IPI increased.

      Reviewer #2 (Public review):

      This study explores the underlying causes of the generalized movement slowness observed in astronauts in weightlessness compared to their performance on Earth. The authors argue that this movement slowness stems from an underestimation of mass rather than a deliberate reduction in speed for enhanced stability and safety.

      Overall, this is a fascinating and well-written work. The kinematic analysis is thorough and comprehensive. The design of the study is solid, the collected dataset is rare, and the model tends to add confidence to the proposed conclusions. That being said, I have several comments that could be addressed to consolidate interpretations and improve clarity.

      Main comments:

      (1) Mass underestimation

      a) While this interpretation is supported by data and analyses, it is not clear whether this gives a complete picture of the underlying phenomena. The two hypotheses (i.e., mass underestimation vs deliberate speed reduction) can only be distinguished in terms of velocity/acceleration patterns, which should display specific changes during the flight with a mass underestimation. The experimental data generally shows the expected changes but for the 45° condition, no changes are observed during flight compared to the pre- and post-phases (Figure 4). In Figure 5E, only a change in the primary submovement peak velocity is observed for 45°, but this finding relies on a more involved decomposition procedure. It suggests that there is something specific about 45° (beyond its low effective mass). In such planar movements, 45° often corresponds to a movement which is close to single-joint, whereas 90° and 135° involve multi-joint movements. If so, the increased proportion of submovements in 90° and 135° could indicate that participants had more difficulties in coordinating multi-joint movements during flight. Besides inertia, Coriolis and centripetal effects may be non-negligible in such fast planar reaching (Hollerbach & Flash, Biol Cyber, 1982) and, interestingly, they would also be affected by a mass underestimation (thus, this is not necessarily incompatible with the author's view; yet predicting the effects of a mass underestimation on Coriolis/centripetal torques would require a two-link arm model). Overall, I found the discrepancy between the 45° direction and the other directions under-exploited in the current version of the article. In sum, could the corrective submovements be due to a misestimation of Coriolis/centripetal torques in the multi-joint dynamics (caused specifically -or not- by a mass underestimation)?

      Response (6): Thank you for raising these important questions. We unpacked the whole paragraph into two concerns: 1) the possibility that misestimation of Coriolis and centripetal torques might lead to corrective submovements, and 2) the weak effect in the 45° direction unexploited. These two concerns are valid but addressable, and they did not change our general conclusions based on our empirical findings (see Supplementary note 2. Coriolis and centripetal torques have minimal impact).

      Possible explanation for the 45° discrepancy

      We agree with the reviewer that the 45° direction likely involves more single-joint (elbow-dominant) movement, whereas the 90° and 135° directions require greater multi-joint (elbow + shoulder) coordination. This is particularly relevant when the workspace is near body midline (e.g., Haggard & Richardson, 1995), as the case in our experimental setup. To demonstrate this, we examined the curvature of the hand trajectories across directions. Using cumulative curvature (positive = counterclockwise), we obtained average values of 6.484° ± 0.841°, 1.539° ± 0.462°, and 2.819° ± 0.538° for the 45°, 90°, and 135° directions, respectively. The significantly larger curvature in the 45° condition suggests that these movements deviate more from a straight-line path, a hallmark of more elbow-dominant movements.

      Importantly, this curvature pattern was present in both the pre-flight and in-flight phases, indicating that it is a general movement characteristic rather than a microgravity-induced effect. Thus, the 45° reaches are less suitable for modeling with a simplified two-link arm model compared to the other two directions. We believe this is the main reason why the model predictions based on effective mass become less consistent with the empirical data for the 45° direction.

      We have now incorporated this new analysis in the Results and discussed it in the revised Discussion.

      Citation: Haggard, P., Hutchinson, K., & Stein, J. (1995). Patterns of coordinated multi-joint movement. Experimental Brain Research, 107(2), 254-266.

      b) Additionally, since the taikonauts are tested after 2 or 3 weeks in flight, one could also assume that neuromuscular deconditioning explains (at least in part) the general decrease in movement speed. Can the authors explain how to rule out this alternative interpretation? For instance, weaker muscles could account for slower movements within a classical time-effort trade-off (as more neural effort would be needed to generate a similar amount of muscle force, thereby suggesting a purposive slowing down of movement). Therefore, could the observed results (slowing down + more submovements) be explained by some neuromuscular deconditioning combined with a difficulty in coordinating multi-joint movements in weightlessness (due to a misestimation or Coriolis/centripetal torques) provide an alternative explanation for the results?

      Response (7): Neuromuscular deconditioning is indeed a space effect; thanks for bringing this up as we omitted the discussion of this confounds in our original manuscript. Prolonged stay in microgravity can lead to a reduction of muscle strength, but this is mostly limited to lower limb. For example, a recent well-designed large-sample study have shown that while lower leg muscle showed significant strength reductions, no changes in mean upper body strength was found (Scott et al., 2023), consistent with previous propositions that muscle weakness is less for upper-limb muscles than for postural and lower-limb muscles (Tesch et al., 2005). Furthermore, the muscle weakness is unlikely to play a major role here since our reaching task involves small movements (~12cm) with joint torques of a magnitude of ~2N·m. Of course, we cannot completely rule out the contribution of muscle weakness; we can only postulate, based on the task itself (12 cm reaching) and systematic microgravity effect (the increase in submovements, the increase in the inter-submovements intervals, and their significant prediction on movement slowing), that muscle weakness is an unlikely major contributor for the movement slowing.

      The reviewer suggests that poor coordination in microgravity might contribute to slowing down + more submovements. This is also a possibility, but we did not find evidence to support it. First, there is no clear evidence or reports about poor coordination for simple upper-limb movements like reaching investigated here. Note that reaching or aiming movement is one of the most studied tasks among astronauts. Second, we further analyzed our reaching trajectories and found no sign of curvature increase, a hallmark of poor coordination of Coriolis/centripetal torques, in our large collection of reaching movements. We probably have the largest dataset of reaching movements collected in microgravity thus far, given that we had 12 taikonauts and each of them performed about 480 to 840 reaching trials during their spaceflight. We believe the probability of Type II error is quite low here.

      Citation: Tesch, P. A., Berg, H. E., Bring, D., Evans, H. J., & LeBlanc, A. D. (2005). Effects of 17-day spaceflight on knee extensor muscle function and size. European journal of applied physiology, 93(4), 463-468.

      Scott J, Feiveson A, English K, et al. Effects of exercise countermeasures on multisystem function in long duration spaceflight astronauts. npj Microgravity. 2023;9(11).

      (2) Modelling

      a) The model description should be improved as it is currently a mix of discrete time and continuous time formulations. Moreover, an infinite-horizon cost function is used, but I thought the authors used a finite-horizon formulation with the prefixed duration provided by the movement utility maximization framework of Shadmehr et al. (Curr Biol, 2016). Furthermore, was the mass underestimation reflected both in the utility model and the optimal control model? If so, did the authors really compute the feedback control gain with the underestimated mass but simulate the system with the real mass? This is important because the mass appears both in the utility framework and in the LQ framework. Given the current interpretations, the feedforward command is assumed to be erroneous, and the feedback command would allow for motor corrections. Therefore, it could be clarified whether the feedback command also misestimates the mass or not, which may affect its efficiency. For instance, if both feedforward and feedback motor commands are based on wrong internal models (e.g., due to the mass underestimation), one may wonder how the astronauts would execute accurate goal-directed movements.

      b) The model seems to be deterministic in its current form (no motor and sensory noise). Since the framework developed by Todorov (2005) is used, sensorimotor noise could have been readily considered. One could also assume that motor and sensory noise increase in microgravity, and the model could inform on how microgravity affects the number of submovements or endpoint variance due to sensorimotor noise changes, for instance.

      c) Finally, how does the model distinguish the feedforward and feedback components of the motor command that are discussed in the paper, given that the model only yields a feedback control law? Does 'feedforward' refer to the motor plan here (i.e., the prefixed duration and arguably the precomputed feedback gain)?

      Response (8): We thank the reviewer for raising these important and technically insightful points regarding our modeling framework. We first clarify the structure of the model and key assumptions, and then address the specific questions in points (a)–(c) below.

      We used Todorov’s (2005) stochastic optimal control method to compute a finite-horizon LQG policy under sensory noise and signal-dependent motor noise (state noise set to zero). The cost function is: (see details in updated Methods). The resulting time-varying gains {L<sub>k</sub>, K<sub>k</sub>} correspond to the feedforward mapping and the feedback correction gain, respectively. The control law can be expressed as:

      where u<sub>k</sub> is the control input, is the nominal planned state, is the estimated state, L<sub>k</sub> is the feedforward (nominal) control associated with the planned trajectory, and K<sub>k</sub> is the time-varying feedback gain that corrects deviations from the plan.

      To define the motor plan for comparison with behavior, we simulate the deterministic open-loop

      trajectory by turning off noise and disabling feedback corrections, i.e., . In this framework, “feedforward” refers to this nominal motor plan. Thus, sensory and signal-dependent noise influence the computed policy (via the gains), but are not injected when generating the nominal trajectory. This mirrors the minimum-jerk practice used to obtain nominal kinematics in prior utility-based work (Shadmehr, 2016), while optimal control provides a more physiologically grounded nominal plan. In the revision, we have updated the equations, provided more modeling details, and moved the model description to the main text to reduce possible confusions.

      In the implementation of the “mass underestimation” condition, the mass used to compute the policy is the underestimated mass (), whereas the actual mass is used when simulating the feedforward trajectories. Corrective submovements are analyzed separately and are not required for the planning-deficit findings reported here.

      Answers of the three specific questions:

      a) We mistakenly wrote a continuous-time infinite-horizon cost function in our original manuscript, whereas our controller is actually implemented as a discrete-time finite-horizon LQG with a terminal cost, over a horizon set by the utility-based optimal movement duration T<sub>opt</sub>. The underestimated mass is used in both the utility model (to determine T<sub>opt</sub>) and in the control computation (i.e., internal model), while the true mass is used when simulating the movement. This mismatch captures the central idea of feedforward planning based on an incorrect internal model.

      b) As described, our model includes signal-dependent motor noise and sensory noise, following Todorov (2005). We also evaluated whether increased noise levels in microgravity could account for the observed behavioral changes. Simulation results showed that increasing either source of noise did not alter the main conclusions or reverse the trends in our key metrics. Moreover, our experimental data showed no significant increase in endpoint variability in microgravity (see analyses and results in Figure 2—figure supplement 3 & 4), making it unlikely that increased sensorimotor noise alone accounts for the observed slowing and submovement changes.

      c) In our framework, the time-varying gains {L<sub>K</sub>,K<sub>K</sub>}define the feedforward and feedback components of the control policy. While both gains are computed based on a stochastic optimal control formulation (including noise), for comparison with behavior we simulate only the nominal feedforward plan, by turning off both noise and feedback: . This defines a deterministic open-loop trajectory, which we use to capture planning-level effects such as peak timing shifts under mass underestimation. Feedback corrections via gains exist in the full model but are not involved in these specific analyses. We clarified this modeling choice and its behavioral relevance in the revised text.

      We have updated the equations and moved the model description into the main text in the revised manuscript to avoid confusion.

      (3) Brevity of movements and speed-accuracy trade-off

      The tested movements are much faster (average duration approx. 350 ms) than similar self-paced movements that have been studied in other works (e.g., Wang et al., J Neurophysiology, 2016; Berret et al., PLOS Comp Biol, 2021, where movements can last about 900-1000 ms). This is consistent with the instructions to reach quickly and accurately, in line with a speed-accuracy trade-off. Was this instruction given to highlight the inertial effects related to the arm's anisotropy? One may however, wonder if the same results would hold for slower self-paced movements (are they also with reduced speed compared to Earth performance?). Moreover, a few other important questions might need to be addressed for completeness: how to ensure that astronauts did remember this instruction during the flight? (could the control group move faster because they better remembered the instruction?). Did the taikonauts perform the experiment on their own during the flight, or did one taikonaut assume the role of the experimenter?

      Response (9): Thanks for highlighting the brevity of movements in our experiment. Our intention in emphasizing fast movements is to rigorously test whether movement is indeed slowed down in microgravity. The observed prolonged movement duration clearly shows that microgravity affects people’s movement duration, even when they are pushed to move fast. The second reason for using fast movement is to highlight that feedforward control is affected in microgravity. Mass underestimation specifically affects feedforward control in the first place, shown by the microgravity-related changes in peak velocity/acceleration. Slow movement would inevitably have online corrections that might obscure the effect of mass underestimation. Note that movement slowing is not only observed in our speed-emphasized reaching task, but also in whole-arm pointing in other astronauts’ studies (Berger, 1997; Sangals, 1999), which have been quoted in our paper. We thus believe these findings are generalizable.

      Regarding the consistency of instructions: all our experiments conducted in the Tiangong space station were monitored in real time by experimenters in the control center located in Beijing. The task instructions were presented on the initial display of the data acquisition application and ample reading time was allowed. All the pre-, in-, and post-flight test sessions were administered by the same group of personnel with the same instruction. It is common that astronauts serve both as participants and experimenters at the same time. And, they were well trained for this type of role on the ground. Note that we had multiple pre-flight test sessions to familiarize them with the task. All these rigorous measures were in place to obtain high-quality data. In the revision, we included these experimental details for readers that are not familiar with space studies, and provided the rationales for emphasizing fast movements.

      Citations:

      Berger, M., Mescheriakov, S., Molokanova, E., Lechner-Steinleitner, S., Seguer, N., & Kozlovskaya, I. (1997). Pointing arm movements in short- and long-term spaceflights. Aviation, Space, and Environmental Medicine, 68(9), 781–787.

      Sangals, J., Heuer, H., Manzey, D., & Lorenz, B. (1999). Changed visuomotor transformations during and after prolonged microgravity. Experimental Brain Research. Experimentelle Hirnforschung. Experimentation Cerebrale, 129(3), 378–390.

      (4) No learning effect

      This is a surprising effect, as mentioned by the authors. Other studies conducted in microgravity have indeed revealed an optimal adaptation of motor patterns in a few dozen trials (e.g., Gaveau et al., eLife, 2016). Perhaps the difference is again related to single-joint versus multi-joint movements. This should be better discussed given the impact of this claim. Typically, why would a "sensory bias of bodily property" persist in microgravity and be a "fundamental constraint of the sensorimotor system"?

      Response (10): We believe that the presence or absence of adaptation between our study and Gaveau et al.’s study cannot be simply attributed to single-joint versus multi-joint movements. Their adaptation concerned incorporating microgravity into movement control to minimize effort, whereas ours concerned accurately perceiving body mass. Gaveau et al.’s task involved large-amplitude vertical reaching, a scenario in which gravity strongly affects joint torques and movement execution. Thus, adaptation to microgravity can lead to better execution, providing a strong incentive for learning. By contrast, our task consisted of small-amplitude horizontal movements, where the gravitational influence on biomechanics is minimal.

      More importantly, we believe the lack of adaptation for mass underestimation is not totally surprising. When an inertial change is perceived (such as an extra weight attached to the forearm, as in previous motor adaptation studies), people can adapt their reaching within tens of trials. In that case, sensory cues are veridical, as they correctly signal the inertial perturbation. However, in microgravity, reduced gravitational pull and proprioceptive inputs constantly inform the controller that the body mass is less than its actual magnitude. In other words, sensory cues in space are misleading for estimating body mass. The resulting sensory bias prevents the sensorimotor system from adapting. Our initial explanation on this matter was too brief; we expanded it in the revised Discussion.

      Reviewer #3 (Public review):

      Summary:

      The authors describe an interesting study of arm movements carried out in weightlessness after a prolonged exposure to the so-called microgravity conditions of orbital spaceflight. Subjects performed radial point-to-point motions of the fingertip on a touch pad. The authors note a reduction in movement speed in weightlessness, which they hypothesize could be due to either an overall strategy of lowering movement speed to better accommodate the instability of the body in weightlessness or an underestimation of body mass. They conclude for the latter, mainly based on two effects. One, slowing in weightlessness is greater for movement directions with higher effective mass at the end effector of the arm. Two, they present evidence for an increased number of corrective submovements in weightlessness. They contend that this provides conclusive evidence to accept the hypothesis of an underestimation of body mass.

      Strengths:

      In my opinion, the study provides a valuable contribution, the theoretical aspects are well presented through simulations, the statistical analyses are meticulous, the applicable literature is comprehensively considered and cited, and the manuscript is well written.

      Weaknesses:

      Nevertheless, I am of the opinion that the interpretation of the observations leaves room for other possible explanations of the observed phenomenon, thus weakening the strength of the arguments.

      First, I would like to point out an apparent (at least to me) divergence between the predictions and the observed data. Figures 1 and S1 show that the difference between predicted values for the 3 movement directions is almost linear, with predictions for 90º midway between predictions for 45º and 135º. The effective mass at 90º appears to be much closer to that of 45º than to that of 135º (Figure S1A). But the data shown in Figure 2 and Figure 3 indicate that movements at 90º and 135º are grouped together in terms of reaction time, movement duration, and peak acceleration, while both differ significantly from those values for movements at 45º.

      Furthermore, in Figure 4, the change in peak acceleration time and relative time to peak acceleration between 1g and 0g appears to be greater for 90º than for 135º, which appears to me to be at least superficially in contradiction with the predictions from Figure S1. If the effective mass is the key parameter, wouldn't one expect as much difference between 90º and 135º as between 90º and 45º? It is true that peak speed (Figure 3B) and peak speed time (Figure 4B) appear to follow the ordering according to effective mass, but is there a mathematical explanation as to why the ordering is respected for velocity but not acceleration? These inconsistencies weaken the author's conclusions and should be addressed.

      Response (11): Indeed, the model predicts an almost equal separation between 45° and 90° and between 90° and 135°, while the data indicate that the spacing between 45° and 90° is much smaller than between 90° and 135°. We do not regard the divergence as evidence undermining our main conclusion since 1) the model is a simplification of the actual situation. For example, the model simulates an ideal case of moving a point mass (effective mass) without friction and without considering Coriolis and centripetal torques. 2) Our study does not make quantitative predictions of all the key kinematic measures; that will require model fitting, parameter estimation, and posture-constrained reaching experiments; instead, our study uses well-established (though simplified) models to qualitatively predict the overall behavioral pattern we would observe. For this purpose, our results are well in line with our expectations: though we did not find equal spacing between direction conditions, we do confirm that the key kinematic measures (Figure 2 and Figure 3 as questioned) show consistent directional trends between model predictions and empirical data. We added new analysis results on this matter: the directional effect we observed (how the key measures changed in microgravity across direction condition) is significantly correlated with our model predictions in most cases. Please check our detailed response (2) above. These results are also added in the revision.

      We also highlight in the revision that our modeling is not to quantitatively predict reaching behaviors in space, but to qualitatively prescribe that how mass underestimation, but not the conservative control strategy, can lead to divergent predictions about key kinematic measures of fast reaching.

      Then, to strengthen the conclusions, I feel that the following points would need to be addressed:

      (1) The authors model the movement control through equations that derive the input control variable in terms of the force acting on the hand and treat the arm as a second-order low-pass filter (Equation 13). Underestimation of the mass in the computation of a feedforward command would lead to a lower-than-expected displacement to that command. But it is not clear if and how the authors account for a potential modification of the time constants of the 2nd order system. The CNS does not effectuate movements with pure torque generators. Muscles have elastic properties that depend on their tonic excitation level, reflex feedback, and other parameters. Indeed, Fisk et al. showed variations of movement characteristics consistent with lower muscle tone, lower bandwidth, and lower damping ratio in 0g compared to 1g. Could the variations in the response to the initial feedforward command be explained by a misrepresentation of the limbs' damping and natural frequency, leading to greater uncertainty about the consequences of the initial command? This would still be an argument for unadapted feedforward control of the movement, leading to the need for more corrective movements. But it would not necessarily reflect an underestimation of body mass.

      Fisk, J. O. H. N., Lackner, J. R., & DiZio, P. A. U. L. (1993). Gravitoinertial force level influences arm movement control. Journal of neurophysiology, 69(2), 504-511.

      Response (12): We agree that muscle properties, tonic excitation level, proprioception-mediated reflexes all contribute to reaching control. Fisk et al. (1993) study indeed showed that arm movement kinematics change, possibly owing to lower muscle tone and/or damping. However, reduced muscle damping and reduced spindle activity are more likely to affect feedback-based movements. Like in Fisk et al.’s study, people performed continuous arm movements with eyes closed; thus their movements largely relied on proprioceptive control. Our major findings are about the feedforward control, i.e., the reduced and “advanced” peak velocity/acceleration in discrete and ballistic reaching movements. Note that the peak acceleration happens as early as approximately 90-100ms into the movements, clearly showing that feedforward control is affected -- a different effect from Fisk et al’s findings. It is unlikely that people “advanced” their peak velocity/acceleration because they feel the need for more later corrective movements. Thus, underestimation of body mass remains the most plausible explanation.

      (2) The movements were measured by having the subjects slide their finger on the surface of a touch screen. In weightlessness, the implications of this contact are expected to be quite different than those on the ground. In weightlessness, the taikonauts would need to actively press downward to maintain contact with the screen, while on Earth, gravity will do the work. The tangential forces that resist movement due to friction might therefore be different in 0g. This could be particularly relevant given that the effect of friction would interact with the limb in a direction-dependent fashion, given the anisotropy of the equivalent mass at the fingertip evoked by the authors. Is there some way to discount or control for these potential effects?

      Response (13): We agree that friction might play a role here, but normal interaction with a touch screen typically involves friction between 0.1N and 0.5N (e.g., Ayyildiz et al., 2018). We believe that the directional variation of the friction is even smaller than 0.1N. It is very small compared to the force used to accelerate the arm for the reaching movement (10N-15N). Thus, friction anisotropy is unlikely to explain our data. Indeed, our readers might have the same concern, we thus added some discussion about possible effect of friction.

      Citation: Ayyildiz M, Scaraggi M, Sirin O, Basdogan C, Persson BNJ. Contact mechanics between the human finger and a touchscreen under electroadhesion. Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):12668-12673.

      (3) The carefully crafted modelling of the limb neglects, nevertheless, the potential instability of the base of the arm. While the taikonauts were able to use their left arm to stabilize their bodies, it is not clear to what extent active stabilization with the contralateral limb can reproduce the stability of the human body seated in a chair in Earth gravity. Unintended motion of the shoulder could account for a smaller-than-expected displacement of the hand in response to the initial feedforward command and/or greater propensity for errors (with a greater need for corrective submovements) in 0g. The direction of movement with respect to the anchoring point could lead to the dependence of the observed effects on movement direction. Could this be tested in some way, e.g., by testing subjects on the ground while standing on an unstable base of support or sitting on a swing, with the same requirement to stabilize the torso using the contralateral arm?

      Response (14): Body stabilization is always a challenge for human movement studies in space. We minimized its potential confounding effects by using left-hand grasping and foot straps for postural support throughout the experiment. We think shoulder stability is an unlikely explanation because unexpected shoulder instability should not affect the feedforward (early) part of the ballistic reaching movement: the reduced peak acceleration and its early peak were observed at about 90-100ms after movement initiation. This effect is too early to be explained by an expected stability issue. This argument is now mentioned in the revised Discussion.

      The arguments for an underestimation of body mass would be strengthened if the authors could address these points in some way.

      Recommendations for the authors:

      Reviewing Editor Comments:

      General recommendation

      Overall, the reviewers agreed this is an interesting study with an original and strong approach. Nonetheless, there were significant weaknesses identified. The main criticism is that there is insufficient evidence for the claim that the movement slowing is due to mass underestimation, rather than other explanations for the increased feedback corrections. To bolster this claim, the reviewers have requested a deeper quantitative analysis of the directional effect and comparison to model predictions. They have also suggested that a 2-dof arm model could be used to predict how mass underestimation would influence multi-joint kinematics, and this should be compared to the data. Alternatively, or additionally, a control experiment could be performed (described in the reviews). We do realize that some of these options may not be feasible or practical. Ultimately, we leave it to you to determine how best to strengthen and solidify the argument for mass underestimation, rather than other causes.

      As an alternative approach, you could consider tempering the claim regarding mass underestimation and focus more on the result that slower movements in microgravity are not simply a feedforward, rescaling of the movement trajectories, but rather, have greater feedback corrections. In this case, the reviewers feel it would still be critical to explain and discuss potential reasons for the corrections beyond mass underestimation.

      We hope that these points are addressable, either with new analyses, experiments, or with a tempering of the claims. Addressing these points would help improve the eLife assessment.

      Reviewer #1 (Recommendations for the authors):

      (1) Move model descriptions to the main text to present modelling choices in more detail

      Response (15): Thank you for the suggestion. We have moved the model descriptions to the main text to present the modeling choices in more detail and to allow readers to better cross-reference the analyses.

      (2) Perform quantitative comparisons of the directional effect with the model's predictions, and add raw kinematic traces to illustrate the effect in more detail.

      Response (16): Thanks for the suggestion, we have added the raw kinematics figure from a representative participant and please refer to Response (2) above for the comparisons of directional effect.

      (3) Explore the effect of varying cost parameters in addition to mass estimation error to estimate the proportion of data explained by the underestimation hypothesis.

      Response (17): Thank you for the suggestion. This has already been done—please see Response (1) above.

      Reviewer #2 (Recommendations for the authors):

      Minor comments:

      (1) It must be justified early on why reaction times are being analyzed in this work. I understood later that it is to rule out any global slowing down of behavioral responses in microgravity.

      Response (18): Exactly, RT results are informative about the absence of a global slowing down. Contrary to the conservative-strategy hypothesis, taikonauts did not show generalized slowing; they actually had faster reaction times during spaceflight, incompatible with a generalized slowing strategy. Thanks for point out; we justified that early in the text.

      (2) Since the results are presented before the methods, I suggest stressing from the beginning that the reaching task is performed on a tablet and mentioning the instructions given to the participants, to improve the reading experience. The "beep" and "no beep" conditions also arise without obvious justification while reading the paper.

      Response (19): Great suggestions. We now give out some experimental details and rationales at the beginning of Results.

      (3) Figure 1C: The vel profiles are not returning to 0 at the end, why? Is it because the feedback gain is computed based on the underestimated mass or because a feedforward controller is applied here? Is it compatible with the experimental velocity traces?

      Response (20): Figure. 1C shows the forward simulation under the optimal control policy. In our LQG formulation the terminal velocity is softly penalized (finite weight) rather than hard-constrained to zero; with a fixed horizon° the optimal solution can therefore end with a small residual velocity.

      In the behavioral data, the hand does come to rest: this is achieved by corrective submovements during the homing phase.

      (4) Left-skewed -> I believe this is right-skewed since the peak velocity is earlier.

      Response (21): Yes, it should be right-skewed, thanks for point that out.

      (5) What was the acquisition frequency of the positional data points? (on the tablet).

      Response (22): The sampling frequency is 100 Hz. Thanks for pointing that out; we’ve added this information to the Methods.

      (6) Figure S1. The planned duration seems to be longer than in the experiment (it is more around 500 ms for the 135-degree direction in simulation versus less than 400 ms in the experiment). Why?

      Response (23): We apologize for a coding error that inadvertently multiplied the body-mass parameter by an extra factor, making the simulated mass too high. We have corrected the code, rerun the simulations, and updated Figures 1 and S1; all qualitative trends remain unchanged, and the revised movement durations (≈300–400 ms) are closer to the experimental values.

      (7) After Equation 13: "The control law is given by". This is not the control law, which should have a feedback form u=K*x in the LQ framework. This is just the dynamic equations for the auxiliary state and the force. Please double-check the model description.

      Response (24): Thank you for point this out. We have updated and refined all model equations and descriptions, and moved the model description from the Supplementary Materials to the main text; please see the revised manuscript.

      Reviewer #3 (Recommendations for the authors):

      (1) I have a concern about the interpretation of the anisotropic "equivalent mass". From my understanding, the equivalent mass would be what an external actor would feel as an equivalent inertia if pushing on the end effector from the outside. But the CNS does not push on the arm with a pure force generator acting at the hand to effectuate movement. It applies torque around the joints by applying forces across joints with muscles, causing the links of the arm to rotate around the joints. If the analysis is carried out in joint space, is the effective rotational inertia of the arm also anisotropic with respect to the direction of the movement of the hand? In other words, can the authors reassure me that the simulations are equivalent to an underestimation of the rotational inertia of the links when applied to the joints of the limb? It could be that these are mathematically the same; I have not delved into the mathematics to convince myself either way. But I would appreciate it if the authors could reassure me on this point.

      Response (25): Thank you for raising this point. In our work, “equivalent mass” denotes the operational-space inertia projected along the hand-movement direction u, computed as:

      This formulation describes the effective mass perceived at the end effector along a given direction, and is standard in operational-space control.

      Although the motor command can be coded as either torque/force in the CNS, the actual executions are equivalent no matter whether it is specified as endpoint forces or joint torques, since force and torque are related by . For small excursions as investigated here, this makes the directional anisotropy in endpoint inertia consistent with the anisotropy of the effective joint-space inertia required to produce the same endpoint motion. Conceptually, therefore, our “mass underestimation” manipulation in operational space corresponds to underestimating the required joint-space inertia mapped through the Jacobian. Since our behavioral data are hand positions, using the operational-space representation is the most direct and appropriate way for modeling.

      (2) I would also like to suggest one more level of analysis to test their hypothesis. The authors decomposed the movements into submovements and measured the prevalence of corrective submovements in weightlessness vs. normal gravity. The increase in corrective submovements is consistent with the hypothesis of a misestimation of limb mass, leading to an unexpectedly smaller displacement due to the initial feedforward command, leading to the need for corrections, leading to an increased overall movement duration. According to this hypothesis, however, the initial submovement, while resulting in a smaller than expected displacement, should have the same duration as the analogous movements performed on Earth. The authors could check this by analyzing the duration of the extracted initial submovements.

      Response (26): We appreciate the reviewer’s suggestion regarding the analysis of the initial submovement duration. In our decomposition framework, each submovement is modeled as a symmetric log-normal (bell-shaped) component, such that the time to peak speed is always half of the component duration. Thus, the initial submovement duration is directly reflected in the initial submovement peak-speed time already reported in our original manuscript (Figure. 5F).

      However, we respectfully disagree with the assumption that mass underestimation would necessarily yield the same submovement duration as on Earth. Under mass underestimation, the movement is effectively under-actuated, and the initial submovement can terminate prematurely, leading to a shorter duration. This is indeed what we observed in the data. Therefore, our reported metrics already address the reviewer’s proposal and support the conclusion that mass underestimation reduces the initial submovement duration in microgravity. Per your suggestion, we now added one more sentence to explain to the reader that initial submovement peak-speed time reflect the duration of the initial submovement.

      Some additional minor suggestions:

      (1) I believe that it is important to include the data from the control subjects, in some form, in the main article. Perhaps shading behind the main data from the taikonauts to show similarities or differences between groups. It is inconvenient to have to go to the supplementary material to compare the two groups, which is the main test of the experiment.

      Response (27): Thank you for the suggestion. For all the core performance variables, the control group showed flat patterns, with no changes across test sessions at all. Thus, including these figures (together with null statistical results) in the main text would obscure our central message, especially given the expanded length of the revised manuscript (we added model details and new analysis results). Instead, following eLife’s format, we have reorganized the Supplementary Material so that each experimental figure has a corresponding supplementary figure showing the control data. This way, readers can quickly locate the control results and directly compare them with the experimental data, while keeping the main text focused.

      (2) "Importantly, sensory estimate of bodily property in microgravity is biased but evaded from sensorimotor adaptation, calling for an extension of existing theories of motor learning." Perhaps "immune from" would be a better choice of words.

      Response (28): Thanks for the suggestion, we edited our text accordingly.

      (3) "First, typical reaching movement exhibits a symmetrical bell-shaped speed profile, which minimizes energy expenditure while maximizing accuracy according to optimal control principles (Todorov, 2004)." While Todorov's analysis is interesting and well accepted, it might be worthwhile citing the original source on the phenomenon of bell-shaped velocity profiles that minimize jerk (derivative of acceleration) and therefore, in some sense, maximize smoothness. Flash and Hogan, 1985.

      Response (29): Thanks for the suggestion, we added the citation of minimum jerk.

      (4) "Post-hoc analyses revealed slower reaction times for the 45° direction compared to both 90° (p < 0.001, d = 0.293) and 135° (p = 0.003, d = 0.284). Notably, reactions were faster during the in-flight phase compared to pre-flight (p = 0.037, d = 0.333), with no significant difference between in-flight and post-flight phases (p = 0.127)." What can one conclude from this?

      Response (30): Although these decreases reached statistical significance, their magnitudes were small. The parallel pattern across groups suggests the effect is not driven by microgravity, but is more plausibly a mild learning/practice effect. We now mentioned this in the Discussion.

      (5) "In line with predictions, peak acceleration appeared significantly earlier in the 45° direction than other directions (45° vs. 90°, p < 0.001, d = 0.304; 45° vs. 135°, p < 0.001, d = 0.271)." Which predictions? Because the effective mass is greater at 45º? Could you clarify the prediction?

      Response (31): We should be more specific here; thank you for raising this. The predictions are the ones about peak acceleration timing (shown in Fig. 1H). We now modified this sentence as:

      “In line with model predictions (Figure 1H), ….”.

      (6) Figure 2: Why do 45º movements have longer reaction times but shorter movement durations?

      Response (32): Appreciate your careful reading of the results. We believe this is possibly due to flexible motor control across conditions and trials, i.e., people tend to move faster when people react slower with longer reaction time. This has been reflected in across-direction comparisons (as spotted by the reviewer here), and it has also been shown within participant and across participants: For both groups, we found a significant negative correlation between movement duration (MD) and reaction time (RT), both across and within individuals (Figure 2—figure supplement 5). This finding indicates that participants moved faster when their RT was slower, and vice versa. This flexible motor adjustment, likely due to the task requirement for rapid movements, remained consistent during spaceflight.

    1. Author response:

      In response to the comments raised, we outline below the revisions we plan to strengthen the manuscript.

      First, we will expand the Introduction and Discussion sections to provide clearer comparison with prior experimental and computational studies of ectodomain tilting, MPER–TMD conformational heterogeneity, and membrane deformation, and to discuss how our simulations reproduce and extend these earlier observations.

      Second, we plan to add analyses that more directly assess the coupling between ectodomain and TMD motions. We will also revise the text to emphasize the limits imposed by sampling and model dependence and to discuss the potential benefits of enhanced sampling methods.

      Third, we will clarify the rationale for the chosen membrane composition and discuss how differences in lipid content between host plasma membranes and HIV virions may influence bilayer properties and Env dynamics.

      Fourth, we will supplement the Methods section to improve clarity and address issues of citation throughout the manuscript.

      Finally, we intend to deposit MD trajectories to a public research data repository to the extent permitted by available storage capacity.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors present a novel usage of fluorescence lifetime imaging microscopy (FLIM) to measure NAD(P)H autofluorescence in the Drosophila brain, as a proxy for cellular metabolic/redox states. This new method relies on the fact that both NADH and NADPH are autofluorescent, with a different excitation lifetime depending on whether they are free (indicating glycolysis) or protein-bound (indicating oxidative phosphorylation). The authors successfully use this method in Drosophila to measure changes in metabolic activity across different areas of the fly brain, with a particular focus on the main center for associative memory: the mushroom body.

      Strengths:

      The authors have made a commendable effort to explain the technical aspects of the method in accessible language. This clarity will benefit both non-experts seeking to understand the methodology and researchers interested in applying FLIM to Drosophila in other contexts.

      Weaknesses:

      (1) Despite being statistically significant, the learning-induced change in f-free in α/β Kenyon cells is minimal (a decrease from 0.76 to 0.73, with a high variability). The authors should provide justification for why they believe this small effect represents a meaningful shift in neuronal metabolic state.

      We agree with the reviewer that the observed f_free shift averaged per individual, while statistically significant, is small. However, to our knowledge, this is the first study to investigate a physiological (i.e., not pharmacologically induced) variation in neuronal metabolism using FLIM. As such, there are no established expectations regarding the amplitude of the effect. In the revised manuscript, we have included an additional experiment involving the knockdown of ALAT in α/β Kenyon cells, which further supports our findings. We have also expanded the discussion to expose two potential reasons why this effect may appear modest.

      (2) The lack of experiments examining the effects of long-term memory (after spaced or massed conditioning) seems like a missed opportunity. Such experiments could likely reveal more drastic changes in the metabolic profiles of KCs, as a consequence of memory consolidation processes.

      We agree with the reviewer that investigating the effects of long-term memory on metabolism represent a valuable future path of investigation. An intrinsic caveat of autofluorescence measurement, however, is to identify the cellular origin of the observed changes. To this respect, long-term memory formation is not an ideal case study as its essential feature is expected to be a metabolic activation localized to Kenyon cells’ axons in the mushroom body vertical lobes (as shown in Comyn et al., 2024), where many different neuron subtypes send intricate processes. This is why we chose to first focus on middle-term memory, where changes at the level of the cell bodies could be expected from our previous work (Rabah et al., 2022). But our pioneer exploration of the applicability of NAD(P)H FLIM to brain metabolism monitoring in vivo now paves the way to extending it to the effect of other forms of memory.

      (3) The discussion is mostly just a summary of the findings. It would be useful if the authors could discuss potential future applications of their method and new research questions that it could help address.

      The discussion has been expanded by adding interpretations of the findings and remaining challenges.

      Reviewer #2 (Public review):

      This manuscript presents a compelling application of NAD(P)H fluorescence lifetime imaging (FLIM) to study metabolic activity in the Drosophila brain. The authors reveal regional differences in oxidative and glycolytic metabolism, with a particular focus on the mushroom body, a key structure involved in associative learning and memory. In particular, they identify metabolic shifts in α/β Kenyon cells following classical conditioning, consistent with their established role in energy-demanding middle- and long-term memories.

      These results highlight the potential of label-free FLIM for in-vivo neural circuit studies, providing a powerful complement to genetically encoded sensors. This study is well-conducted and employs rigorous analysis, including careful curve fitting and well-designed controls, to ensure the robustness of its findings. It should serve as a valuable technical reference for researchers interested in using FLIM to study neural metabolism in vivo. Overall, this work represents an important step in the application of FLIM to study the interactions between metabolic processes, neural activity, and cognitive function.

      Reviewer #3 (Public review):

      This study investigates the characteristics of the autofluorescence signal excited by 740 nm 2-photon excitation, in the range of 420-500 nm, across the Drosophila brain. The fluorescence lifetime (FL) appears bi-exponential, with a short 0.4 ns time constant followed by a longer decay. The lifetime decay and the resulting parameter fits vary across the brain. The resulting maps reveal anatomical landmarks, which simultaneous imaging of genetically encoded fluorescent proteins helps to identify. Past work has shown that the autofluorescence decay time course reflects the balance of the redox enzyme NAD(P)H vs. its protein-bound form. The ratio of free-to-bound NADPH is thought to indicate relative glycolysis vs. oxidative phosphorylation, and thus shifts in the free-to-bound ratio may indicate shifts in metabolic pathways. The basics of this measure have been demonstrated in other organisms, and this study is the first to use the FLIM module of the STELLARIS 8 FALCON microscope from Leica to measure autofluorescence lifetime in the brain of the fly. Methods include registering the brains of different flies to a common template and masking out anatomical regions of interest using fluorescence proteins.

      The analysis relies on fitting an FL decay model with two free parameters, f_free and t_bound. F_free is the fraction of the normalized curve contributed by a decaying exponential with a time constant of 0.4 ns, thought to represent the FL of free NADPH or NADH, which apparently cannot be distinguished. T_bound is the time constant of the second exponential, with scalar amplitude = (1-f_free). The T_bound fit is thought to represent the decay time constant of protein-bound NADPH but can differ depending on the protein. The study shows that across the brain, T_bound can range from 0 to >5 ns, whereas f_free can range from 0.5 to 0.9 (Figure 1a). These methods appear to be solid, the full range of fits are reported, including maximum likelihood quality parameters, and can be benchmarks for future studies.

      The authors measure the properties of NADPH-related autofluorescence of Kenyon Cells(KCs) of the fly mushroom body. The results from the three main figures are:

      (1) Somata and calyx of mushroom bodies have a longer average tau_bound than other regions (Figure 1e);

      (2) The f_free fit is higher for the calyx (input synapses) region than for KC somata (Figure 2b);

      (3) The average across flies of average f_free fits in alpha/beta KC somata decreases from 0.734 to 0.718. Based on the first two findings, an accurate title would be "Autofluorecense lifetime imaging reveals regional differences in NADPH state in Drosophila mushroom bodies."

      The third finding is the basis for the title of the paper and the support for this claim is unconvincing. First, the difference in alpha/beta f_free (p-value of 4.98E-2) is small compared to the measured difference in f_free between somas and calyces. It's smaller even than the difference in average soma f_free across datasets (Figure 2b vs c). The metric is also quite derived; first, the model is fit to each (binned) voxel, then the distribution across voxels is averaged and then averaged across flies. If the voxel distributions of f_free are similar to those shown in Supplementary Figure 2, then the actual f_free fits could range between 0.6-0.8. A more convincing statistical test might be to compare the distributions across voxels between alpha/beta vs alpha'/beta' vs. gamma KCs, perhaps with bootstrapping and including appropriate controls for multiple comparisons.

      The difference observed is indeed modest relative to the variability of f_free measurements in other contexts. The fact that the difference observed between the somata region and the calyx is larger is not necessarily surprising. Indeed, these areas have different anatomical compositions that may result in different basal metabolic profiles. This is suggested by Figure 1b which shows that the cortex and neuropile have different metabolic signatures. Differences in average f_free values in the somata region can indeed be observed between naive and conditioned flies. However, all comparisons in the article were performed between groups of flies imaged within the same experimental batches, ensuring that external factors were largely controlled for. This absence of control makes it difficult to extract meaningful information from the comparison between naive and conditioned flies.

      We agree with the reviewer that the choice of the metric was indeed not well justified in the first manuscript. In the new manuscript, we have tried to illustrate the reasons for this choice with the example of the comparison of f_free in alpha/beta neurons between unpaired and paired conditioning (Dataset 8). First, the idea of averaging across voxels is supported by the fact that the distributions of decay parameters within a single image are predominantly unimodal. Examples for Dataset 8 are now provided in the new Sup. Figure 14. Second, an interpretable comparison between multiple groups of distributions is, to our knowledge, not straightforward to implement. It is now discussed in Supplementary information. To measure interpretable differences in the shapes of the distributions we computed the first three moments of distributions of f_free for Dataset 8 and compared the values obtained between conditions (see Supplementary information and new Sup. Figure 15). Third, averaging across individuals allows to give each experimental subject the same weight in the comparisons.

      I recommend the authors address two concerns. First, what degree of fluctuation in autofluorescence decay can we expect over time, e.g. over circadian cycles? That would be helpful in evaluating the magnitude of changes following conditioning. And second, if the authors think that metabolism shifts to OXPHOS over glycolosis, are there further genetic manipulations they could make? They test LDH knockdown in gamma KCs, why not knock it down in alpha/beta neurons? The prediction might be that if it prevents the shift to OXPHOS, the shift in f_free distribution in alpha/beta KCs would be attenuated. The extensive library of genetic reagents is an advantage of working with flies, but it comes with a higher standard for corroborating claims.

      In the present study, we used control groups to account for broad fluctuations induced by external factors such as the circadian cycle. We agree with the reviewer that a detailed characterization of circadian variations in the decay parameters would be valuable for assessing the magnitude of conditioning-induced shifts. We have integrated this relevant suggestion in the Discussion. Conducting such an investigation lies unfortunately beyond the scope and means of the current project.

      In line with the suggestion of the reviewer, we have included a new experiment to test the influence of the knockdown of ALAT on the conditioning-induced shift measured in alpha/beta neurons. This choice is motivated in the new manuscript. The obtained result shows that no shift is detected in the mutant flies, in accordance with our hypothesis.

      FLIM as a method is not yet widely prevalent in fly neuroscience, but recent demonstrations of its potential are likely to increase its use. Future efforts will benefit from the description of the properties of the autofluorescence signal to evaluate how autofluorescence may impact measures of FL of genetically engineered indicators.

      Recommendations for the authors

      Reviewer #1 (Recommendations for the authors):

      (1) Y axes in Figures 1e, 2c, 3b,c are misleading. They must start at 0.

      Although we agree that making the Y axes start at 0 is preferable, in our case it makes it difficult to observe the dispersion of the data at the same time (your next suggestion). To make it clearer to the reader that the axes do not start at 0, a broken Y-axis is now displayed in every concerned figure.

      (2) These same plots should have individual data points represented, for increased clarity and transparency.

      Individual data points were added on all boxplots.

      Reviewer #2 (Recommendations for the authors):

      I am evaluating this paper as a fly neuroscientist with experience in neurophysiology, including calcium imaging. I have little experience with FLIM but anticipate its use growing as more microscopes and killer apps are developed. From this perspective, I value the opportunity to dig into FLIM and try to understand this autofluorescence signal. I think the effort to show each piece of the analysis pipeline is valuable. The figures are quite beautiful and easy to follow. My main suggestion is to consider moving some of the supplemental data to the main figures. eLife allows unlimited figures, moving key pieces of the pipeline to the main figures would make for smoother reading and emphasize the technical care taken in this study.

      We thank the reviewer for their feedback. Following their advice we have moved panels from the supplementary figures to the main text (see new Figure 2).

      Unfortunately, the scientific questions and biological data do not rise to the typical standard in the field to support the claims in the title, "In vivo autofluorescence lifetime imaging of the Drosophila brain captures metabolic shifts associated with memory formation". The authors also clearly state what the next steps are: "hypothesis-driven approaches that rely on metabolite-specific sensors" (Intro). The advantage of fly neuroscience is the extensive library of genetic reagents that enable perturbations. The key manipulation in this study is the electric shock conditioning paradigm that subtly shifts the distribution of a parameter fit to an exponential decay in the somas of alpha/beta KCs vs others. This feels like an initial finding that deserves follow-up; but is it a large enough result to motivate a future student to pick this project up? The larger effect appears to be the gradients in f_free across KCs overall (Figure 2b). How does this change with conditioning?

      We acknowledge that the observed metabolic shift is modest relative to the variability of f_free and agree that additional corroborating experiments would further strengthen this result. Nevertheless, we believe it remains a valid and valuable finding that will be of interest to researchers in the field. The reviewer is right in pointing out that the gradient across KCs is higher in magnitude, however, the fact that this technique can also report experience-dependent changes, in addition to innate heterogeneities across different cell types, is a major incentive for people who could be interested in applying NAD(P)H FLIM in the future. For this reason, we consider it appropriate to retain mention of the memory-induced shift in the title, while making it less assertive and adding a reference to the structural heterogeneities of f_free revealed in the study. We have also rephrased the abstract to adopt a more cautious tone and expanded the discussion to clarify why a low-magnitude shift in f_free can still carry biological significance in this context. Finally, we have added the results of a new set of data involving the knockdown of ALAT in Kenyon cells, to further support the relevance of our observation relative to memory formation, despite its small magnitude. We believe that these elements together form a good basis for future investigations and that the manuscript merits publication in its present form.

      Together, I would recommend reshaping the paper as a methods paper that asks the question, what are the spatial properties of NADPH FL across the brain? The importance of this question is clear in the context of other work on energy metabolism in the MBs. 2P FLIM will likely always have to account for autofluorescence, so this will be of interest. The careful technical work that is the strength of the manuscript could be featured, and whether conditioning shifts f_free could be a curio that might entice future work.

      By transferring panels of the supplementary figures to the main text (see new Figure 2) as suggested by Reviewer 2, we have reinforced the methodological part of the manuscript. For the reasons explained above, we however still mention the ‘biological’ findings in the title and abstract.

      Minor recommendations on science:

      Figure 2C. Plotting either individual data points or distributions would be more convincing.

      Individual data points were added on all boxplots.

      There are a few mentions of glia. What are the authors' expectations for metabolic pathways in glia vs. neurons? Are glia expected to use one more than the other? The work by Rabah suggests it should be different and perhaps complementary to neurons. Can a glial marker be used in addition to KC markers? This seems crucial to being able to distinguish metabolic changes in KC somata from those in glia.

      Drosophila cortex glia are thought to play a similar role as astrocytes in vertebrates (see Introduction). In that perspective, we expect cortex glia to display a higher level of glycolysis than neurons. The work by Rabah et al. is coherent with this hypothesis. Reviewer 2 is right in pointing out that using a glial marker would be interesting. However, current technical limitations make such experiments challenging. These limitations are now exposed in the discussion.

      The question of whether KC somata positions are stereotyped can probably be answered in other ways as well. For example, the KCs are in the FAFB connectomic data set and the hemibrain. How do the somata positions compare?

      The reviewer’s suggestion is indeed interesting. However, the FAFB and hemibrain connectomic datasets are based on only two individual flies, which probably limits their suitability for assessing the stereotypy of KC subtype distributions. In addition, aligning our data with the FAFB dataset would represent substantial additional work.

      The free parameter tau_bound is mysterious if it can be influenced by the identity of the protein. Are there candidate NADPH binding partners that have a spatial distribution in confocal images that could explain the difference between somas and calyx?

      There are indeed dozens of NADH- or NADPH-binding proteins. For this reason, in all studies implementing exponential fitting of metabolic FLIM data, tau_bound is considered a complex combination of the contributions from many different proteins. In addition, one should keep in mind that the number of cell types contributing to the autofluorescence signal in the mushroom body calyx (Kenyon cells, astrocyte-like and ensheathing glia, APL neurons, olfactory projection neurons, dopamine neurons) is much higher than in the somas (only Kenyon cells and cortex glia). This could also participate in the observed difference. Hence, focusing on intracellular heterogeneities of potential NAD(P)H binding partners seems premature at that stage.

      The phrase "noticeable but not statistically significant" is misleading.

      We agree with the reviewer and have removed “noticeable but” from the sentence in the new version of the manuscript.

      Minor recommendations on presentation:

      The Introduction can be streamlined.

      We agree that some parts of the Introduction can seem a bit long for experts of a particular field. However, we think that this level of detail makes the article easily accessible for neuroscientists working on Drosophila and other animal models but not necessarily with FLIM, as well as for experts in energy metabolism that may be familiar with FLIM but not with Drosophila neuroscience.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript by Wang et al. reports the potential involvement of an asymmetric neurocircuit in the sympathetic control of liver glucose metabolism.

      Strengths:

      The concept that the contralateral brain-liver neurocircuit preferentially regulates each liver lobe may be interesting.

      Weaknesses:

      However, the experimental evidence presented did not support the study's central conclusion.

      We sincerely thank the reviewer for recognizing the conceptual novelty of our work and for constructive comments aimed at enhancing its rigor and clarity. In response, we will carry out targeted experiments to address the points raised, including: (i) further characterization of LPGi projections to vagal and sympathetic circuits; (ii) evaluation of potential pancreatic involvement; and (ii) validation of the specificity of chemogenetic activation within the proposed circuit. We anticipate completing the revised version within 8 weeks.

      (1) Pseudorabies virus (PRV) tracing experiment:

      The liver not only possesses sympathetic innervations but also vagal sensory innervations. The experimental setup failed to distinguish whether the PRV-labeling of LPGi (Lateral Paragigantocellular Nucleus) is derived from sympathetic or vagal sensory inputs to the liver.

      Thank you for raising this important point. We fully agree that the liver receives both sympathetic and vagal sensory innervation, and we acknowledge that PRV-based tracing alone does not definitively distinguish between these two pathways. This represents a limitation of the original experimental design.

      Based on established anatomical literature as well as our experimental observations, vagal sensory neuron cell bodies reside in the nodose ganglion (NG), and their central projections terminate predominantly in the nucleus of the solitary tract (NTS) (Nature. 2023;623(7986):387-396; Curr Biol. 2020;30(20):3986-3998.e5.), which is located in the dorsomedial medulla. In contrast, the LPGi, together with other sympathetic-related nuclei, is predominantly distributed in the ventral medulla (Cell Metab. 2025;37(11):2264-2279.e10; Nat Commun. 2022;13(1):5079.).

      To directly assess the contribution of vagal sensory pathways, we will perform an additional PRV tracing experiment using two groups of mice: one with bilateral nodose ganglion (NG) removal and a sham-operated control group. Identical PRV injections will be delivered to the liver in both groups, and PRV labeling in the LPGi will be quantitatively compared. Preservation of LPGi labeling following NG ablation would indicate that PRV transmission occurs primarily via sympathetic, rather than vagal sensory, pathways. These data will be incorporated into the revised manuscript and are expected to be completed within 3 weeks.

      (2) Impact on pancreas:

      The celiac ganglia not only provide sympathetic innervations to the liver but also to the pancreas, the central endocrine organ for glucose metabolism. The chemogenetic manipulation of LPGi failed to consider a direct impact on the secretion of insulin and glucagon from the pancreas.

      Thank you for this important comment. We agree that the celiac ganglia (CG) provide sympathetic innervation not only to the liver but also to the pancreas, which plays a central role in glucose homeostasis through the secretion of both insulin and glucagon. Therefore, the potential pancreatic implications associated with LPGi chemogenetic manipulation worth careful consideration.

      To address this concern, we examined circulating glucagon levels following chemogenetic manipulation of the LPGi. As shown in the Supplementary Figure below, plasma glucagon (GCG) concentrations were not significantly altered at 30, 60, 90, or 120 minutes compared with control mice (n = 6), indicating that LPGi manipulation does not measurably affect glucagon secretion under our experimental conditions.

      We acknowledge that insulin secretion was not assessed in the study, which represents an important limitation given the pancreatic innervation of the CG. To further strengthen our interpretation, we are performing additional experiments in newly prepared mice to measure circulating insulin levels following LPGi manipulation. These data together with Author response image 1 below will be included in the revised manuscript upon completion.

      Author response image 1.

      Plasma concentrations of GCG in mice following LPGi GABAergic neurons activation.

      (3) Neuroanatomy of the brain-liver neurocircuit:<br /> The current study and its conclusion are based on a speculative brain-liver sympathetic circuit without the necessary anatomical information downstream of LPGi.

      Thank you for raising this important point. A clear anatomical definition of the downstream pathways linking the brain to the liver is essential for interpreting the proposed brain-liver sympathetic circuit.

      However, the present study (Figure 4A) provides direct anatomical evidence supporting the organization of the brain–liver sympathetic neurocircuit. These observations are consistent with our recent detailed characterization of the brain-liver sympathetic circuit published in Cell Metabolism (Cell Metab. 2025;37(11):2264–2279), LPGi GABAergic neurons inhibit GABAergic neurons in the caudal ventrolateral medulla (CVLM). Disinhibition of CVLM reduces GABAergic suppression of rostral ventrolateral medulla (RVLM) neurons, which are key excitatory drivers of sympathetic tone. RVLM neurons project to sympathetic preganglionic neurons in the sympathetic chain (Syc). These neurons synapse with postganglionic sympathetic neurons in ganglia such as the celiac-superior mesenteric ganglion (CG-SMG). Postganglionic sympathetic fibers then innervate the liver, releasing NE to activate hepatic β<sub>2</sub>-adrenergic receptors and stimulate HGP.

      Together, these data establish a coherent anatomical basis for the proposed brain-liver sympathetic pathway and clarify the downstream organization relevant to the functional experiments presented here.

      Author response image 2.

      Tracing scheme (Left) and whole-mount imaging (Right) of PRV-labeled brain-liver neurocircuit. Scale bars, 3,000 (whole mount) or 1,000 (optical sections) μm.

      (4) Local manipulation of the celiac ganglia:<br /> The left and right ganglia of mice are not separate from each other but rather anatomically connected. The claim that the local injection of AAV in the left or right ganglion without affecting the other side is against this basic anatomical feature.

      Thank you for raising this important anatomical point. We fully acknowledge that the left and right celiac ganglia (CG) in mice are interconnected, and that unilateral viral injection could theoretically affect the contralateral side. The celiac–superior mesenteric ganglion (CG-SMG) complex serves as a major sympathetic hub that regulates visceral organ functions. Recent transcriptomic, anatomical, and functional studies have revealed that the CG-SMG is not a homogeneous structure but is composed of molecularly and functionally distinct neuronal populations. These populations exhibit specialized projection patterns and regulate different aspects of gastrointestinal physiology, supporting a model of modular sympathetic control. (Nature. 2025 Jan;637(8047):895-902). Therefore, we were aware of this phenomenon during the initial stages of these experiments.

      To minimize unintended spread to the contralateral CG, we took two complementary approaches.

      First, we optimized the injection strategy by using an extremely small injection volume (100 nL per site), with a very slow infusion rate (50 nL/min), and fine glass micropipettes. With these refinements, contralateral viral spread was rarely observed.

      Second, and importantly, all animals included in the final analyses were subjected to post hoc anatomical verification. After completion of the experiments, CG were collected, sectioned, and examined for viral expression. As shown in Supplementary Figure 5F, only mice in which viral expression was strictly confined to the targeted CG, with no detectable infection in the contralateral ganglion, were included in the presented data.

      Together, these measures ensure that the reported effects are attributable to local manipulation of the intended CG. We will ensure that the Methods section more explicitly details these technical precautions and that the legend for Figure S5F clearly states its role in validating injection specificity.

      Reviewer #2 (Public review):

      Summary:

      The manuscript by Wang and colleagues aims to determine whether the left and right LPGi differentially regulate hepatic glucose metabolism and to reveal decussation of hepatic sympathetic nerves.

      The authors used tissue clearing to identify sympathetic fibers in the liver lobes, then injected PRV into the hepatic lobes. Five days post-injection, PRV-labeled neurons in the LPGi were identified. The results indicated contralateral dominance of premotor neurons and partial innervation of more than one lobe. Then the authors activated each side of the LPGi, resulting in a greater increase in blood glucose levels after right-sided activation than after left-sided activation, as well as changes in protein expression in the liver lobes. These data suggested modulation of HGP (hepatic glucose production) in a lobe-specific manner. Chemical denervation of a particular lobe did not affect glucose levels due to compensation by the other lobes. In addition, nerve bundles decussate in the hepatic portal region.

      We thank the reviewer for the thorough and constructive evaluation of our manuscript. In direct response, we will undertake comprehensive revisions to enhance the rigor and clarity of the study, including: (i) correcting ambiguous or misleading terminology pertaining to anatomical resolution and sympathetic circuit organization; (ii) expanding the Methods section with complete experimental details, improved image presentation, and explicit justification of our viral and genetic approaches; and (iii) strengthening data interpretation by addressing issues related to sparse PRV labeling, projection heterogeneity, and the functional implications of double-labeled neurons. All revisions are expected to be completed within 8 weeks.

      Strengths:

      The manuscript is timely and relevant. It is important to understand the sympathetic regulation of the liver and the contribution of each lobe to hepatic glucose production. The authors use state-of-the-art methodology.

      Weaknesses:

      (1) The wording/terminology used in the manuscript is misleading, and it is not used in the proper context. For instance, the goal of the study is "to investigate whether cerebral hemispheres differentially regulate hepatic glucose metabolism..." (see abstract); however, the authors focus on the brainstem (a single structure without hemispheres). Similarly, symmetric is not the best word for the projections.

      We thank the reviewer for raising these critical points regarding terminology and conceptual framing. We acknowledge that certain phrases in our original manuscript may have been overly broad or ambiguous, particularly in describing the scope of sympathetic heterogeneity and the specificity of neural projections. Due to practical constraints and the scope of our study, our investigation is focused on the brainstem, which represents the final common pathway for these lateralized commands. We acknowledge that terms referring to the cerebral hemispheres do not accurately describe our study.

      We are revising the manuscript to ensure accurate and consistent terminology and will submit the revised version with these corrections.

      (2) Sparse labeling of liver-related neurons was shown in the LPGi (Figure 1). It would be ideal to have lower magnification images to show the area. Higher quality images would be necessary, as it is difficult to identify brainstem areas. The low number of labeled neurons in the LPGi after five days of inoculation is surprising. Previous findings showed extensive labeling in the ventral brainstem at four days post-inoculation (Desmoulins et al., 2025). Unfortunately, it is not possible to compare the injection paradigm/methods because the PRV inoculation is missing from the methods section. If the PRV is different from the previously published viral tracers, time-dependent studies to determine the order of neurons and the time course of infection would be necessary.

      We sincerely thank the reviewer for these detailed and constructive comments regarding the PRV tracing experiments. We fully agree that careful presentation and interpretation of the anatomical data are essential for ensuring rigor and transparency. We address each point in detail below.

      (1) Image magnification and anatomical context of LPGi labeling

      We agree that the original images did not sufficiently convey the broader anatomical context of the LPGi. In the revised manuscript, we will replace the original panels in Figure 1 with new images that include lower-magnification overviews of the brainstem, alongside higher-magnification views of the LPGi. These images clearly delineate the LPGi with respect to established anatomical landmarks and atlas boundaries. Image contrast and resolution will also be optimized to allow unambiguous identification of PRV-labeled neurons and surrounding structures.

      (2) Sparse LPGi labeling at 5 days post-injection and methodological details

      We apologize for the omission of the detailed PRV injection protocol in the original Methods section. We deliberately used small-volume, focal injections (1 µL per liver lobe) to minimize viral spread and to restrict labeling to circuits specifically connected to the targeted hepatic region. Under these conditions, early-stage or intermediate-order upstream nuclei such as the LPGi are expected to exhibit relatively sparse labeling compared to more proximal autonomic nuclei. This information will add, including the PRV strain, viral titer, injection volume, precise injection coordinates, and surgical procedures.

      (3) Not all LPGi cells are liver-related. Was the entire LPGi population stimulated, or was it done in a cell-type-specific manner? What was the strain, sex, and age of the mice? What was the rationale for using the particular viral constructs?

      We thank the reviewer for this insightful and important question. We agree that not all neurons within the LPGi are liver-related, and we apologize that our rationale was not clearly articulated in the original manuscript.

      (1) Our decision to target GABAergic neurons in the LPGi using Gad1-Cre mice was based on prior experimental evidence rather than an assumption about the entire LPGi population. In our previous study (Cell Metab. 2025;37(11):2264-2279.e10), we performed single-cell RNA sequencing on retrogradely labeled LPGi neurons following liver tracing. These analyses revealed that the majority of liver-projecting LPGi neurons are GABAergic in nature. Based on these findings, we chose to selectively manipulate GABAergic neurons in the LPGi rather than the entire LPGi neuronal population, in order to achieve greater cellular specificity and to minimize potential confounding effects arising from heterogeneous neuron types within this region. We regret that this rationale was not clearly described in the original submission and have now revised the manuscript to explicitly state this reasoning.

      (2) In addition, we apologize for the omission of mouse strain, sex, and age information in the Methods section. These details will be fully added.

      (3) We selected AAV-based viral vectors, specifically the AAV9 serotype, due to their well-established efficiency in transducing neurons in the brainstem, relatively low toxicity, and widespread use in circuit-level chemogenetic and optogenetic studies. When combined with Cre-dependent viral constructs in Gad1-Cre mice, this approach enabled selective and reliable manipulation of LPGi GABAergic neurons.

      (4) The authors should consider the effect of stimulation of double-labeled neurons (innervating more than one lobe) and potential confounding effects regarding other physiological functions.

      We thank the reviewer for raising this important point. We agree that neurons innervating more than one liver lobe could, in principle, introduce potential confounding effects and may reflect higher-order integrative autonomic neurons.

      This consideration is consistent with a key finding of the cited study: the celiac-superior mesenteric ganglion (CG-SMG) contains molecularly distinct sympathetic neuron populations (e.g., RXFP1<sup>+</sup> vs. SHOX2<sup>+</sup>) that exhibit complementary organ projections and separate, non‑overlapping functions. Specifically, RXFP1<sup>+</sup> neurons innervate secretory organs (pancreas, bile duct) to regulate secretion, while SHOX2<sup>+</sup> neurons innervate the gastrointestinal tract to control motility. This functional segregation supports the concept of specialized autonomic modules rather than a uniform,“fight or flight”response, reinforcing the need for careful interpretation of circuit-specific manipulations. (Nature. 2025;637(8047):895-902; Neuron. Published online December 10, 2025).

      In our PRV tracing experiments, the proportion of double-labeled neurons was relatively small, suggesting that the majority of labeled LPGi neurons preferentially associate with individual hepatic lobes. Nevertheless, we recognize that activation of this minority population could contribute to broader physiological effects beyond strictly lobe-specific regulation. We acknowledge that the absence of single-cell-level resolution in the current study limits our ability to further dissect the functional heterogeneity of these projection-defined neurons, and we will explicitly state this as a limitation in the revised manuscript. We will explicitly acknowledge this possibility in the revised manuscript and included it as a limitation of the current study. We thank the reviewer for highlighting this important conceptual consideration.

      (5) The authors state that "central projections directly descend along the sympathetic chain to the celiac-superior mesenteric ganglia". What they mean is unclear. Do the authors refer to pre-ganglionic neurons or premotor neurons? How does it fit with the previous literature?

      We thank the reviewer for pointing out this imprecise wording. We agree that the original phrasing was anatomically inaccurate and potentially confusing. The pathways we intended to describe involve brainstem premotor neurons that project to sympathetic preganglionic neurons in the spinal cord. These preganglionic neurons then innervate neurons in the celiac–superior mesenteric ganglia, which in turn provide postganglionic input to the liver.

      We are revising the manuscript to clearly distinguish premotor from preganglionic neurons and to describe this pathway in a manner consistent with the established organization of sympathetic autonomic circuits reported in the previous literature. The revised wording will explicitly reflect this hierarchical relay structure.

      (6) How was the chemical denervation completed for the individual lobes?

      We thank the reviewer for raising this important methodological concern. We agree that potential diffusion of 6-OHDA is a critical issue when performing lobe-specific chemical denervation, and we apologize that our original description did not sufficiently clarify how this was controlled.

      In the revised Methods section, we will provide a detailed description of the denervation procedure, including the injection volume and concentration of 6-OHDA, as well as the physical separation and isolation of individual hepatic lobes during application to minimize diffusion to adjacent tissue.

      To directly assess the specificity of the chemical denervation, we included immunofluorescence and Western blot analyses demonstrating a selective reduction of sympathetic markers in the targeted lobe, with minimal effects on non-targeted lobes. These results support the effectiveness and relative spatial confinement of the 6-OHDA treatment under our experimental conditions.

      We thank the reviewer for highlighting this point, which has helped us improve both the clarity and rigor of the manuscript.

      (7) The Western Blot images look like they are from different blots, but there are no details provided regarding protein amount (loading) or housekeeping. What was the reason to switch beta-actin and alpha-tubulin? In Figures 3F -G, the GS expression is not a good representative image. Were chemiluminescence or fluorescence antibodies used? Were the membranes reused?

      We thank the reviewer for this careful and detailed evaluation of the Western blot data. We apologize that insufficient methodological detail was provided in the original submission.

      (1) We would like to clarify that the protein bands shown within each panel were derived from the same membrane. To improve transparency, we will provide full, uncropped images of the corresponding membranes in the supplementary materials. In addition, detailed information regarding protein loading amounts, gel conditions, and housekeeping controls will be added to the Methods section.

      (2) The use of different loading controls (β-actin or α-tubulin) reflects a technical consideration rather than an experimental inconsistency. In our experiments, the molecular weight of the TH (62kDa) was too close to α-tubulin (55kDa), and β-actin (42kDa) was therefore used to avoid band overlap and to ensure accurate quantification.

      (3) Regarding the GS signal shown in Figures 3F–G, we agree that the original representative image was suboptimal. This appears to be related to antibody performance rather than sample quality. To address this, we are repeating the GS Western blot using a newly validated antibody. The original tissue samples had been aliquoted and stored at −80 °C, allowing reliable re-analysis. This work will be done in 8 weeks.

      (4) All Western blot experiments were detected using chemiluminescence, and membrane stripping and reprobing procedures are now explicitly described in the Methods section.

      We thank the reviewer for highlighting these issues, which significantly improve the rigor and clarity of our data presentation.

      (8) Key references using PRV for liver innervation studies are missing (Stanley et al, 2010 [PMID: 20351287]; Torres et al., 2021 [PMID: 34231420]; Desmoulins et al., 2025 [PMID: 39647176]).

      We thank the reviewer for pointing out these important and highly relevant references that were inadvertently omitted in our initial submission. The studies by Stanley et al. (Proc Natl Acad Sci U S A, 2010), Torres et al. (Am J Physiol Regul Integr Comp Physiol, 2021), and Desmoulins et al. (Auton Neurosci, 2025) represent key PRV-based retrograde tracing work that has mapped central neural circuits innervating the liver and thus provide essential context for our anatomical analyses.

      We agree that inclusion of these studies is necessary to properly situate our findings within the existing literature. Accordingly, we will incorporate citations to these references in the revised manuscript and discuss their relationship to our results.

      Reviewer #3 (Public review):

      Summary:

      This study found a lobe-specific, lateralized control of hepatic glucose metabolism by the brain and provides anatomical evidence for sympathetic crossover at the porta hepatis. The findings are particularly insightful to the researchers in the field of liver metabolism, regeneration, and tumors.

      Strengths:

      Increasing evidence suggests spatial heterogeneity of the liver across many aspects of metabolism and regenerative capacity. The current study has provided interesting findings: neuronal innervation of the liver also shows anatomical differences across lobes. The findings could be particularly useful for understanding liver pathophysiology and treatment, such as metabolic interventions or transplantation.

      Weaknesses:

      Inclusion of detailed method and Discussion:

      We sincerely thank the reviewer for the positive and constructive feedback, which will significantly enhance both the methodological rigor and the broader biological interpretation of our study. In direct response, we will revise the Discussion to elaborate on the potential physiological advantages of a lateralized and lobe-specific pattern of liver innervation. Furthermore, we will expand the Methods section to include a comprehensive description of the quantitative analysis applied to PRV-labeled neurons. Together, these revisions will strengthen the manuscript’s clarity, depth, and relevance to researchers in hepatic metabolism, regeneration, and disease. We expect to complete all updates within 8 weeks.

      (1) The quantitative results of PRV-labeled neurons are presented, and please include the specific quantitative methods.

      We thank the reviewer for this helpful suggestion. We will add a detailed description of the quantitative methods used to analyze PRV-labeled neurons in the revised Methods section. This includes information on the counting criteria, the brain regions analyzed, how the regions of interest were delineated, and the normalization procedures applied to obtain the reported neuron counts.

      (2) The Discussion can be expanded to include potential biological advantages of this complex lateralized innervation pattern.

      We appreciate the reviewer’s suggestion. We will expand the Discussion to include a paragraph addressing the potential biological significance of lateralized liver innervation. We highlight that this asymmetric organization could allow for more precise, lobe-specific regulation of hepatic metabolism, enable integration of distinct physiological signals, and potentially provide robustness against perturbations. These points will discuss in the revised manuscript.

      Reviewer #4 (Public review):

      Summary:

      The studies here are highly informative in terms of anatomical tracing and sympathetic nerve function in the liver related to glucose levels, but given that they are performed in a single species, it is challenging to translated them to humans, or to determine whether these neural circuits are evolutionarily conserved. Dual-labeling anatomical studies are elegant, and the addition of chemogenetic and optogenetic studies is mechanistically informative. Denervation studies lack appropriate controls, and the role of sensory innervation in the liver is overlooked.

      We sincerely appreciate the reviewer's thoughtful evaluation and fully agree that findings derived from a single-species model must be interpreted with caution in relation to human physiology. In direct response, we will revise the manuscript to explicitly clarify that all experimental data were obtained in mice and to provide a discussion of the limitations regarding direct extrapolation to humans. Concurrently, we will expand the Discussion section by integrating our findings with recent human and translational studies, including a multicenter clinical trial demonstrating that catheter-based endovascular denervation of the celiac and hepatic arteries significantly improved glycemic control in patients with poorly controlled type 2 diabetes, without major adverse events (Signal Transduct Target Ther. 2025;10(1):371). While our current work focuses on defining the anatomical organization and functional asymmetry of this circuit in mice, the clinical findings suggest that the core principles, sympathetic control of hepatic glucose metabolism via CG-liver pathways, may be conserved and of translational relevance. Additionally, we will clarify the interpretation of tyrosine hydroxylase labeling and expand the discussion of hepatic sensory and parasympathetic innervation, acknowledging their important roles in liver–brain communication and identifying them as key directions for future research. Collectively, these revisions will provide a more balanced, clinically informed, and rigorous framework for interpreting our findings, and we aim to complete all updates within 8 weeks.

      Specific Weaknesses - Major:

      (1) The species name should be included in the title.

      We thank the reviewer for this suggestion. We agree that the species should be clearly indicated. The findings presented in this study were obtained in mice using tissue clearing and whole-organ imaging approaches. Due to technical limitations, these observations are currently limited to the mouse strain. We will update the title and clarified the species used throughout the manuscript.

      (2) Tyrosine hydroxylase was used to mark sympathetic fibers in the liver, but this marker also hits a portion of sensory fibers that need to be ruled out in whole-mount imaging data

      We thank the reviewer for pointing this out. We acknowledge that tyrosine hydroxylase (TH) labels not only sympathetic fibers but also a subset of sensory fibers. We will add a limitation of this point in the revised manuscript. In addition, ongoing experiments using retrograde PRV labeling from the liver, combined with sectioning, are being used to distinguish sympathetic fibers from vagal and dorsal root ganglion–derived sensory fibers. These data will be included in a forthcoming update of the manuscript and are expected to be completed in approximately 6 weeks.

      (3) Chemogenetic and optogenetic data demonstrating hyperglycemia should be described in the context of prior work demonstrating liver nerve involvement in these processes. There is only a brief mention in the Discussion currently, but comparing methods and observations would be helpful.

      We thank the reviewer for this suggestion. Previous studies largely relied on electrical stimulation to modulate liver innervation, which provides relatively coarse control of neural activity (Eur J Biochem. 1992;207(2):399-411). By contrast, our use of chemogenetic and optogenetic approaches allows selective, cell-type–specific manipulation of LPGi neurons. We will revise the Discussion to place our functional data in the context of prior work, highlighting how these more precise approaches improve understanding of the contribution of liver-innervating neurons to hyperglycemia.

      (4) Sympathetic denervation with 6-OHDA can drive compensatory increases to tissue sensory innervation, and this should be measured in the liver denervation studies to implicate potential crosstalk, especially given the increase in LPGi cFOS that may be due to afferent nerve activity. Compensatory sympathetic drive may not be the only culprit, though it is clearly assumed to be. The sensory or parasympathetic/vagal innervation of the liver is altogether ignored in this paper and could be better described in general.

      We thank the reviewer for this insightful comment and agree that chemical sympathetic denervation with 6-OHDA may induce compensatory changes in non-sympathetic hepatic inputs, including sensory and parasympathetic (vagal) innervation. As the reviewer correctly points out, increased LPGi cFOS activity may reflect afferent nerve engagement rather than solely compensatory sympathetic drive.

      More broadly, we agree that the central nervous system functions as an integrated homeostatic network that continuously processes diverse afferent signals, including hepatic sensory and vagal inputs, as well as other interoceptive cues. From this perspective, the LPGi cFOS changes observed in our study likely represent one component of a complex integrative response rather than evidence for a single dominant pathway.

      We acknowledge that the present study did not directly assess hepatic sensory or parasympathetic innervation, which represents a limitation in scope. In the revised manuscript, we will expand the Discussion to explicitly note this limitation and provide a more balanced consideration of potential crosstalk among sympathetic, sensory, and parasympathetic pathways in shaping LPGi activity following hepatic denervation.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Although the findings are interesting, this reviewer has major concerns about the experimental design, methodology, results, and interpretation of the data. Experimental details are lacking, including basic information (age, sex, strain of mice, procedures, magnification, etc.).

      We thank the reviewer for this important recommendation. We agree that comprehensive reporting of experimental details is essential for rigor and reproducibility.

      In the revised manuscript, we will add complete information regarding mouse strain, sex, age, and sample size for each experiment. In addition, detailed descriptions of surgical procedures, viral constructs, injection parameters, imaging magnification, and analysis methods have been incorporated into the Methods section.

      These revisions ensure that all experiments are described with sufficient technical detail and clarity to allow accurate interpretation and replication of our findings.

      Reviewer #3 (Recommendations for the authors):

      Addressing a few questions might help:

      (1) The study found that liver-associated LPGi neurons are predominantly GABAergic. It would be informative to molecularly characterize the PRV-traced, liver-projecting LPGi neurons to determine their neurochemical phenotypes.

      We thank the reviewer for this insightful suggestion. We agree that molecular characterization of liver-projecting LPGi neurons is important for understanding their functional identity.

      This issue has been addressed in detail in our recent study (Cell Metab. 2025;37(11):2264-2279.e10), in which we performed single-cell RNA sequencing on retrogradely traced LPGi neurons connected to the liver. These analyses demonstrated that the majority of liver-projecting LPGi neurons are GABAergic, with a defined transcriptional profile distinct from neighboring non–liver-related populations.

      Based on these findings, the current study selectively targets GABAergic LPGi neurons using Gad1-Cre mice. We are now explicitly referencing and summarizing these molecular results in the revised manuscript to clarify the neurochemical identity of the PRV-traced LPGi neurons.

      (2) Is it possible to do a local microinjection of a sodium channel blocker (e.g., lidocaine) or an adrenergic receptor antagonist into the porta hepatis? That would potentially provide additional evidence for the porta hepatis as the functional crossover point.

      We appreciate the reviewer’s thoughtful suggestion. While pharmacological blockade at the porta hepatis could modulate local neural activity, the proposed approach may not fully capture the distinction between ipsilateral and contralateral inputs, and may not conclusively establish neural crossover at this particular site.

      In our view, the anatomical evidence provided by whole-mount tissue clearing, dual-labeled tracing, and direct visualization of decussating nerve bundles at the porta hepatis offers a more definitive demonstration of sympathetic crossover. Pharmacological blockade would affect both crossed and uncrossed fibers simultaneously and therefore would not specifically resolve the anatomical organization of this decussation.

      Nevertheless, we agree that functional interrogation of the porta hepatis represents an interesting direction for future work, and we will now acknowledge this possibility in the Discussion.

      (3) It is possible to investigate the effects of unilateral LPGi manipulation or ablation of one side of CG/SMG on liver metabolism, such as hyperglycemia?

      We thank the reviewer for this important suggestion. We agree that unilateral ablation or silencing of the CG-SMG could provide additional insight into lateralized sympathetic control of liver metabolism.

      However, precise and selective ablation of one side of the CG-SMG through 6-OHDA without affecting the contralateral ganglion or adjacent autonomic structures remains technically challenging, particularly given the anatomical connectivity between the two sides. We are currently optimizing approaches to achieve reliable unilateral manipulation.

      If successful within the revision timeframe, we will include these experiments and corresponding metabolic analyses in the revised manuscript. If not, we will explicitly discuss this experimental limitation and the predicted metabolic consequences of unilateral CG-SMG ablation as an important direction for future studies. This work will be done in 6 weeks.

      Reviewer #4 (Recommendations for the authors):

      In the abstract and elsewhere, the use of the term 'sympathetic release' is unclear - do you mean release of nerve products, such as the neurotransmitter norepinephrine? This should be more clearly defined.

      We thank the reviewer for pointing out this ambiguity. We agree that the term “sympathetic release” was imprecise. In the revised manuscript, we will explicitly refer to the release of sympathetic neurotransmitters, primarily norepinephrine, from postganglionic sympathetic fibers.

      We will revise the wording throughout the manuscript to ensure accurate and consistent terminology and to avoid potential confusion regarding the underlying neurobiological mechanisms.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews

      Reviewer #1 (Public review):

      Summary:

      In this paper, the authors investigate the effects of Miro1 on VSMC biology after injury. Using conditional knockout animals, they provide the important observation that Miro1 is required for neointima formation. They also confirm that Miro1 is expressed in human coronary arteries. Specifically, in conditions of coronary diseases, it is localized in both media and neointima, and, in atherosclerotic plaque, Miro1 is expressed in proliferating cells.

      However, the role of Miro1 in VSMC in CV diseases is poorly studied, and the data available are limited; therefore, the authors decided to deepen this aspect. The evidence that Miro-/- VSMCs show impaired proliferation and an arrest in S phase is solid and further sustained by restoring Miro1 to control levels, normalizing proliferation. Miro1 also affects mitochondrial distribution, which is strikingly changed after Miro1 deletion. Both effects are associated with impaired energy metabolism due to the ability of Miro1 to participate in MICOS/MIB complex assembly, influencing mitochondrial cristae folding. Interestingly, the authors also show the interaction of Miro1 with NDUFA9, globally affecting super complex 2 assembly and complex I activity.

      Finally, these important findings also apply to human cells and can be partially replicated using a pharmacological approach, proposing Miro1 as a target for vasoproliferative diseases.

      Strengths:

      The discovery of Miro1 relevance in neointima information is compelling, as well as the evidence in VSMC that MIRO1 loss impairs mitochondrial cristae formation, expanding observations previously obtained in embryonic fibroblasts.

      The identification of MIRO1 interaction with NDUFA9 is novel and adds value to this paper. Similarly, the findings that VSMC proliferation requires mitochondrial ATP support the new idea that these cells do not rely mostly on glycolysis.

      Weaknesses:

      (1) Figure 3:

      I appreciate the system used to assess mitochondrial distribution; however, I believe that time-lapse microscopy to evaluate mitochondrial movements in real time should be mandatory. The experimental timing is compatible with time-lapse imaging, and these experiments will provide a quantitative estimation of the distance travelled by mitochondria and the fraction of mitochondria that change position over time. I also suggest evaluating mitochondrial shape in control and MIRO1-/- VSMC to assess whether MIRO1 absence could impact mitochondrial morphology, altering fission/fusion machinery, since mitochondrial shape could differently influence the mobility.

      Mitochondrial motility experiments. WT and Miro1-/- VSMCs were transiently transfected with mito-ds-red and untargeted GFP adenoviruses to fluorescently label mitochondria and cytosol, respectively. Live-cell fluorescence confocal microscopy was used to acquire mitochondrial images at one-minute intervals over a 25-30-minute period. WT cells exhibited dynamic reorganization of the mitochondrial network, whereas Miro1-/- VSMCs displayed minimal mitochondrial movement, characterized only by limited oscillatory behavior without network remodeling (Supplemental Video 1).

      Mitochondrial shape (form factor) was assessed by confocal microscopy in WT and Miro1-/- VSMCs. Analysis of the mitochondrial form factor (defined as the ratio of mitochondrial length to width) during cell cycle progression revealed morphological changes in wild type (WT) cells, characterized by an increase in form factor. In contrast, Miro1-/- cells exhibited no significant alterations in mitochondrial morphology (Figure 3- Figure supplement 1B).

      (2) Figure 6:

      The evidence of MIRO1 ablation on cristae remodeling is solid; however, considering that the mechanism proposed to explain the finding is the modulation of MICOS/MIB complex, as shown in Figure 6D, I suggest performing EM analysis in each condition. In my mind, Miro1 KK and Miro1 TM should lead to different cristae phenotypes according to the different impact on MICOS/MIB complex assembly. Especially, Miro1 TM should mimic Miro1 -/- condition, while Miro1 KK should drive a less severe phenotype. This would supply a good correlation between Miro1, MICOS/MIB complex formation and cristae folding.

      I also suggest performing supercomplex assembly and complex I activity with each plasmid to correlate MICOS/MIB complex assembly with the respiratory chain efficiency.

      Complex I activity assays revealed that overexpression of MIRO1-WT fully restored enzymatic activity in MIRO1-/- cells, whereas MIRO1-KK provided partial rescue. In contrast, a MIRO1 mutant lacking the transmembrane domain failed to restore activity and resembled the Miro1-/- phenotype (Figure 6- Figure supplement 2).

      The Complex I activity in each Miro1 mutant correlated with the degree of MICOS/MIB complex assembly in pulldown assays, implying a functional link between Miro1 and mitochondrial cristae organization.

      Moreover, an in-gel Complex V activity assay was performed to evaluate the enzymatic activity of mitochondrial ATP synthase in a native gel following electrophoresis. To normalize the activity signal, a Blue Native PAGE of the same samples was probed for the ATP5F1 subunit. A modest, yet statistically significant reduction in Complex V activity was observed in Miro1-/- cells (Figure 6- Figure supplement 1).

      (3) I noticed that none of the in vitro findings have been validated in an in vivo model. I believe this represents a significant gap that would be valuable to address. In your animal model, it should not be too complex to analyze mitochondria by electron microscopy to assess cristae morphology. Additionally, supercomplex assembly and complex I activity could be evaluated in tissue homogenates to corroborate the in vitro observations.

      We appreciate the reviewer’s comment. However, our currently available samples have been processed by light microscopy and are therefore not suitable for embedding for light for electron microscopy.

      (4) I find the results presented in Figure S7 somewhat unclear. The authors employ a pharmacological strategy to reduce Miro1 and validate the findings previously obtained with the genetic knockout model. They report increased mitophagy and a reduction in mitochondrial mass. However, in my opinion, these changes alone could significantly impact cellular metabolism. A lower number of mitochondria would naturally result in decreased ATP production and reduced mitochondrial respiration. This, in turn, weakens the proposed direct link between Miro1 deletion and impaired metabolic function or altered electron transport chain (ETC) activity. I believe this section would benefit from additional experiments and a more in-depth discussion.

      We initially conducted experiments using the MIRO1 reducer to explore the translational potential of our findings. These experiments aimed to provide a foundation in vivo studies. However, despite multiple attempts, we were unable to demonstrate a significant effect of MIRO1reducer, delivered via a Pluronic gel, on the mitochondria of the vascular wall. Of note, he role of MIRO1 in mitophagy has been well-established in several studies (for example, PMID: 34152608), which show that genetic deletion of Miro1 delays the translocation of the E3 ubiquitin ligase Parkin onto damaged mitochondria, thereby reducing mitochondrial clearance in fibroblasts and cultured neurons. Furthermore, loss of Miro1 in the hippocampus and cortex increases mitofusin levels with the appearance of hyperfused mitochondria and activation of the integrated stress response. Thus, MIRO1 deletion in genetic models does not result in a substantial reduction of mitochondria but causes hyperfused mitochondria. The rationale for developing the MIRO1 reducer stems from genetic forms of Parkinson’s disease, where Miro1 is retained in PD cells but degraded in healthy cells following mitochondrial depolarization (PMID: 31564441). Thus, the degradation of mutant MIRO1 by the reducer does not phenocopy the effects of genetic MIRO1 depletion. Thus, we believe the data with the reducer demonstrate that MIRO1 can be acutely targeted in vitro, but the mechanism of action (as the reviewer points out, the reduction of mitochondrial mass may lead to decreased ATP levels, potentially reducing cell proliferation) differs from that of chronic genetic deletion. In fact, we observe somewhat increased mitochondrial length in MIRO1-/- cells. We acknowledge that this is complex and have revised the paragraph to clarify the use of the MIRO1 reducer.

      Reviewer #2 (Public review):

      Summary:

      This study identifies the outer mitochondrial GTPase MIRO1 as a central regulator of vascular smooth muscle cell (VSMC) proliferation and neointima formation after carotid injury in vivo and PDGF-stimulation ex vivo. Using smooth muscle-specific knockout male mice, complementary in vitro murine and human VSMC cell models, and analyses of mitochondrial positioning, cristae architecture, and respirometry, the authors provide solid evidence that MIRO1 couples mitochondrial motility with ATP production to meet the energetic demands of the G1/S cell cycle transition. However, a component of the metabolic analyses is suboptimal and would benefit from more robust methodologies. The work is valuable because it links mitochondrial dynamics to vascular remodeling and suggests MIRO1 as a therapeutic target for vasoproliferative diseases, although whether pharmacological targeting of MIRO1 in vivo can effectively reduce neointima after carotid injury has not been explored. This paper will be of interest to those working on VSMCs and mitochondrial biology.

      Strengths:

      The strength of the study lies in its comprehensive approach, assessing the role of MIRO1 in VSMC proliferation in vivo, ex vivo, and importantly in human cells. The subject provides mechanistic links between MIRO1-mediated regulation of mitochondrial mobility and optimal respiratory chain function to cell cycle progression and proliferation. Finally, the findings are potentially clinically relevant given the presence of MIRO1 in human atherosclerotic plaques and the available small molecule MIRO1.

      Weaknesses:

      (1) There is a consistent lack of reporting across figure legends, including group sizes, n numbers, how many independent experiments were performed, or whether the data is mean +/- SD or SEM, etc. This needs to be corrected.

      These data were added in the revised manuscript.

      (2) The in vivo carotid injury experiments are in male mice fed a high-fat diet; this should be explicitly stated in the abstract, as it's unclear if there are any sex- or diet-dependent differences. Is VSMC proliferation/neointima formation different in chow-fed mice after carotid injury?

      This is an important point, and we appreciate the feedback. In this model, the transgene is located on the Y chromosome. As a result, only male mice can be studied. However, in our previous experiments, we have not observed any sex-dependent changes in neointimal formation. Additionally, please note that smooth muscle cell proliferation in neointimal formation is enhanced in models of cholesterol-fed mice on a high-fat diet.

      (3) The main body of the methods section is thin, and it's unclear why the majority of the methods are in the supplemental file. The authors should consider moving these to the main article, especially in an online-only journal.

      We thank the reviewer for this suggestion. We moved the methods to the main manuscript.

      (4) Certain metabolic analyses are suboptimal, including ATP concentration and Complex I activity measurements. The measurement of ATP/ADP and ATP/AMP ratios for energy charge status (luminometer or mass spectrometry), while high-resolution respirometry (Oroboros) to determine mitochondrial complex I activity in permeabilized VSMCs would be more informative.

      ATP/ADP and ATP/AMP ratios were assessed on samples from WT and Miro1-/- VSMCs using an ATP/ADP/AMP Assay Kit (Cat#: A-125) purchased from Biomedical Research Service, University at Buffalo, New York). Miro1-/- samples exhibited reduced ATP levels accompanied by elevated concentrations of ADP and AMP. As a result, both ATP/ADP and ATP/AMP ratios were significantly lower in MIRO1-/- cells compared to WT, indicating impaired cellular energy homeostasis (Figure 5B, C).

      (5) The statement that 'mitochondrial mobility is not required for optimal ATP production' is poorly supported. XF Seahorse analysis should be performed with nocodazole and also following MIRO1 reconstitution +/- EF hands.

      To evaluate the metabolic effects of Nocodazole, we conducted Seahorse metabolic assays on vascular smooth muscle cells with various conditions (VSMCs). We used WT VSMCs, Miro1-/- VSMCs, and Miro1-/- VSMCs that expressed either MIRO1-WT, KK, or ΔTM mutants.Our results demonstrate that Nocodazole exposure did not compromise mitochondrial respiratory activity. However, Miro1-/- VSMCs displayed a trend toward reduced basal and maximal mitochondrial respiration when compared to WT cells. This deficit was only partially corrected by the expression of the MIRO1-KK mutant. In contrast, reintroducing MIRO1-WT through adenoviral delivery fully restored mitochondrial respiration to normal levels (Figure 5- Figure supplement 1).

      (6) The authors should consider moving MIRO1 small molecule data into the main figures. A lot of value would be added to the study if the authors could demonstrate that therapeutic targeting of MIRO1 could prevent neointima formation in vivo.

      We appreciate the reviewer's comment and attempted the suggested in vivo experiments using the commercially available Miro1 reducer. For these experiments, we used a pluronic gel to deliver the reducer to the adventitial area surrounding the carotid artery. Despite numerous attempts to optimize the experimental conditions, we were unable to reliably detect a significant effect of the reducer on mitochondria in the vascular wall.

      Reviewer #3 (Public review):

      Summary:

      This study addresses the role of MIRO1 in vascular smooth muscle cell proliferation, proposing a link between MIRO1 loss and altered growth due to disrupted mitochondrial dynamics and function. While the findings are potentially useful for understanding the importance of mitochondrial positioning and function in this specific cell type within health and disease contexts, the evidence presented appears incomplete, with key bioenergetic and mechanistic claims lacking adequate support.

      Strengths:

      (1)The study focuses on an important regulatory protein, MIRO1, and its role in vascular smooth muscle cell (VSMC) proliferation, a relatively underexplored context.

      (2) It explores the link between smooth muscle cell growth, mitochondrial dynamics, and bioenergetics, which is a potentially significant area for both basic and translational biology.

      (3) The use of both in vivo and in vitro systems provides a potentially useful experimental framework to interrogate MIRO1 function in this context.

      Weaknesses:

      (1) The central claim that MIRO1 loss impairs mitochondrial bioenergetics is not convincingly demonstrated, with only modest changes in respiratory parameters and no direct evidence of functional respiratory chain deficiency.

      (2) The proposed link between MIRO1 and respiratory supercomplex assembly or function is speculative, lacking mechanistic detail and supported by incomplete or inconsistent biochemical data.

      (3) Key mitochondrial assays are either insufficiently controlled or poorly interpreted, undermining the strength of the conclusions regarding oxidative phosphorylation.

      (4) The study does not adequately assess mitochondrial content or biogenesis, which could confound interpretations of changes in respiratory activity.

      (5) Overall, the evidence for a direct impact of MIRO1 on mitochondrial respiratory function in the experimental setting is weak, and the conclusions overreach the data.

      Recommendations for the authors:

      Reviewer #3 (Recommendations for the authors):

      (1)  Throughout the manuscript, the authors incorrectly use "mobility" to describe the active transport of mitochondria. The appropriate term is "mitochondrial motility," which refers to active, motor-driven movement. "Mobility" implies passive diffusion and is not scientifically accurate in this context.

      (2) "Super complex" should be consistently written as "supercomplex," in line with accepted mitochondrial biology terminology.

      We thank the reviewer for this comment and revised the text accordingly.

      (3) A significant limitation of the in vivo model is the mild phenotype observed, which is expected from an inducible knockout system. The authors should clarify whether a constitutive, tissue-specific knockout was considered and, if not, whether embryonic lethality or another limitation prevented its generation.

      This genetic model was originally developed by Dr. Janet Shaw at the University of Utah. In the original publication, Miro1 was constitutively knocked out in neurons. Germline inactivation of Miro1 was achieved by crossing mice harboring the Miro1F allele with a mouse line expressing Cre recombinase under the control of the hypoxanthine-guanine phosphoribosyltransferase (HPRT) promoter. Mating Miro1+/− mice resulted in Miro1−/− animals, which were cyanotic and died shortly after birth. Due to this outcome, we opted to develop an inducible, smooth muscle-specific model. Additionally, we considered testing whether the acute use of an inhibitor or a knockdown system targeting Miro1 could be evaluated as a potential therapeutic approach.

      (4) In Figure 1A and S1A, the authors use Western blotting to validate the knockout in the aorta and IHC in carotid arteries. The choice of different methods does not seem justified, and qPCR data are shown only for the aorta. IHC appears to be suboptimal for assessing MIRO1 levels in vascular tissue due to high autofluorescence, and IHC in Figure S1A is merely qualitative, with no quantification provided.

      We present complementary approaches to validate the deletion of Miro1. For Western blot analysis, we used the aorta because it provides more material for analysis. The autofluorescence observed via immunofluorescence is characteristic of elastin fibers within the media layer, making our results typical for this technique. As shown in Figure 1- Figure supplement 1, our data demonstrate a significant decrease, if not a complete knockout, of the target protein specifically in smooth muscle cells.

      (5) In Figure 1G, the bottom left panel (magnification) shows a lower green signal than the top left panel, suggesting these may have been collected with different signal intensity. This raises concerns about image consistency and representation.

      Top images in Figure 1G are taken at magnification 63x. Bottom images were made at magnification 20x. The intensity is different between the two magnifications, but similar between genotypes.

      (6) In Figure S3, the sampling is uncontrolled: the healthy subject and the patient differ markedly in age. The claim of colocalization is not substantiated with any quantitative analysis.

      As outlined in the Methods section, our heart samples were obtained from LVAD patients or explanted hearts from transplant recipients. Due to the limited availability of such samples, there is indeed a difference in age between the healthy subject and the patient. While we acknowledge this limitation, the scarcity of samples made it challenging to control for age. Additionally, we determined that performing a quantitative analysis of colocalization would not yield robust or meaningful data given the constraints of our sample size and variability. 

      (7) Figure S4A lacks statistical analysis, which is necessary for interpreting the data shown.

      This appears to be a misunderstanding. In this manuscript, we do present statistically significant differences and focus on those that are biologically meaningful. Specifically, we highlight differences between PDGF treatment versus no treatment within the same genotype, as well as differences between the two genotypes under the same treatment condition (control or PDGF treatment). In this particular case, there is only a statistical difference between WT+PDGF and SM-Miro1-/, but since this is not a meaningful comparison, it is not shown. Please note that this approach applies to all figures in the manuscript. Including all comparisons—whether statistically significant or not, and whether biologically meaningful or not—may appear rigorous but in our opinion, ultimately detracts from the main message of this paper.

      (8) The authors state, "given the generally poor proliferation of VSMCs from SM-MIRO1-/- mice, in later experiments we used VSMCs from MIRO1fl/fl mice and infected them with adenovirus expressing cre." This is not convincing, especially since in vivo cre efficiency is generally lower than in vitro. Moreover, the methods indicate that "VSMCs from littermate controls were subjected to the same procedure with empty vector control adenovirus," yet in Figure 2A, the control appears to be MIRO1fl/fl VSMCs transduced with Ad-EV. The logic and consistency of the controls used need clarification.

      For the initial experiments, cells were explanted from SM-MIRO1-/- mice (Figure 2- Figure supplement 1). In these mice, Cre recombination had occurred in vivo, and the cells exhibited very poor growth. In fact, their growth was so limited that we decided not to pursue this experimental approach after three independent experiments.

      For subsequent experiments, cells were explanted from Miro1fl/fl mice and passaged several times, which allowed us to generate the number of cells required for the experiments (Figure 2B). Once sufficient Miro1fl/fl cells were obtained, they were treated with adenovirus expressing Cre, as described in the Methods section. Control cells were treated with an empty vector adenovirus. To clarify, the control cells are Miro1fl/fl cells infected with an empty vector adenovirus, while the MIRO1-/- cells are Miro1fl/fl cells infected with adenovirus expressing Cre. The statement that “littermate controls were used” is incorrect as in fact, Miro1fl/fl cells from the same preparation were either infected with an empty vector adenovirus, or with adenovirus expressing Cre. As mentioned, the knockdown was confirmed by Western blotting.

      (9) Figure 2C shows a growth delay in MIRO1-/- cells. Have the authors performed additional time points to determine when these cells return to G1 and quantify the duration of the lag?

      This is an excellent suggestion. So far, we have not performed this experiment.

      (10) In the 24 h time point of Figure 2C, MIRO1-/- cells appear to be cycling, yet no cyclin E signal is detected. How do the authors explain this inconsistency? Additionally, in Figure 2H, the quantification of cyclin E is unreliable, given that lanes 3 and 4 show no detectable signal.

      We agree with the reviewer—the inconsistency is driven by the exposure of the immunoblot presented. We revisited the data, reviewed the quantification, and performed an additional experiment. We are now presenting an exposure that demonstrates levels of cyclin E (Figure 2G).

      (11) In Figure 3D, the authors present mitochondrial probability map vs. distance from center curves. How was the "center" defined in this analysis? Were radial distances normalized across cells (e.g., to the cell radius or maximum extent)? If not, variation in cell and/or nucleus size or shape could significantly affect the resulting profiles. No statistical analysis is provided for this assessment, which undermines its quantitative value. Furthermore, the rationale behind the use of mito95 values is not clearly explained.

      The center refers to the center of the microchip's Y-shaped pattern, to which each cell is attached. Since all Y-shapes on the chip are identical in size, normalization is not required. The size of the optimal Y-shapes was tested as recommended by CYTOO. For further context, please refer to the papers by the Kittler group.

      Additionally, a graph demonstrating the percentage of mitochondria localized at specific distances can be produced for any given distance. Notably, the further from the center of the chip, the more pronounced the differences become.

      (12) The authors apply a 72 h oligomycin treatment to assess proliferation and a 16 h treatment to measure ATP levels. This discrepancy in experimental design is not justified in the manuscript. The length of treatment directly impacts the interpretation of the data in Figures 4C, 4D, and 4E, and needs to be addressed.

      Thank you for this comment. We have performed additional experiments to align these time points. In the revised manuscript, we now present proliferation and ATP production measured at the same time point (Figure 4A, B for proliferation and ATP levels).

      (13) The manuscript repeatedly suggests that MIRO1 loss causes a defect in mitochondrial ATP production, yet no direct demonstration of a bioenergetic defect is provided. The claim relies on a modest decrease in supercomplex species (of undefined composition) and a mild reduction in complex I activity that does not support a substantial OXPHOS defect. Notably, the respirometry data in Figure 5I do not align with the BN-PAGE results in Figure 6I. There is increasing evidence that respiratory chain supercomplexes do not confer a catalytic advantage. The authors should directly assess the enzymatic activities of all respiratory complexes. Reported complex I activity in MIRO1-/- cells appears rotenone-like (virtually zero, figure 3K) or ~30% residual (Figure 3L), suggesting a near-total loss of functional complex I, which is not reflected in the BN-PAGE. Additionally, complex I activity has not been normalized to a mitochondrial reference, such as citrate synthase.

      Given that we work in primary cells and are limited by the number of cells we can generate, we concentrated on ETC1 and 5 and performed experiments in cells after expression of MIRO1 WT and MIRO1 mutants (Figure 6- Figure supplement 1). Please note that the addition of Rotenone abolishes the slope of NADH consumptions (Figure 6- Figure supplement 2F).

      While the ETC1 activity is measured in Fig. 6K, the blue native gel shown in Figure 6I is performed without substrate and thus, indicative of protein complex abundance rather than complex activity.

      In additional experiments, we normalized the activity to citrate synthase as requested.

      (14) In the methods section, the complex I activity assay is incorrectly described: complex I is a NADH dehydrogenase, so the assay measures NADH oxidation, not NADPH.

      We thank the reviewer for his comment and revised the manuscript accordingly.

      (15) The authors have not assessed mitochondrial mass, which is a critical omission. Differences in mitochondrial biogenesis or content could underlie several observed phenotypes and should be controlled for.

      A qPCR assay was used to assess mitochondrial DNA copy number in WT and Miro1-/- VSMCs. We determined the abundance of COX1 and MT-RNR1 DNA as mitochondrial gene targets and NDUFV DNA as the nuclear reference gene. While the results in Miro1-/- cells were highly variable, no statistically significant reduction of copy numbers was detected (Figure 3- Figure supplement 1B).

      (16) Complex IV signal is missing in Figure 6I. Its omission is not acknowledged or explained.

      Thank you for this comment. We believe this is due to a technical issue. Complex IV can be challenging to detect consistently, as its visibility is highly dependent on sample preparation conditions. In this specific case, we suspect that the buffer used during the isolation process may have influenced the detection of Complex IV.

      (17) Figure 6D does not appear representative of the quantifications shown. C-MYC signal is visibly reduced in the mutant, consistent with the lower levels of interactors such as Sam50 and NDUFA9. Additionally, the SDHA band is aligned at the bottom of the blot box. The list of antibodies used, and their catalog number is missing, or it was not provided to the reviewers. It seems plausible that the authors used a cocktail antibody set (e.g., Abcam ab110412), which includes anti-NDUFA9. This would contradict the claim of reduced complex I and SC levels, as the steady-state levels of NDUFA9 appear unchanged.

      We acknowledge that the expression of the myc-MIRO1 mutant is lower compared to myc-MIRO1 WT or myc-MIRO1 KK. Achieving identical expression levels when overexpressing multiple MIRO1 constructs is challenging. We agree that the lower expression of this mutant contributes to a reduced pull-down. Our quantification shows a reduction in association, although it is not statistically significant.

      A list of the antibodies was provided in the Methods section.

      We would like to clarify that we did not use an antibody cocktail in our experiments.

      (18) The title of Figure 6, "Loss of Miro1 leads to dysregulation of ETC activity under growth conditions," is vague. The term "dysregulation" should be replaced with a more specific mechanistic descriptor-what specific regulatory defect is meant?

      We thank the reviewer for this suggestion and rephrased the title.

      (19) In the results text for Figure 6, the authors state: "These data demonstrate that MIRO1 associates with MIB/MICOS and that this interaction promotes the formation of mitochondrial super complexes and the activity of ETC complex I." This conclusion is speculative and not mechanistically supported by the data presented.

      We appreciate the reviewer's feedback. We have revised the text to clarify the relationship between MIRO1, MIB/MICOS, supercomplex formation, and ETC activity. The updated text now states: "These data demonstrate that MIRO1 associates with MIB/MICOS. Additionally, MIRO1 promotes the formation of mitochondrial supercomplexes and enhances the activity of ETC complex I.”

      (20) In Figure 7A, it is unclear what the 3x siControl/siMiro1 pairs represent-are these different cell lines or technical replicates of the same line? No loading control is shown. If changes in mitochondrial protein abundance are being evaluated, using COX4 as a loading control is inappropriate. The uneven COX4 signal across samples further complicates interpretation

      Please note that we used primary cells, not cell lines. The three siControl/siMiro1 pairs represent independent cell isolations, each transfected with either siControl or. siMIRO1 mRNA. While the possibility of a difference in mitochondrial mass is an interesting question, the primary objective of this experiment is to demonstrate that the technique effectively results in the knockdown of Miro1, which is exclusively localized to mitochondria and not present in the cytosol. As such, we believe that Cox4 serves as a reasonable loading control. Although Miro1 knockdown may lead to a reduction in mitochondrial mass, the focus of this experiment is not to assess mitochondrial mass but to confirm the reduction in Miro1 protein levels on mitochondria. We also performed anti-VDAC immunoblots on the same membranes as alternative loading control (Author response image 1).

      Author response image 1.

      (21) Figure 7G is difficult to interpret. Why did the authors choose to use a sensor-based method instead of the chemiluminescent assay to measure ATP in these samples?

      Both methods were employed to assess ATP levels in human samples. ATP measurements obtained with luminescent assay are provided.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Here, the authors have addressed the recruitment and firing patterns of motor units (MUs) from the long and lateral heads of the triceps in the mouse. They used their newly developed Myomatrix arrays to record from these muscles during treadmill locomotion at different speeds, and they used template-based spike sorting (Kilosort) to extract units. Between MUs from the two heads, the authors observed differences in their firing rates, recruitment probability, phase of activation within the locomotor cycle, and interspike interval patterning. Examining different walking speeds, the authors find increases in both recruitment probability and firing rates as speed increases. The authors also observed differences in the relation between recruitment and the angle of elbow extension between motor units from each head. These differences indicate meaningful variation between motor units within and across motor pools and may reflect the somewhat distinct joint actions of the two heads of triceps.

      Strengths:

      The extraction of MU spike timing for many individual units is an exciting new method that has great promise for exposing the fine detail in muscle activation and its control by the motor system. In particular, the methods developed by the authors for this purpose seem to be the only way to reliably resolve single MUs in the mouse, as the methods used previously in humans and in monkeys (e.g. Marshall et al. Nature Neuroscience, 2022) do not seem readily adaptable for use in rodents.

      The paper provides a number of interesting observations. There are signs of interesting differences in MU activation profiles for individual muscles here, consistent with those shown by Marshall et al. It is also nice to see fine-scale differences in the activation of different muscle heads, which could relate to their partially distinct functions. The mouse offers greater opportunities for understanding the control of these distinct functions, compared to the other organisms in which functional differences between heads have previously been described.

      The Discussion is very thorough, providing a very nice recounting of a great deal of relevant previous results.

      We thank the Reviewer for these comments.

      Weaknesses:

      The findings are limited to one pair of muscle heads. While an important initial finding, the lack of confirmation from analysis of other muscles acting at other joints leaves the general relevance of these findings unclear.

      The Reviewer raises a fair point. While outside the scope of this paper, future studies should certainly address a wider range of muscles to better characterize motor unit firing patterns across different sets of effectors with varying anatomical locations. Still, the importance of results from the triceps long and lateral heads should not be understated as this paper, to our knowledge, is the first to capture the difference in firing patterns of motor units across any set of muscles in the locomoting mouse.

      While differences between muscle heads with somewhat distinct functions are interesting and relevant to joint control, differences between MUs for individual muscles, like those in Marshall et al., are more striking because they cannot be attributed potentially to differences in each head's function. The present manuscript does show some signs of differences for MUs within individual heads: in Figure 2C, we see what looks like two clusters of motor units within the long head in terms of their recruitment probability. However, a statistical basis for the existence of two distinct subpopulations is not provided, and no subsequent analysis is done to explore the potential for differences among MUs for individual heads.

      We agree with the Reviewer and have revised the manuscript to better examine potential subpopulations of units within each muscle as presented in Figure 2C. We performed Hartigan’s dip test on motor units within each muscle to test for multimodal distributions. For both muscles, p > 0.05, so we cannot reject the null hypothesis that the units in each muscle come from a multimodal distribution. However, Hartigan’s test and similar statistical methods have poor statistical power for the small sample sizes (n=17 and 16 for long and lateral heads, respectively) considered here, so the failure to achieve statistical significance might reflect either the absence of a true difference or a lack of statistical resolution.

      Still, the limited sample size warrants further data collection and analysis since the varying properties across motor units may lead to different activation patterns. Given these results, we have edited the text as follows:

      “A subset of units, primarily in the long head, were recruited in under 50% of the total strides and with lower spike counts (Figure 2C). This distribution of recruitment probabilities might reflect a functionally different subpopulation of units. However, the distribution of recruitment probabilities were not found to be significantly multimodal (p>0.05 in both cases, Hartigan’s dip test; Hartigan, 1985). However, Hartigan’s test and similar statistical methods have poor statistical power for the small sample sizes (n=17 and 16 for long and lateral heads, respectively) considered here, so the failure to achieve statistical significance might reflect either the absence of a true difference or a lack of statistical resolution.”

      The statistical foundation for some claims is lacking. In addition, the description of key statistical analysis in the Methods is too brief and very hard to understand. This leaves several claims hard to validate.

      We thank the Reviewer for these comments and have clarified the text related to key statistical analyses throughout the manuscript, as described in our other responses below.

      Reviewer #2 (Public review):

      The present study, led by Thomas and collaborators, aims to describe the firing activity of individual motor units in mice during locomotion. To achieve this, they implanted small arrays of eight electrodes in two heads of the triceps and performed spike sorting using a custom implementation of Kilosort. Simultaneously, they tracked the positions of the shoulder, elbow, and wrist using a single camera and a markerless motion capture algorithm (DeepLabCut). Repeated one-minute recordings were conducted in six mice at five different speeds, ranging from 10 to 27.5 cm·s<sup>-1</sup>.

      From these data, the authors reported that:

      (1) a significant portion of the identified motor units was not consistently recruited across strides,

      (2) motor units identified from the lateral head of the triceps tended to be recruited later than those from the long head,

      (3) the number of spikes per stride and peak firing rates were correlated in both muscles, and

      (4) the probability of motor unit recruitment and firing rates increased with walking speed.

      The authors conclude that these differences can be attributed to the distinct functions of the muscles and the constraints of the task (i.e., speed).

      Strengths:

      The combination of novel electrode arrays to record intramuscular electromyographic signals from a larger muscle volume with an advanced spike sorting pipeline capable of identifying populations of motor units.

      We thank the Reviewer for this comment.

      Weaknesses:

      (1) There is a lack of information on the number of identified motor units per muscle and per animal.

      The Reviewer is correct that this information was not explicitly provided in the prior submission. We have therefore added Table 1 that quantifies the number of motor units per muscle and per animal.

      (2) All identified motor units are pooled in the analyses, whereas per-animal analyses would have been valuable, as motor units within an individual likely receive common synaptic inputs. Such analyses would fully leverage the potential of identifying populations of motor units.

      Please see our answer to the following point, where we address questions (2) and (3) together.

      (3) The current data do not allow for determining which motor units were sampled from each pool. It remains unclear whether the sample is biased toward high-threshold motor units or representative of the full pool.

      We thank the Reviewer for these comments. To clarify how motor unit responses were distributed across animals and muscle targets, we updated or added the following figures:  

      Figure 2C

      Figure 4–figure supplement 1

      Figure 5–figure supplement 2

      Figure 6–figure supplement 2

      These provide a more complete look at the range of activity within each motor pool, suggesting that we do measure from units with different activation thresholds within the same motor pool, rather than this variation being due to cross-animal differences. For example, Figure 2C illustrates that motor units from the same muscle and animal show a wide variety of recruitment probabilities. However, the limited number of motor units recorded from each individual animal does not allow a statistically rigorous test for examining cross-animal differences.

      (4) The behavioural analysis of the animals relies solely on kinematics (2D estimates of elbow angle and stride timing). Without ground reaction forces or shoulder angle data, drawing functional conclusions from the results is challenging.

      The Reviewer is correct that we did not measure muscular force generation or ground reaction forces in the present study. Although outside the scope of this study, future work might employ buckle force transducers as used in larger animals (Biewener et al., 1988; Karabulut et al., 2020) to examine the complex interplay between neural commands, passive biomechanics, and the complex force-generating properties of muscle tissue.

      Major comments:

      (1) Spike sorting

      The conclusions of the study rely on the accuracy and robustness of the spike sorting algorithm during a highly dynamic task. Although the pipeline was presented in a previous publication (Chung et al., 2023, eLife), a proper validation of the algorithm for identifying motor unit spikes is still lacking. This is particularly important in the present study, as the experimental conditions involve significant dynamic changes. Under such conditions, muscle geometry is altered due to variations in both fibre pennation angles and lengths.

      This issue differs from electrode drift, and it is unclear whether the original implementation of Kilosort includes functions to address it. Could the authors provide more details on the various steps of their pipeline, the strategies they employed to ensure consistent tracking of motor unit action potentials despite potential changes in action potential waveforms, and the methods used for manual inspection of the spike sorting algorithm's output?

      This is an excellent point and we agree that the dynamic behavior used in this investigation creates potential new challenges for spike sorting. In our analysis, Kilosort 2.5 provides key advantages in comparing unit waveforms across multiple channels and in detecting overlapping spikes. We modified this version of Kilosort to construct unit waveform templates using only the channels within the same muscle (Chung et al., 2023), as clarified in the revised Methods section (see “Electromyography (EMG)”):

      “A total of 33 units were identified across all animals. Each unit’s isolation was verified by confirming that no more than 2% of inter-spike intervals violated a 1 ms refractory limit. Additionally, we manually reviewed cross-correlograms to ensure that each waveform was only reported as a single motor unit.”

      The Reviewer is correct that our ability to precisely measure a unit’s activity based on its waveform will depend on the relationship between the embedded electrode and the muscle geometry, which alters over the course of the stride. As a follow-up to the original text, we have included new analyses to characterize the waveform activity throughout the experiment and stride (also in Methods):

      “We further validated spike sorting by quantifying the stability of each unit’s waveform across time (Figure 1–figure supplement 1). First, we calculated the median waveform of each unit across every trial to capture long-term stability of motor unit waveforms. Additionally, we calculated the median waveform through the stride binned in 50 ms increments using spiking from a single trial. This second metric captures the stability of our spike sorting during the rapid changes in joint angles that occur during the burst of an individual motor unit. In doing so, we calculated each motor unit’s waveforms from the single channel in which that unit’s amplitude was largest and did not attempt to remove overlapping spikes from other units before measuring the median waveform from the data. We then calculated the correlation between a unit’s waveform over either trials or bins in which at least 30 spikes were present. The high correlation of a unit waveform over time, despite potential changes in the electrodes’ position relative to muscle geometry over the dynamic task, provides additional confidence in both the stability of our EMG recordings and the accuracy of our spike sorting.”

      (2) Yield of the spike sorting pipeline and analyses per animal/muscle

      A total of 33 motor units were identified from two heads of the triceps in six mice (17 from the long head and 16 from the lateral head). However, precise information on the yield per muscle per animal is not provided. This information is crucial to support the novelty of the study, as the authors claim in the introduction that their electrode arrays enable the identification of populations of motor units. Beyond reporting the number of identified motor units, another way to demonstrate the effectiveness of the spike sorting algorithm would be to compare the recorded EMG signals with the residual signal obtained after subtracting the action potentials of the identified motor units, using a signal-to-residual ratio.

      Furthermore, motor units identified from the same muscle and the same animal are likely not independent due to common synaptic inputs. This dependence should be accounted for in the statistical analyses when comparing changes in motor unit properties across speeds and between muscles.

      We thank the Reviewer for this comment. Regarding motor unit yield, as described above the newly-added Table 1 displays the yield from each animal and muscle.

      Regarding spike sorting, while signal-to-residual is often an excellent metric, it is not ideal for our high-resolution EMG signals since isolated single motor units are typically superimposed on a “bulk” background consisting of the low-amplitude waveforms of other motor units. Because these smaller units typically cannot be sorted, it is challenging to estimate the “true” residual after subtracting (only) the largest motor unit, since subtracting each sorted unit’s waveform typically has a very small effect on the RMS of the total EMG signal. To further address concerns regarding spike sorting quality, we added Figure 1–figure supplement 1 that demonstrates motor units’ consistency over the experiment, highlighting that the waveform maintains its shape within each stride despite muscle/limb dynamics and other possible sources of electrical noise or artifact.

      Finally, the Reviewer is correct that individual motor units in the same muscle are very likely to receive common synaptic inputs. These common inputs may reflect in sparse motor units being recruited in overlapping rather than different strides. Indeed, in the following added to the Results, we identified that motor units are recruited with higher probability when additional units are recruited.

      “Probabilistic recruitment is correlated across motor units

      Our results show that the recruitment of individual motor units is probabilistic even within a single speed quartile (Figure 5A-C) and predicts body movements (Figure 6), raising the question of whether the recruitment of individual motor units are correlated or independent. Correlated recruitment might reflect shared input onto the population of motor units innervating the muscle (De Luca, 1985; De Luca & Erim, 1994; Farina et al., 2014). For example, two motor units, each with low recruitment probabilities, may still fire during the same set of strides. To assess the independence of motor unit recruitment across the recorded population, we compared each unit’s empirical recruitment probability across all strides to its conditional recruitment probability during strides in which another motor unit from the same muscle was recruited (Figure 7). Doing this for all motor unit pairs revealed that motor units in both muscles were biased towards greater recruitment when additional units were active (p<0.001, Wilcoxon signed-rank tests for both the lateral and long heads of triceps). This finding suggests that probabilistic recruitment reflects common synaptic inputs that covary together across locomotor strides.”

      (3) Representativeness of the sample of identified motor units

      However, to draw such conclusions, the authors should exclusively compare motor units from the same pool and systematically track violations of the recruitment order. Alternatively, they could demonstrate that the motor units that are intermittently active across strides correspond to the smallest motor units, based on the assumption that these units should always be recruited due to their low activation thresholds.

      One way to estimate the size of motor units identified within the same muscle would be to compare the amplitude of their action potentials, assuming that all motor units are relatively close to the electrodes (given the selectivity of the recordings) and that motoneurons innervating more muscle fibres generate larger motor unit action potentials.

      We thank the Reviewer for this comment. Below, we provide more detailed analyses of the relationships between motor unit spike amplitude and the recruitment probability as well as latency (relative to stride onset) of activation.

      We generated the below figures to illustrate the relationship between the amplitude of motor units and their firing properties. As suspected, units with larger-amplitude waveforms fired with lower probability and produced their first spikes later in the stride. If we were comfortable assuming that larger spike amplitudes mean higher-force units, then this would be consistent with a key prediction of the size principle (i.e. that higher-force units are recruited later). However, we are hesitant to base any conclusions on this assumption or emphasize this point with a main-text figure, since EMG signal amplitude may also vary due to the physical properties of the electrode and distance from muscle fibers. Thus it is possible that a large motor unit may have a smaller waveform amplitude relative to the rest of the motor pool.

      Author response image 1.

      Relation between motor unit amplitude and (A) recruitment probability and (B) mean first spike time within the stride. Colored lines indicate the outcome of linear regression analyses.

      Currently, the data seem to support the idea that motor units that are alternately recruited across strides have recruitment thresholds close to the level of activation or force produced during slow walking. The fact that recruitment probability monotonically increases with speed suggests that the force required to propel the mouse forward exceeds the recruitment threshold of these "large" motor units. This pattern would primarily reflect spatial recruitment following the size principle rather than flexible motor unit control.

      We thank the Reviewer for this comment. We agree with this interpretation, particularly in relation to the references suggested in later comments, and have added the following text to the Discussion to better reflect this argument:

      “To investigate the neuromuscular control of locomotor speed, we quantified speed-dependent changes in both motor unit recruitment and firing rate. We found that the majority of units were recruited more often and with larger firing rates at faster speeds (Figure 5, Figure5–figure supplement 1). This result may reflect speed-dependent differences in the common input received by populations of motor neurons with varying spiking thresholds (Henneman et al., 1965). In the case of mouse locomotion, faster speeds might reflect a larger common input, increasing the recruitment probability as more neurons, particularly those that are larger and generate more force, exceed threshold for action potentials (Farina et al., 2014).”

      (4) Analysis of recruitment and firing rates

      The authors currently report active duration and peak firing rates based on spike trains convolved with a Gaussian kernel. Why not report the peak of the instantaneous firing rates estimated from the inverse of the inter-spike interval? This approach appears to be more aligned with previous studies conducted to describe motor unit behaviour during fast movements (e.g., Desmedt & Godaux, 1977, J Physiol; Van Cutsem et al., 1998, J Physiol; Del Vecchio et al., 2019, J Physiol).

      We thank the Reviewer for this comment. In the revised Discussion (see ‘Firing rates in mouse locomotion compared to other species’) we reference several examples of previous studies that quantified spike patterns based on the instantaneous firing rate. We chose to report the peak of the smoothed firing rate because that quantification includes strides with zero spikes or only one spike, which occur regularly in our dataset (and for which ISI rate measures, which require two spikes to define an instantaneous firing rate, cannot be computed). Regardless, in the revised Figure 4B, we present an analysis that uses inter-spike intervals as suggested, which yielded similar ranges of firing rates as the primary analysis.

      (5) Additional analyses of behaviour

      The authors currently analyse motor unit recruitment in relation to elbow angle. It would be valuable to include a similar analysis using the angular velocity observed during each stride, re broadly, comparing stride-by-stride changes in firing rates with changes in elbow angular velocity would further strengthen the final analyses presented in the results section.

      We thank the Reviewer for this comment. To address this, we have modified Figure 6 and the associated Supplemental Figures, to show relationships in unit activation with both the range of elbow extension and the range of elbow velocity for each stride. These new Supplemental Figures show that the trends shown in main text Figure 6C and 6E (which show data from all speed quartiles on the same axes) are also apparent in both the slower and faster quartiles individually, although single-quartile statistical tests (with smaller sample size than the main analysis) not reach statistical significance in all cases.

      Reviewer #3 (Public review):

      Summary:

      Using the approach of Myomatrix recording, the authors report that:

      (1) Motor units are recruited differently in the two types of muscles.

      (2) Individual units are probabilistically recruited during the locomotion strides, whereas the population bulk EMG has a more reliable representation of the muscle.

      (3) The recruitment of units was proportional to walking speed.

      Strengths:

      The new technique provides a unique data set, and the data analysis is convincing and well-performed.

      We thank the Reviewer for the comment.

      Weaknesses:

      The implications of "probabilistical recruitment" should be explored, addressed, and analyzed further.

      Comments:

      One of the study's main findings (perhaps the main finding) is that the motor units are "probabilistically" recruited. The authors do not define what they mean by probabilistically recruited, nor do they present an alternative scenario to such recruitment or discuss why this would be interesting or surprising. However, on page 4, they do indicate that the recruitment of units from both muscles was only active in a subset of strides, i.e., they are not reliably active in every step.

      If probabilistic means irregular spiking, this is not new. Variability in spiking has been seen numerous times, for instance in human biceps brachii motor units during isometric contractions (Pascoe, Enoka, Exp physiology 2014) and elsewhere. Perhaps the distinction the authors are seeking is between fluctuation-driven and mean-driven spiking of motor units as previously identified in spinal motor networks (see Petersen and Berg, eLife 2016, and Berg, Frontiers 2017). Here, it was shown that a prominent regime of irregular spiking is present during rhythmic motor activity, which also manifests as a positive skewness in the spike count distribution (i.e., log-normal).

      We thank the Reviewer for this comment and have clarified several passages in response. The Reviewer is of course correct that irregular motor unit spiking has been described previously and may reflect motor neurons’ operating in a high-sensitivity (fluctuation-driven) regime. We now cite these papers in the Discussion (see ‘Firing rates in mouse locomotion compared to other species’). Additionally, the revision clarifies that “probabilistically” - as defined in our paper - refers only to the empirical observation that a motor unit spikes during only a subset of strides, either when all locomotor speeds are considered together (Figure 2) or separately (Figure 5A-C):

      “Motor units in both muscles exhibited this pattern of probabilistic recruitment (defined as a unit’s firing on only a fraction of strides), but with differing distributions of firing properties across the long and lateral heads (Figure 2).”

      “Our findings (Figure 4) highlight that even with the relatively high firing rates observed in mice, there are still significant changes in firing rate and recruitment probability across the spikes within bursts (Figure 4B) and across locomotor speeds (Figure 5F). Future studies should more carefully examine how these rapidly changing spiking patterns derive from both the statistics of synaptic inputs and intrinsic properties of motor neurons (Manuel & Heckman, 2011; Petersen & Berg, 2016; Berg, 2017).”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      As mentioned above, there are several issues with the statistics that need to be corrected to properly support the claims made in the paper.

      The authors compare the fractions of MUs that show significant variation across locomotor speeds in their firing rate and recruitment probability. However, it is not statistically founded to compare the results of separate statistical tests based on different kinds of measurements and thus have unconstrained differences in statistical power. The comparison of the fractional changes in firing rates and recruitment across speeds that follow is helpful, though in truth, by contemporary standards, one would like to see error bars on these estimates. These could be generated using bootstrapping.

      The Reviewer is correct, and we have revised the manuscript to better clarify which quantities should or should not be compared, including the following passage (see “Motor unit mechanisms of speed control” in Results):

      “Speed-dependent increases in peak firing rate were therefore also present in our dataset, although in a smaller fraction of motor units (22/33) than changes in recruitment probability (31/33). Furthermore, the mean (± SE) magnitude of speed-dependent increases was smaller for spike rates (mean rate<sub>fast</sub>/rate<sub>slow</sub> of 111% ± 20% across all motor units) than for recruitment probabilities (mean p(recruitment) <sub>fast</sub>/p(recruitment) <sub>slow</sub> of 179% ± 3% across all motor units). While fractional changes in rate and recruitment probability are not readily comparable given their different upper limits, these findings could suggest that while both recruitment and peak rate change across speed quartiles, increased recruitment probability may play a larger role in driving changes in locomotor speed.”

      The description in the Methods of the tests for variation in firing rates and recruitment probability across speeds are extremely hard to understand - after reading many times, it is still not clear what was done, or why the method used was chosen. In the main text, the authors quote p-values and then state "bootstrap confidence intervals," which is not a statistical test that yields a p-value. While there are mathematical relationships between confidence intervals and statistical tests such that a one-to-one correspondence between them can exist, the descriptions provided fall short of specifying how they are related in the present instance. For this reason, and those described in what follows, it is not clear what the p-values represent.

      Next, the authors refer to fitting a model ("a Poisson distribution") to the data to estimate firing rate and recruitment probability, that the model results agree with their actual data, and that they then bootstrapped from the model estimates to get confidence intervals and compute p-values. Why do this? Why not just do something much simpler, like use the actual spike counts, and resample from those? I understand that it is hard to distinguish between no recruitment and just no spikes given some low Poisson firing rate, but how does that challenge the ability to test if the firing rates or the number of spiking MUs changes significantly across speeds? I can come up with some reasons why I think the authors might have decided to do this, but reasoning like this really should be made explicit.

      In addition, the authors would provide an unambiguous description of the model, perhaps using an equation and a description of how it was fit. For the bootstrapping, a clear description of how the resampling was done should be included. The focus on peak firing rate instead of mean (or median) firing rate should also be justified. Since peaks are noisier, I would expect the statistical power to be lower compared to using the mean or median.

      We thank the Reviewer for the comments and have revised and expanded our discussion of the statistical tests employed. We expanded and clarified our description of these techniques in the updated Methods section:

      “Joint model of rate and recruitment

      We modeled the recruitment probability and firing rate based on empirical data to best characterize firing statistics within the stride. Particularly, this allowed for multiple solutions to explain why a motor unit would not spike within a stride. From the empirical data alone, strides with zero spikes would have been assumed to have no recruitment of a unit. However, to create a model of motor unit activity that includes both recruitment and rate, it must be possible that a recruited unit can have a firing rate of zero. To quantify the firing statistics that best represent all spiking and non-spiking patterns, we modeled recruitment probability and peak firing rate along the following piecewise function:

      where y denotes the observed peak firing rate on a given stride (determined by convolving motor unit spike times with a Gaussian kernel as described above), p denotes the probability of recruitment, and λ denotes the expected peak firing rate from a Poisson distribution of outcomes. Thus, an inactive unit on a given stride may be the result of either non-recruitment or recruitment with a stochastically zero firing rate. The above equations were fit by minimizing the negative log-likelihood of the parameters given the data.

      “Permutation test for joint model of rate and recruitment and type 2 regression slopes

      To quantify differences in firing patterns across walking speeds, we subdivided each mouse’s total set of strides into speed quartiles and calculated rate (𝜆, Eq. 1 and 2, Fig. 5A-C) and recruitment probability terms (p, Eq. 1 and 2, Fig. 5D-F) for each unit in each speed quartile. Here we calculated the difference in both the rate and recruitment terms across the fastest and slowest speed quartiles (p<sub>fast</sub>-p<sub>slow</sub> and 𝜆<sub>fast</sub>-𝜆<sub>slow</sub>). To test whether these model parameters were significantly different depending on locomotor speed, we developed a null model combining strides from both the fastest and slowest speed quartiles. After pooling strides from both quartiles, we randomly distributed the pooled set of strides into two groups with sample sizes equal to the original slow and fast quartiles. We then calculated the null model parameters for each new group and found the difference between like terms. To estimate the distribution of possible differences, we bootstrapped this result using 1000 random redistributions of the pooled set of strides. Following the permutation test, the 95% confidence interval of this final distribution reflects the null hypothesis of no difference between groups. Thus, the null hypothesis can be rejected if the true difference in rate or recruitment terms exceeds this confidence interval.

      We followed a similar procedure to quantify cross-muscle differences in the relationship between firing parameters. For each muscle, we estimated the slope across firing parameters for each motor unit using type 2 regression. In this case, the true difference was the difference in slopes between muscles. To test the null hypothesis that there was no difference in slopes, the null model reflected the pooled set of units from both muscles. Again, slopes were calculated for 1000 random resamplings of this pooled data to estimate the 95% confidence interval.”

      The argument for delayed activation of the lateral head is interesting, but I am not comfortable saying the nervous system creates a delay just based on observations of the mean time of the first spike, given the potential for differential variability in spike timing across muscles and MUs. One way to make a strong case for a delay would be to show aggregate PSTHs for all the spikes from all the MUs for each of the two heads. That would distinguish between a true delay and more gradual or variable activation between the heads.

      This is a good point and we agree that the claim made about the nervous system is too strong given the results. Even with Author response image 2 below that the Reviewer suggested, there is still not enough evidence to isolate the role of the nervous system in the muscles’ activation.

      Author response image 2.

      Aggregate peristimulus time histogram (PSTH) for all motor unit spike times in the long head (top) and lateral head (bottom) within the stride.

      In the ideal case, we would have more simultaneous recordings from both muscles to make a more direct claim on the delay. Still, within the current scope of the paper, to correct this and better describe the difference in timing of muscle activity, we edited the text to the following:

      “These findings demonstrate that despite the synergistic (extensor) function of the long and lateral heads of the triceps at the elbow, the motor pool for the long head becomes active roughly 100 ms before the motor pool supplying the lateral head during locomotion (Figure 3C).”

      The results from Marshall et al. 2022 suggest that the recruitment of some MUs is not just related to muscle force, but also the frequency of force variation - some of their MUs appear to be recruited only at certain frequencies. Figure 5C could have shown signs of this, but it does not appear to. We do not really know the force or its frequency of variation in the measurements here. I wonder whether there is additional analysis that could address whether frequency-dependent recruitment is present. It may not be addressable with the current data set, but this could be a fruitful direction to explore in the future with MU recordings from mice.

      We agree that this would be a fruitful direction to explore, however the Reviewer is correct that this is not easily addressable with the dataset. As the Reviewer points out, stride frequency increases with increased speed, potentially offering the opportunity to examine how motor unit activity varies with the frequency, phase, and amplitude of locomotor movements. However, given our lack of force data (either joint torques or ground reaction forces), dissociating the frequency/phase/amplitude of skeletal kinematics from the frequency/phase/amplitude of muscle force. Marshall et al. (2022) mitigated these issues by using an isometric force-production task (Marshall et al., 2022). Therefore, while we agree that it would be a major contribution to extend such investigations to whole-body movements like locomotion, given the complexities described above we believe this is a project for the future, and beyond the scope of the present study.

      Minor:

      Page 5: "Units often displayed no recruitment in a greater proportion of strides than for any particular spike count when recruited (Figures 2A, B)," - I had to read this several times to understand it. I suggest rephrasing for clarity.

      We have changed the text to read:

      “Units demonstrated a variety of firing patterns, with some units producing 0 spikes more frequently than any non-zero spike count (Figure 2A, B),...”

      Figure 3 legend: "Mean phase ({plus minus} SE) of motor unit burst duration across all strides.": It is unclear what this means - durations are not usually described as having a phase. Do we mean the onset phase?

      We have changed the text to read:

      “Mean phase ± SE of motor unit burst activity within each stride”

      Page 9: "suggesting that the recruitment of individual motor units in the lateral and long heads might have significant (and opposite) effects on elbow angle in strides of similar speed (see Discussion)." I wouldn't say "opposite" here - that makes it sound like the authors are calling the long head a flexor. The authors should rephrase or clarify the sense in which they are opposite.

      This is a fair point and we agree we should not describe the muscles as ‘opposite’ when both muscles are extensors. We have removed the phrase ‘and opposite’ from the text.

      Page 11: "in these two muscles across in other quadrupedal species" - typo.

      We have corrected this error.

      Page 16: This reviewer cannot decipher after repeated attempts what the first two sentences of the last paragraph mean. - “Future studies might also use perturbations of muscle activity to dissociate the causal properties of each motor unit’s activity from the complex correlation structure of locomotion. Despite the strong correlations observed between motor unit recruitment and limb kinematics (Fig. 6, Supplemental Fig. 3), these results might reflect covariations of both factors with locomotor speed rather than the causal properties of the recorded motor unit.”

      For better clarity, we have changed the text to read:

      “Although strong correlations were observed between motor unit recruitment and limb kinematics during locomotion (Figure 6, Figure 6–figure supplement 1), it remains unclear whether such correlations actually reflect the causal contributions that those units make to limb movement. To resolve this ambiguity, future studies could use electrical or optical perturbations of muscle contraction levels (Kim et al., 2024; Lu et al., 2024; Srivastava et al., 2015, 2017) to test directly how motor unit firing patterns shape locomotor movements. The short-latency effects of patterned motor unit stimulation (Srivastava et al., 2017) could then reveal the sensitivity of behavior to changes in muscle spiking and the extent to which the same behaviors can be performed with many different motor commands.”

      Reviewer #2 (Recommendations for the authors):

      Minor comments:

      Introduction:

      (1) "Although studies in primates, cats, and zebrafish have shown that both the number of active motor units and motor unit firing rates increase at faster locomotor speeds (Grimby, 1984; Hoffer et al., 1981, 1987; Marshall et al., 2022; Menelaou & McLean, 2012)." I would remove Marshall et al. (2022) as their monkeys performed pulling tasks with the upper limb. You can alternatively remove locomotor from the sentence and replace it with contraction speed.

      Thank you for the comment. While we intended to reference this specific paper to highlight the rhythmic activity in muscles, we agree that this deviates from ‘locomotion’ as it is referenced in the other cited papers which study body movement. We have followed the Reviewer’s suggestion to remove the citation to Marshall et al.

      (2) "The capability and need for faster force generation during dynamic behavior could implicate motor unit recruitment as a primary mechanism for modulating force output in mice."

      The authors could add citations to this sentence, of works that showed that recruitment speed is the main determinant of the rate of force development (see for example Dideriksen et al. (2020) J Neurophysiol; J. L. Dideriksen, A. Del Vecchio, D. Farina, Neural and muscular determinants of maximal rate of force development. J Neurophysiol 123, 149-157 (2020)).

      Thank you for pointing out this important reference. We have included this as a citation as recommended.

      Results:

      (3) "Electrode arrays (32-electrode Myomatrix array model RF-4x8-BHS-5) were implanted in the triceps brachii (note that Figure 1D shows the EMG signal from only one of the 16 bipolar recording channels), and the resulting data were used to identify the spike times of individual motor units (Figure 1E) as described previously (Chung et al., 2023)."

      This sentence can be misleading for the reader as the array used by the researchers has 4 threads of 8 electrodes. Would it be possible to specify the number of electrodes implanted per head of interest? I assume 8 per head in most mice (or 4 bipolar channels), even if that's not specifically written in the manuscript.

      Thank you for the suggestion. As described above, we have added Table 1, which includes all array locations, and we edited the statement referenced in the comment as follows:

      “Electrode arrays (32-electrode Myomatrix array model RF-4x8-BHS-5) were implanted in forelimb muscles (note that Figure 1D shows the EMG signal from only one of the 16 bipolar recording channels), and the resulting data were used to identify the spike times of individual motor units in the triceps brachii long and lateral heads (Table 1, Figure 1E) as described previously (Chung et al., 2023).“

      (4) "These findings demonstrate that despite the overlapping biomechanical functions of the long and lateral heads of the triceps, the nervous system creates a consistent, approximately 100 ms delay (Figure 3C) between the activation of the two muscles' motor neuron pools. This timing difference suggests distinct patterns of synaptic input onto motor neurons innervating the lateral and long heads."

      Both muscles don't have fully overlapping biomechanical functions, as one of them also acts on the shoulder joint. Please be more specific in this sentence, saying that both muscles are synergistic at the elbow level rather than "have overlapping biomechanical functions".

      We agree with the above reasoning and that our manuscript should be clearer on this point. We edited the above text in accordance with the Reviewer suggestion as follows:

      "These findings demonstrate that despite the synergistic (extensor) function of the long and lateral heads of the triceps at the elbow, …”  

      (5) "Together with the differences in burst timing shown in Figure 3B, these results again suggest that the motor pools for the lateral and long heads of the triceps receive distinct patterns of synaptic input, although differences in the intrinsic physiological properties of motor neurons innervating the two muscles might also play an important role."

      It is difficult to draw such an affirmative conclusion on the synaptic inputs from the data presented by the authors. The differences in firing rates may solely arise from other factors than distinct synaptic inputs, such as the different intrinsic properties of the motoneurons or the reception of distinct neuromodulatory inputs.

      To better explain our findings, we adjusted the above text in the Results (see “Motor unit firing patterns in the long and lateral heads of the triceps”):

      “Together with the differences in burst timing shown in Figure 3B, these results again suggest that the motor pools for the lateral and long heads of the triceps receive distinct patterns of synaptic input, although differences in the intrinsic physiological properties of motor neurons innervating the two muscles might also play an important role.”

      We also included the following distinction in the Discussion (see “Differences in motor unit activity patterns across two elbow extensors”) to address the other plausible mechanisms mentioned.

      “The large differences in burst timing and spike patterning across the muscle heads suggest that the motor pools for each muscle receive distinct inputs. However, differences in the intrinsic physiological properties of motor units and neuromodulatory inputs across motor pools might also make substantial contributions to the structure of motor unit spike patterns (Martínez-Silva et al., 2018; Miles & Sillar, 2011).”

      (6) "We next examined whether the probabilistic recruitment of individual motor units in the triceps and elbow extensor muscle predicted stride-by-stride variations in elbow angle kinematics."

      I'm not sure that the wording is appropriate here. The analysis does not predict elbow angle variations from parameters extracted from the spiking activity. It rather compares the average elbow angle between two conditions (motor unit active or not active).

      We thank the Reviewer for this comment and agree that the wording could be improved here to better reflect our analysis. To lower the strength of our claim, we replaced usage of the word ‘predict’ with ‘correlates’ in the above text and throughout the paper when discussing this result.

      Methods:

      (7) "Using the four threads on the customizable Myomatrix array (RF-4x8-BHS-5), we implanted a combination of muscles in each mouse, sometimes using multiple threads within the same muscle. [...] Some mice also had threads simultaneously implanted in their ipsilateral or contralateral biceps brachii although no data from the biceps is presented in this study."

      A precise description of the localisation of the array (muscles and the number of arrays per muscle) for each animal would be appreciated.

      (8) "A total of 33 units were identified and manually verified across all animals." A precise description of the number of motor units concurrently identified per muscle and per animal would be appreciated. Moreover, please add details on the manual inspection. Does it involve the manual selection of missing spikes? What are the criteria for considering an identified motor unit as valid?

      As discussed earlier, we added Table 1 to the main text to provide the details mentioned in the above comments.

      Regarding spike sorting, given the very large number of spikes recorded, we did not rely on manual adjusting mislabeled spikes. Instead, as described in the revised Methods section, we verified unit isolation by ensuring units had >98% of spikes outside of 1ms of each other. Moreover, as described above we have added new analyses (Figure 1–figure supplement 1) confirming the stability of motor unit waveforms across both the duration of individual recording sessions (roughly 30 minutes) and across the rapid changes in limb position within individual stride cycles (roughly 250 msec).

      Reviewer #3 (Recommendations for the authors):

      Figure 2 (and supplement) show spike count distributions with strong positive skewness, which is in accordance with the prediction of a fluctuation-driven regime. I suggest plotting these on a logarithmic x-axis (in addition to the linear axis), which should reveal a bell-shaped distribution, maybe even Gaussian, in a majority of the units.

      We thank the Reviewer for the suggestion. We present the requested analysis below, which shows bell-shaped distributions for some (but not all) distributions. However, we believe that investigating why some replotted distributions are Gaussian and others are not falls beyond the scope of this paper, and likely requires a larger dataset than the one we were able to obtain.

      Author response image 3.

      Spike count distributions for each motor unit on a logarithmic x-axis.

      Why not more data? I tried to get an overview of how much data was collected.

      Supplemental Figure 1 has all the isolated units, which amounts to 38 (are the colors the two muscle types?). Given there are 16 leads in each myomatrix, in two muscles, of six mice, this seems like a low yield. Could the authors comment on the reasons for this low yield?

      Regarding motor unit yield, even with multiple electrodes per muscle and a robust sorting algorithm, we often isolated only a few units per muscle. This yield likely reflects two factors. First, because of the highly dynamic nature of locomotion and high levels of muscle contraction, isolating individual spikes reliably across different locomotor speeds is inherently challenging, regardless of the algorithm being employed. Second, because the results of spike-train analyses can be highly sensitive to sorting errors, we have only included the motor units that we can sort with the highest possible confidence across thousands of strides.

      Minor:

      Figure captions especially Figure 6: The text is excessively long. Can the text be shortened?

      We thank the Reviewer for this comment. Generally, we seek to include a description of the methods and results within the figure captions, but we concede that we can condense the information in some cases. In a number of cases, we have moved some of the descriptive text from the caption to the Methods section.

      References

      Berg, R. W. (2017). Neuronal Population Activity in Spinal Motor Circuits: Greater Than the Sum of Its Parts. Frontiers in Neural Circuits, 11. https://doi.org/10.3389/fncir.2017.00103

      Biewener, A. A., Blickhan, R., Perry, A. K., Heglund, N. C., & Taylor, C. R. (1988). Muscle Forces During Locomotion in Kangaroo Rats: Force Platform and Tendon Buckle Measurements Compared. Journal of Experimental Biology, 137(1), 191–205. https://doi.org/10.1242/jeb.137.1.191

      Chung, B., Zia, M., Thomas, K. A., Michaels, J. A., Jacob, A., Pack, A., Williams, M. J., Nagapudi, K., Teng, L. H., Arrambide, E., Ouellette, L., Oey, N., Gibbs, R., Anschutz, P., Lu, J., Wu, Y., Kashefi, M., Oya, T., Kersten, R., … Sober, S. J. (2023). Myomatrix arrays for high-definition muscle recording. eLife, 12, RP88551. https://doi.org/10.7554/eLife.88551

      De Luca, C. J. (1985). Control properties of motor units. Journal of Experimental Biology, 115(1), 125–136. https://doi.org/10.1242/jeb.115.1.125

      De Luca, C. J., & Erim, Z. (1994). Common drive of motor units in regulation of muscle force. Trends in Neurosciences, 17(7), 299–305. https://doi.org/10.1016/0166-2236(94)90064-7

      Farina, D., Negro, F., & Dideriksen, J. L. (2014). The effective neural drive to muscles is the common synaptic input to motor neurons. The Journal of Physiology, 592(16), 3427–3441. https://doi.org/10.1113/jphysiol.2014.273581

      Hartigan, P. M. (1985). Algorithm AS 217: Computation of the Dip Statistic to Test for Unimodality. Applied Statistics, 34(3), 320. https://doi.org/10.2307/2347485

      Henneman, E., Somjen, G., & Carpenter, D. O. (1965). FUNCTIONAL SIGNIFICANCE OF CELL SIZE IN SPINAL MOTONEURONS. Journal of Neurophysiology, 28(3), 560–580. https://doi.org/10.1152/jn.1965.28.3.560

      Karabulut, D., Dogru, S. C., Lin, Y.-C., Pandy, M. G., Herzog, W., & Arslan, Y. Z. (2020). Direct Validation of Model-Predicted Muscle Forces in the Cat Hindlimb During Locomotion. Journal of Biomechanical Engineering, 142(5), 051014. https://doi.org/10.1115/1.4045660

      Kim, J. J., Wyche, I. S., Olson, W., Lu, J., Bakir, M. S., Sober, S. J., & O’Connor, D. H. (2024). Myo-optogenetics: Optogenetic stimulation and electrical recording in skeletal muscles. https://doi.org/10.1101/2024.06.21.600113

      Lu, J., Zia, M., Baig, D. A., Yan, G., Kim, J. J., Nagapudi, K., Anschutz, P., Oh, S., O’Connor, D., Sober, S. J., & Bakir, M. S. (2024). Opto-Myomatrix: μLED integrated microelectrode arrays for optogenetic activation and electrical recording in muscle tissue. https://doi.org/10.1101/2024.07.01.601601

      Manuel, M., & Heckman, C. J. (2011). Adult mouse motor units develop almost all of their force in the subprimary range: A new all-or-none strategy for force recruitment? Journal of Neuroscience, 31(42), 15188–15194. https://doi.org/10.1523/JNEUROSCI.2893-11.2011

      Marshall, N. J., Glaser, J. I., Trautmann, E. M., Amematsro, E. A., Perkins, S. M., Shadlen, M. N., Abbott, L. F., Cunningham, J. P., & Churchland, M. M. (2022). Flexible neural control of motor units. Nature Neuroscience, 25(11), 1492–1504. https://doi.org/10.1038/s41593-022-01165-8

      Martínez-Silva, M. de L., Imhoff-Manuel, R. D., Sharma, A., Heckman, C. J., Shneider, N. A., Roselli, F., Zytnicki, D., & Manuel, M. (2018). Hypoexcitability precedes denervation in the large fast-contracting motor units in two unrelated mouse models of ALS. eLife, 7(2007), 1–26. https://doi.org/10.7554/eLife.30955

      Miles, G. B., & Sillar, K. T. (2011). Neuromodulation of Vertebrate Locomotor Control Networks. Physiology, 26(6), 393–411. https://doi.org/10.1152/physiol.00013.2011

      Petersen, P. C., & Berg, R. W. (2016). Lognormal firing rate distribution reveals prominent fluctuation–driven regime in spinal motor networks. eLife, 5. https://doi.org/10.7554/elife.18805

      Srivastava, K. H., Elemans, C. P. H., & Sober, S. J. (2015). Multifunctional and Context-Dependent Control of Vocal Acoustics by Individual Muscles. The Journal of Neuroscience, 35(42), 14183–14194. https://doi.org/10.1523/JNEUROSCI.3610-14.2015

      Srivastava, K. H., Holmes, C. M., Vellema, M., Pack, A. R., Elemans, C. P. H., Nemenman, I., & Sober, S. J. (2017). Motor control by precisely timed spike patterns. Proceedings of the National Academy of Sciences of the United States of America, 114(5), 1171–1176. https://doi.org/10.1073/pnas.1611734114

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Mazar & Yovel 2025 dissect the inverse problem of how echolocators in groups manage to navigate their surroundings despite intense jamming using computational simulations.

      The authors show that despite the 'noisy' sensory environments that echolocating groups present, agents can still access some amount of echo-related information and use it to navigate their local environment. It is known that echolocating bats have strong small and large-scale spatial memory that plays an important role for individuals. The results from this paper also point to the potential importance of an even lower-level, short-term role of memory in the form of echo 'integration' across multiple calls, despite the unpredictability of echo detection in groups. The paper generates a useful basis to think about the mechanisms in echolocating groups for experimental investigations too.

      Strengths:

      The paper builds on biologically well-motivated and parametrised 2D acoustics and sensory simulation setup to investigate the various key parameters of interest

      The 'null-model' of echolocators not being able to tell apart objects & conspecifics while echolocating still shows agents succesfully emerge from groups - even though the probability of emergence drops severely in comparison to cognitively more 'capable' agents. This is nonetheless an important result showing the direction-of-arrival of a sound itself is the 'minimum' set of ingredients needed for echolocators navigating their environment.

      The results generate an important basis in unraveling how agents may navigate in sensorially noisy environments with a lot of irrelevant and very few relevant cues.

      The 2D simulation framework is simple and computationally tractable enough to perform multiple runs to investigate many variables - while also remaining true to the aim of the investigation.

      Weaknesses:

      Authors have not yet provided convincing justification for the use of different echolocation phases during emergence and in cave behaviour. In the previous modelling paper cited for the details - here the bat-agents are performing a foraging task, and so the switch in echolocation phases is understandable. While flying with conspecifics, the lab's previous paper has shown what they call a 'clutter response' - but this is not necessarily the same as going into a 'buzz'-type call behaviour. As pointed out by another reviewer - the results of the simulations may hinge on the fact that bats are showing this echolocation phase-switching, and thus improving their echo-detection. This is not necessarily a major flaw - but something for readers to consider in light of the sparse experimental evidence at hand currently.

      The use of echolocation phases—defined as the sequential search, approach, and buzz call patterns—has been documented not only during foraging but also in tasks such as landing, obstacle avoidance, clutter navigation, and drinking. Bat call structure has been shown to vary systematically with object proximity, not exclusively in response to prey. During obstacle avoidance, phase transitions were observed, with approach calls emitted in grouped sequences and with reduced durations (Gustafson & Schnitzler, 1979; Schnitzler et al., 1987). In landing contexts, bats have been reported to emit short-duration calls and decrease inter-pulse intervals—buzz-like patterns also observed during prey capture— suggesting shared acoustic strategies across behaviors (Hagino et al., 2007; Hiryu et al., 2008; Melcón et al., 2007, 2009). Comparable patterns have been reported during drinking maneuvers, where “drinking buzzes” have been proposed to guide a precise approach to the water surface, analogous to landing buzzes (Griffiths, 2013; Russo et al., 2016). In response to environmental complexity, bats were found to shorten calls and increase repetition rates when navigating cluttered spaces compared to open ones (Falk et al., 2014; Kalko & Schnitzler, 1993).

      Moreover, field recordings from our study of Rhinopoma microphyllum (Goldshtein et al., 2025) revealed shortened call durations and inter-pulse intervals during dense group flight outside the cave during emergence—patterns consistent with terminal-approach phase that is typical when coming very close to an object (another bat in this case). The Author response image 1 shows an approach sequence recorded from a tagged bat approximately 20 meters from the cave entrance, with self-generated echolocation calls marked. The inter-pulse-interval of ca. 20 ms is used by these bats when a reflective object (another bat in this case) is nearby. 

      Author response image 1.

      These results provide direct evidence that bats actively employ approach-phase echolocation during swarming likely to avoid collision with other bats. This supports the view that echolocation phase transitions are a general proximity-based sensing strategy, adapted across a variety of behavioral scenarios—not limited to hunting alone. 

      In our simulations, bats predominantly emitted calls in the approach phase, with only rare occurrences of buzz-phase calls.

      See lines 355-363 in the revised manuscript.

      The decision to model direction-of-arrival with such high angular resolution (1-2 degrees) is not entirely justifiable - and the authors may wish to do simulation runs with lower angular resolution. Past experimental paradigms haven't really separated out target-strength as a confounding factor for angular resolution (e.g. see the cited Simmons et al. 1983 paper). Moreover, to this reviewer's reading of the cited paper - it is not entirely clear how this experiment provides source-data to support the DoA-SNR parametrisation in this manuscript. The cited paper has two array-configurations, both of which are measured to have similar received levels upon ensonification. A relationship between angular resolution and signal-to-noise ratio is understandable perhaps - and one can formulate such a relationship, but here the reviewer asks that the origin/justification be made clear. On an independent line, also see the recent contrasting results of Geberl, Kugler, Wiegrebe 2019 (Curr. Biol.) - who suggest even poorer angular resolution in echolocation.

      We thank the reviewer for raising this important point. The acuity of 1.5–3° in horizontal direction-of-arrival (DoA) estimation is based on the classical work of Simmons et al. with Eptesicus fuscus (Simmons et al., 1983). Similar precision was later supported by Erwin et al. (Erwin et al., 2001), who modeled azimuth estimation from measured interaural intensity differences (IIDs), reporting an average error of 0.2° with a standard deviation of ~2.2°, consistent with the behavioral data found by Simmons. The decline in acuity with increasing arrival angle has also been demonstrated in behavioral and physiological studies of binaural IID processing (Erwin et al., 2001; Fay, 1995; Razak, 2012; Wohlgemuth et al., 2016). The error model itself was first introduced in our earlier work (Mazar & Yovel, 2020).

      Importantly, Geberl et al. (Geberl et al., 2019) examined the resolution of weak targets masked by nearby strong flankers  and found poor spatial discrimination of ~45 degrees; however, they were studying a detection problem, rather than the horizontal acuity of azimuth estimation. Indeed, our model assumes there is no spatial discrimination at all.

      Overall, while our DoA–SNR parametrization can certainly be critiqued and alternative parameterizations could be tested in future work, we believe it reflects a reasonable and empirically supported assumption. 

      Reviewer #2 (Public review):

      This manuscript describes a detailed model for bats flying together through a fixed geometry. The model considers elements which are faithful to both bat biosonar production and reception and the acoustics governing how sound moves in air and interacts with obstacles. The model also incorporates behavioral patterns observed in bats, like one-dimensional feature following and temporal integration of cognitive maps. From a simulation study of the model and comparison of the results with the literature, the authors gain insight into how often bats may experience destructive interference of their acoustic signals and those of their peers, and how much such interference may actually negatively effect the groups' ability to navigate effectively. The authors use generalized linear models to test the significance of the effects they observe.

      The work relies on a thoughtful and detailed model which faithfully incorporates salient features, such as acoustic elements like the filter for a biological receiver and temporal aggregation as a kind of memory in the system. At the same time, the authors abstract features that are complicating without being expected to give additional insights, as can be seen in the choice of a two-dimensional rather than three-dimensional system. I thought that the level of abstraction in the model was perfect, enough to demonstrate their results without needless details. The results are compelling and interesting, and the authors do a great job discussing them in the context of the biological literature.

      With respect to the first version of the manuscript, the authors have remedied all my outstanding questions or concerns in the current version. The new supplementary figure 5 is especially helpful in understanding the geometry.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Data Availability: This reviewer lauds the authors for switching from a private commercial folder requiring login to one that does not. At the cost of being overtly pedantic - the Github repository is not a long-term archival resource. The ideal solution is to upload the code in an academic repository (Zenodo, OSF, etc.) to periodically create a 'static snapshot' of code for archival, while also hosting a 'live' version on Github.

      We have uploaded to Zenodo repository, and updated the link in the paper:

      How bats exit a crowded colony when relying on echolocation only - a modeling approach

      In one of the rebuttals to Reviewer #3- the authors have cited a wrong paper (Beleyur & Goerlitz 2019) - while discussing broad bandwidth calls improving detection - and may wish to correct this if possible on record.

      We have removed the incorrect citation from the revised version of the manuscript.

      Specific comments on the 2nd manuscript:

      Figure 5: Table 1 says 1, 2,5,10,20,40,100 bats were simulated (line 138-139) but the conclusion (line 398) says '1 to 100 bats' per 3msq. However, the X-axis only stops at 40 and says 'number of bats', while the legend says bats/3msq....what is actually being plotted? Moreover, in the entire paper there is a constant back-and-forth between density and # of bats - perhaps it is explained beforehand, but it is a bit unsettling - and more can be done to clarify these two conventions.

      While most parameters were tested across the full range of 1 to 100 bats per 3 m², a subset of conditions—including misidentification, multi-call clustering, wall target strength, and conspecific target strength—were simulated only up to 40 bats due to significantly longer run-times. This is now clarified in both the main text and the Table 1 caption.

      In our simulations, the primary parameter was the number of bats placed within a 3 m² starting area, which directly determined the initial density (bats per 3 m²). Throughout the manuscript, we use “number of bats” to refer to the simulation input, while “density” denotes the equivalent ecological measure. Figure 5 and related captions have been revised accordingly to note these conventions and to indicate when results are shown only up to 40 bats (see lines 120–122, 314-317 in the revised text).

      Table 1: This was made considerably difficult to read given the visual clutter - and I hope I've understood these changes correctly.

      What is in the square brackets of the effect-size (e.g. first row with values 'Exit prob. (%)' says -0.37/bat [63:100] ? What does this 63:100 refer to?

      What is the 'process flag'

      Values in square brackets indicate the minimum and maximum values of the metric across the tested range (e.g., [63:100] shows the range of exit probabilities observed across different bat densities).

      The term “process flag” has been replaced with “with and without multi-call clustering” for clarity

      Both the table layout and caption have been revised to reduce visual clutter and to make these conventions clearer to the reader. 

      Lines 562-3: "In our study, due to the dense cave environment, the bats are found to operate in the approach phase nearly all of the time, which is consistent with natural cave emergence behavior" - bats are 'found to' implies there is some experimental data or it is an emergent property. See above for the point questioing the implementation of multiple echolocation phases in the model, but also - here the bat-agents are allowed to show different phases and thus they do so -- it is a constraint of the implementation and not a result per se given the size of the cave and the number of bats involved...

      We removed the sentence from the Methods section, since it could be misinterpreted as an experimental finding rather than a model outcome. Instead, we now discuss this in the Discussion, clarifying that the predominance of the approach phase arises from the cluttered cave environment in our simulations, which is consistent with natural emergence behavior (see lines 355-363). In this context, the use of echolocation phases is presented as a biologically plausible modeling choice rather than an empirical result.

      Lines 659-660: The parametrisation between DoA and SNR is supposedly found in 'Equation 10' - which this reviewer could not find in the manuscript

      The equation was accidentally omitted in the previous revision and has now been reinserted into the manuscript. It defines how direction-of-arrival (DoA) error depends on SNR and azimuth angle (see lines 603-605).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      The key discovery of the manuscript is that the authors found that genetically wild type females descended from Khdc3 mutants shows abnormal gene expression relating to hepatic metabolism, which persist over multiple generations and pass through both female and male lineages. They also find dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with Khdc3 mutant ancestry. These data provide solid evidence further support that phenotype can be transmitted to multiple generations without altering DNA sequence, supporting the involvement of epigenetic mechanisms. The authors further performed exploratory studies on the small RNA profiles in the oocytes of Khdc3-null females, and their wild type descendants, suggesting that altered small RNA expression could be a contributor of the observed phenotype transmission, although this has not been functionally validated.

      Reviewer #2 (Public review):

      Summary:

      This manuscript aimed to investigate the non-genetic impact of KHDC3 mutation on the liver metabolism. To do that they analyzed the female liver transcriptome of genetically wild type mice descended from female ancestors with a mutation in the Khdc3 gene. They found that genetically wild type females descended from Khdc3 mutants have hepatic transcriptional dysregulation which persist over multiple generations in the progenies descended from female ancestors with a mutation in the Khdc3 gene. This transcriptomic deregulation was associated with dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with female mutational ancestry. Furthermore, to determine whether small non-coding RNA could be involved in the maternal non-genetic transmission of the hepatic transcriptomic deregulation, they performed small RNA-seq of oocytes from Khdc3-/- mice and genetically wild type female mice descended from female ancestors with a Khdc3 mutation and claimed that oocytes of wild type female offspring from Khdc3-null females has dysregulation of multiple small RNAs.

      Finally, they claimed that their data demonstrates that ancestral mutation in Khdc3 can produce transgenerational inherited phenotypes.

      However, at this stage and considering the information provided in the paper, I think that these conclusions are too preliminary. Indeed, several controls/experiments need to be added to reach those conclusions.

      Additional context you think would help readers interpret or understand the significance of the work

      Line 25: this first sentence is very strong and needs to be documented in the introduction.

      Line 48: Reference 5 is not appropriate since the paper shows the remodeling of small RNA during post-testicular maturation of mammalian sperm and their sensibility to environment. Please, change it

      Line 51: "implies" is too strong and should be replaced by « suggests »

      Line 67: reference is missing

      Database, the accession numbers are lacking.

      References showing the maternal transmission of non-genetically inherited phenotypes in mice via small RNA need to be added

      Line 378: All RNA-Seq and small RNA-Seq data are available in the NCBI GEO

      We have changed references as requested, and updated portions of the introduction in order to mention specifically genes that seem to regulate an RNA-based genetic nurture effect.  We are not aware of any published work that has demonstrated maternal transmission of non-genetic phenotypes via small RNAs; if the reviewer has a specific reference in mind, we would be happy to read it and add it to our manuscript.  We did add a few sentences describing why this work has primarily been performed in males/fathers.

      Reviewer #1 (Recommendations for the authors):

      (1) In addition to the altered hepatic gene expression and metabolites, did the authors notice any overall phenotypes? including body weight, overall growth, eating behavior, etc?

      We have added information on more general phenotypes of the mice, including litter size, birth weights, and weights at 3 and 8 weeks of age.  We have also performed a metabolic analysis of WT****** mice at 8 months of age.  Overall, there are no striking differences in the WT* mice in these broad phenotypic measures, and also no indication that a smaller litter size or larger birthweight are the drivers of our observed hepatic abnormalities.

      (2) When analyzing the small RNAs, the authors mentioned that they have mapped the reads aging rRNAs. This should have resulted in the identifications of many rRNA-derived small RNAs (rsRNAs). The authors should also perform analyses on the differential expression of rsRNAs in this context. Both tsRNAs and rsRNAs has been shown to be involved in epigenetic inheritance (at least in sperm) (Nat Cell Biol 2018, PMID: 29695786).

      In the oocyte small RNA data, we did not notice many differences in either piRNAs or rRNAs between either the WT and KO oocytes, or the WT and WT** oocytes.  The most significant differences by far were in miRNA and tsRNA.  We have added that we do not see any differences in rRNAs.

      Reviewer #2 (Recommendations for the authors):

      To support your conclusion, you should include the following Data/experiments:

      (1) In the abstract, you wrote "Our results demonstrate that ancestral mutation in Khdc3 can produce transgenerational inherited phenotypes". The full phenotypic description of the phenotype (weight at birth, 3-weeks, 8weights old, phenotype of the liver...) of each progeny should carefully described/analyzed.

      Female KHDC3-deficient mice showed reduced fertility with smaller litter. Given the fact that litter size influences early growth and adult physiology (DOI: 10.1016/j.cmet.2020.07.014), all the metabolic effects observed in the paper could be the result of the litter size. Information about the litter size should be provided. Without this information, it is difficult to evaluate the non-genetic impact of KHDC3 mutation on the metabolism of the progenies.

      We have added information on more general phenotypes of the mice, including litter size, birth weights, and weights at 3 and 8 weeks of age (Figure 3). We have also performed a metabolic analysis of WT****** mice at 8 months of age.  Overall, there were no striking differences in the WT* mice in these broad phenotypic measures, and also no indication that a smaller litter size or larger birthweight are the drivers of our observed hepatic abnormalities.

      We have also added a new figure in order to examine the mechanism of transmission of our observed transcriptional abnormalities (Figure 5).  By transferring serum from WT* mice into wild type recipients, we observe alterations to hepatic gene expression, suggesting that serum-based molecules are driving the altered non-genetic factors in the oocyte.  This lends further support to the conclusion that the observed changes in WT* mice are from inherited germ cell abnormalities (informed by somatic metabolic abnormalities and communicated via blood), and not a consequence of litter sizes or growth rates.

      (2) In addition to the lack of phenotypic information of the progenies, the DEG for the small RNA-seq should be filtered on padj(FDR)<0.05 and not on pvalue<0.05. In Figure 4a, the legend is missing.

      We did not alter the filtering on the small RNA-Seq data.  We are not focusing on any specific small RNA, rather we are stating that these groups (miRNA, tsRNA) of small RNAs are dysregulated; accordingly we believe that using pval is not inappropriate in this circumstance.  The analysis was performed similarly to 4 cell embryo RNA-Seq performed by Harris et al, Cell Reports (PMID 38573852).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study addresses the encoding of forelimb movement parameters using a reach-to-grasp task in mice. The authors use a modified version of the water-reaching paradigm developed by Galinanes and Huber. Two-photon calcium imaging was then performed with GCaMP6f to measure activity across both the contralateral caudal forelimb area (CFA) and the forelimb portion of primary somatosensory cortex (fS1) as mice perform the reaching behavior. Established methods were used to extract the activity of imaged neurons in layer 2/3, including methods for deconvolving the calcium indicator's response function from fluorescence time series. Video-based limb tracking was performed to track the positions of several sites on the forelimb during reaching and extract numerous low-level (joint angle) and high-level (reach direction) parameters. The authors find substantial encoding of parameters for both the proximal and distal parts of the limb across both CFA and fS1, with individual neurons showing heterogeneous parameter encoding. Limb movement can be decoded similarly well from both CFA and fS1, though CFA activity enables decoding of reach direction earlier and for a more extended duration than fS1 activity. Collectively, these results indicate involvement of a broadly distributed sensorimotor region in mouse cortex in determining low-level features of limb movement during reach-to-grasp.

      Strengths:

      The technical approach is of very high quality. In particular, the decoding methods are well designed and rigorous. The use of partial correlations to distinguish correlation between cortical activity and either proximal or distal limb parameters or either low- or high-level movement parameters was very nice. The limb tracking was also of extremely high quality, and critical here to revealing the richness of distal limb movement during task performance.

      The task itself also reflects an important extension of the original work by Galinanes and Huber. The demonstration of a clear, trackable grasp component in a paradigm where mice will perform hundreds of trials per day expands the experimental opportunities for the field. This is an exciting development.

      The findings here are important and the support for them is solid. The work represents an important step forward toward understanding the cortical origins of limb control signals. One can imagine numerous extensions of this work to address basic questions that have not been reachable in other model systems.

      Collectively, these strengths made this manuscript a pleasure to read and review.

      Thank you!

      Weaknesses:

      In the last section of the results, the authors purport to examine the representation of "higher-level target-related signals," using the decoding of reach direction. While I think the authors are careful in their phrasing here, I think they should be more explicit about what these signals could be reflecting. The "signals" here that are used to decode direction could relate to anything - low-level signals related to limb or postural muscles, or true high-level commands that dictate only what movement downstream motor centers should execute, rather than the muscle commands that dictate how. One could imagine using a partial correlation-type approach again here to extract a signal uncorrelated with all the measured low-level parameters, but there would still be all the unmeasured ones. Again, I think it is still ok to call these "high-level signals," but I think some explicit discussion of what these signals could reflect is necessary.

      Thank you for this excellent suggestion. We have followed both pieces of the reviewer’s advice. First, we performed the suggested analysis, partialing off the kinematics then performing target classification on the residuals. This is now Figure 6S1. The analysis revealed the presence of target-related information in the neural activity after subtracting off all linear correlations with kinematics, supporting our claims that higher-level information is present in both populations. The exact timing of classifier performances varied substantially across mice, potentially due to differences in reach-to-grasp strategy, kinematic tracking fidelity, and exact spatial locations of each recorded FOV. Following the second suggestion, we have made the relevant text more careful. We now conclude simply that higher-level signals, meaning those signals that are largely unrelated to forelimb joint angle kinematics, are present but with variable timing and strengths in each area. That text now reads:

      “Target decoding performance could result from truly higher-level signals that code abstractly for target location, or alternatively could be supported by strong encoding of kinematic variables that differed between targets. To disambiguate these possibilities, we refit the linear classifier to neural data after regressing off variance related to the joint angle kinematics. The strength and exact time course of the resulting target decoding varied somewhat across animals, but the earliest portion of target decoding performance persisted in all animals after the removal of kinematics and performance remained stronger for M1-fl than S1-fl (Fig. 6S1B). We thus conclude that higher-level signals are present in both areas, but differ in their exact timing and strength. However, we note that other possible signals, such as postural changes, could not be controlled for here.”

      Related to this, I think the manuscript in general does not do an adequate job of explicitly raising the important caveats in interpreting parametric correlations in motor system signals, like those raised by Todorov, 2000. The authors do an expert job of handling the correlations, using PCA to extract uncorrelated components and using the partial correlation approach. However, more clarity about the range of possible signal types the recorded activity could reflect seems necessary.

      This is an important point, and our text could have unintentionally misled readers. We have now attempted to make this point explicit in the Discussion and in the Results for Figure 6. This Discussion text now reads:

      “Moreover, as is widely known (Todorov 2000), the exact role of these kinematically-related signals is challenging to determine from correlative measures alone; thus, determining whether these signals are used for direct movement control or instead indirectly reflect control performed elsewhere is left as a topic for future work.”

      The manuscript could also do a better job of clarifying relevant similarities and differences between the rodent and primate systems, especially given the claims about the rodent being a "first-class" system for examining the cellular and circuit basis of motor control, which I certainly agree with. Interspecies similarities and differences could be better addressed both in the Introduction, where results from both rodents and primates are intermixed (second paragraph), and in the Discussion, where more clarity on how results here agree and disagree with those from primates would be helpful. For example, the ratio of corticospinal projections targeting sensory and motor divisions of the spinal cord differs substantially between rodents and primates. As another example, the relatively high physical proximity between the typical neurons in mouse M1 and S1 compared to primates seems likely to yoke their activity together to a greater extent. There is also the relatively large extent of fS1 from which forelimb movements can be elicited through intracortical microstimulation at current levels similar to those for evoking movement from M1. All of these seem relevant in the context of findings that activity in mouse M1 and S1 are similar.

      We understand two points to address here. The first point is that we needed to be more careful to attribute previous results as being from the rodent vs. monkey. We agree. We have now revised several parts of the paper to make these distinctions clearer. The second point is about the potential benefit of a thorough review of the many ways in which primate and rodent sensorimotor systems differ. We entirely agree that this could be useful for the field. However, this is a sizable endeavor and doing it full justice is beyond what we know how to fit in the space allotted for framing our results here. We therefore sought a compromise, acknowledging how our results correspond to existing results in the primate without exhaustively accounting for how they differ. Future work will be necessary to more carefully disambiguate whether species-specific differences are due to biomechanical, neurological, ethological, or as-of-yet undetermined sources. We have incorporated your final specific points about what could produce similar information in M1 and S1 into the Discussion.

      “This may simply be a consequence of widely distributed representations of movement across mouse cortex (Musall et al. 2019; Steinmetz et al. 2019; Stringer et al. 2019), including forelimb somatosensory areas, or may be a consequence of the close physical proximity of M1-fl and S1-fl hindering development of functionally distinct representations (Tennant et al. 2011).”

      In addition, there are a number of other issues related to the interpretation of findings here that are not adequately addressed. These are described in the Recommendations for improvement.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Grier, Salimian, and Kaufman characterize the relationship between the activity of neurons in sensorimotor cortex and forelimb kinematics in mice performing a reach-to-grasp task. First, they train animals to reach to two cued targets to retrieve water reward, measure limb motion with high resolution, and characterize the stereotyped kinematics of the shoulder, elbow, wrist, and digits. Next, they find that inactivation of the caudal forelimb motor area severely impairs coordination of the limb and prevents successful performance of the task. They then use calcium imaging to measure the activity of neurons in motor and somatosensory cortex, and demonstrate that fine details of limb kinematics can be decoded with high fidelity from this activity. Finally, they show reach direction (left vs right target) can be decoded earlier in the trial from motor than from somatosensory cortex.

      Strengths:

      In my opinion, this manuscript is technically outstanding and really sets a new bar for motor systems neurophysiology in the mouse. The writing and figures are clear, and the claims are supported by the data. This study is timely, as there has been a recent trend towards recording large numbers of neurons across the brain in relatively uncontrolled tasks and inferring a widespread but coarse encoding of high-level task variables. The central finding here, that sensorimotor cortical activity reflects fine details of forelimb movement, argues against the resurgent idea of cortical equipotentiality, and in favor of a high degree of specificity in the responses of individual neurons and of the specialization of cortical areas.

      Thank you!

      Weaknesses:

      It would be helpful for the authors to be more explicit about which models of mouse cortical function their results support or rule out, and how their findings break new conceptual ground.

      We appreciate this feedback and have attempted to make these details clearer through changes to the Introduction and Discussion. One key change is noted below:

      “The presence of detailed kinematic signals in the sensorimotor cortex supports a model of mouse sensorimotor cortex in which M1-fl and S1-fl play a strong role in shaping the fine details of reaching and grasping movements.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In addition to the weaknesses noted above, I suggest the authors also address the following:

      The last results section is generally lacking in statistical support for claims. Statistical support should be added.

      Thank you for pointing this out, we have added more statistical support to this section.

      The consideration in the Discussion of relevant previous findings and potential explanations for the distal limb signals in mouse sensorimotor cortex is somewhat lacking. There are several specific issues:

      (1) In contrast to the present study, the studies cited in regards to a lack of motor cortical involvement did not involve dexterous movements - in fact, Kawai et al. explicitly engineered a task that did not involve dexterity to distinguish the role of motor cortex in learning from its known role in dextrous movement execution. In Kawai et al., the authors note one rat who adopted a more dexterous approach to the lever pressing task; in this rat, a motor cortical lesion did cause a longer-lasting reduction in task performance. In additional experiments reported in Kawai's PhD thesis, performance of a dextrous task does erode with motor cortex lesion, as seen in other studies, like the early rodent reaching work of Whishaw and colleagues.

      (2) Other possible explanations for the persistence of non-dexterous tasks following motor cortical removal are compensation by, or redundant functionality in, other motor system regions.

      (3) It is also worth noting that stimulation in different regions of mouse M1 and S1 evokes alternately, digit, wrist, and elbow movements in fairly similar proportions (Tennant, 2011), suggesting that descending pathways substantially target spinal circuits that control all forelimb joints.

      (4) It also seems relevant that although the recovery time course is longer, nonhuman primates also retain substantial hand control after motor cortical removal (e.g. Lashley, 1925; Glees and Cole, 1950; Passingham et al., 1983). Humans of course, appear to be a different story.

      These are good points. We have tried to make the Discussion better reflect the tension in the literature, including with this new text:

      “However, several other previous results have indirectly suggested that M1 and S1 may be involved in the details of forelimb movement. Performance suffers with inactivation or lesioning of M1 and S1 in skilled, complex manual behaviors (Guo et al 2015, Mizes et al 2024, Whishaw et al 1990) or idiosyncratic use of digits to accomplish non-dexterous tasks (Kawai 2014). The sparing of non-dexterous tasks with these lesions may also reflect redundancy in control as opposed to irrelevance of M1 and S1. Nevertheless, our finding of low-level kinematic information in sensorimotor cortex supports a role for cortex beyond simply providing redundant high-level commands to these subcortical areas.”

      We have avoided mentioning points 3 and 4 in the paper; the stimulation results might follow from activating projections not normally involved in this behavior, and discussing primates in this context would require a long list of caveats. We agree that these points are worth thinking about, but are concerned that they are too circumstantial to include in interpreting the results formally.

      Although similar decoding performance is achieved using neurons from both CFA and fS1, I am left wondering whether you would do substantially better with CFA using activity at additional preceding time points, or when using exclusively time points from the past. The primary model used here appears to use neural signals from corresponding time points to decode limb parameters, but results seemingly could be different when using preceding time points as regressors.

      We appreciate this suggestion and have added the analysis to an additional supplementary panel for Figure 5 (Figure 5S3). Incorporating lags into the decoder via a Wiener filter does indeed improve the decoding performance, but this could simply be due to the increase in the number of predictor variables. This analysis did not, however, further disambiguate M1-fl and S1-fl: the performance improvement was similar across areas for both causal and acausal lag configurations. This could be a consequence of the time resolution of calcium imaging, so further experiments with electrophysiology would be required to rule this possibility out. We now note this new result:

      “Including additional causal (-100 ms preceding) and/or acausal (-100 ms preceding to 100 following) lags improved decoding performance modestly and similarly for both areas (Fig. 5S3E-F).”

      Related to this, I am also worried about the bleeding of signals across time here. If you deconvolve and interpolate between time points, the interpolation seemingly will pull information into the past, up to half the sampling period, which here is on the order of how long it takes signals to travel to and from the limb. The authors do not make any inappropriate claims about the neural signals here reflecting causes or consequences of what is happening at the limb, but readers (like me) will still try to draw these sorts of conclusions. Is it possible that, although decoding from instantaneous signals is similar for the two regions, the M1 signals are actually motor signals related to future limb state while the S1 signals are sensory consequences? Even if many of the relevant details related to conduction times are not known, perhaps the authors could clarify what can and can't be said related to causal interpretation here.

      Thank you for suggesting further explanation here. We agree that our interpretation could be made more specific. We have added text in the Discussion section to speak more directly to what can and cannot be concluded from our analyses. In short, it is hard to be certain of lags in calcium imaging data for many reasons, and using recording methods with finer temporal resolution (like electrophysiology) will be necessary for determining the precise temporal relationships between kinematics and neural activity. In the absence of these recordings, we limit our claim to kinematic information being present in M1-fl and S1-fl neural activity and leave determining the causal role of this information to future work.

      New clarifying text in the Discussion:

      “The use of calcium imaging further prevents strong conclusions about whether activity reflects future limb states or sensory consequences. Confirming this limitation, inclusion of lagged data in the decoding models, whether causal or acausal, resulted in similar performance changes in both areas.”

      An alternative reason why lift onset is less decodable in CFA is that CFA activates substantially before lift onset, as has been observed in previous rodent studies (Kargo and Nitz, 2004; Miri et al., 2017; Veuthey et al., 2020), perhaps as some sort of movement preparation. S1, on the other hand, may not have this early activity, and so may show a clearer transient at onset when the hand and limb start to move. This seems more likely than the explanations provided by the authors.

      This is a valid possible alternative explanation and we have updated the Discussion to reflect this. This difference in the structure of M1-fl activity versus S1-fl is apparent in the projections of Figure 6A, which show M1-fl projections more clearly aligned to cue-onset than S1-fl projections.

      “Our lift time decoding results are consistent with this view and align with recent observations characterizing mouse proprioceptive forelimb cortex, (Alonso et al 2023), although an alternative explanation may be simply that M1-fl activates earlier than S1-fl during reaching (Kargo and Nitz 2004; Miri et al 2017; Veuthey et al 2020).”

      To better clarify relevant similarities and differences between the rodent and primate systems, the Introduction could include some of these similarities and differences exposed by the literature currently cited, and the Discussion could include an additional paragraph specifically relating findings here to previous observations in the primate.

      We appreciate the reviewer’s thoughtfulness on possible framings of our results. When writing this paper, framing was a major challenge for us and we drafted quite a few versions of the Introduction including some that focused more on mouse-primate comparison. In the end, we decided the most critical function of the Intro was to set up our central question, of “levels-of-sensorimotor-control”. The rich primate literature was valuable here, but getting into a protracted compare-and-contrast exercise quickly became a distraction from the point. Further, we sought to highlight the relevance and importance of the question answered in our work as the mouse has gained prominence for filling gaps that are challenging to address with primates. This paper serves as one of many early steps towards the ultimate goal of revealing general properties of sensorimotor cortical function with the mouse model. We have made some subtle changes to the Introduction that we hope will more clearly communicate this narrative. 

      We agree that a Discussion paragraph directly relating our results to those in primates would benefit our conclusions and have added one:

      “These results expand our understanding of the rodent sensorimotor system and highlight similarities to nonhuman primates. We show here evidence in mice of detailed joint angle kinematic signals from the full forelimb in M1 and S1, as has been shown in macaque cortex during tasks involving reaching and grasping objects (Vargas-Irwin et al. 2010; Saleh et al. 2010, 2012; Goodman et al. 2019; Okorokova et al. 2020). Additionally, the earlier onset of movement-related activity in M1-fl compared to S1-fl is similar to macaque M1 and S1 (Tanji and Evarts 1976). Taken together these results suggest that the mouse can be employed to address questions traditionally explored in primates about how cortical activity encodes detailed movement commands.”

      Although this is outside the scope of the present study, it would be interesting to image descending projection neurons to see what signals are conveyed downstream, and to what targets. Some signals observed in layer 2/3 may not be strongly reflected in descending projections.

      We agree that recording from descending projection neurons in this task would be of deep interest – and also agree that these experiments are beyond the scope of the present study. We look forward to performing these additional experiments in future work.

      Minor:

      (1) The use of "CFA" and “fS1” is a bit confusing. S1, like M1, is defined primarily based on histological criteria, while CFA is defined by intracortical microstimulation. CFA contains a substantial fraction of fS1, seemingly most of it based on the maps shown in Tennant et al., 2011. This is not really a criticism, as the field has not reached any sort of consensus on this nomenclature yet.

      We are similarly unhappy with the inconsistency of the terminology in the field, and struggled with how not to make it worse.  After much debate and consultation with colleagues, we decided to use “M1” and “S1” to evoke the century of literature on these areas; and “-fl” to indicate forelimb because it is more intuitive than “-ul” and avoids using the illegible “-ll” for hindlimb (relevant to our subsequent paper). For what we called M1-fl, we recorded where we did because anecdotally we saw similar responses across that swath; but note that this definition is also consistent with the definition of “MOp-ul” found with multimodal mapping by

      Munoz-Castaneda (2021), which extends a little anteriorly of MOp as defined by the Allen CCF. As the field continues to mature, we hope future work can converge on a set of shared terms.

      (2) Page 4: "Inactivations and lesions of M1 and S1 have shown that M1 is required for the execution of dexterous reach-to-grasp movements" - to me, earlier work from Whishaw and colleagues deserves to be cited here.

      We appreciate the suggestion and have updated the references in this section to better reflect the prior work from Whishaw and other researchers.

      (3) Page 5: "evoking sufficient trial-to-trial variability to avoid model overfitting." - what I think the authors are referring to here is a particular kind of "overfitting," the consequence of not exploring the full movement space, as opposed to model overfitting from issues with the model-fitting method itself. Rather than just saying overfitting, the authors could be clearer about what they are referring to.

      The reviewer is right; the phenomenon we intended to refer to is not properly termed overfitting. Specifically, we meant that data with restricted range does not necessarily express global structure, and models can therefore incorrectly fit them. For example, fitting a linear model to data including many periods of a sine wave will correctly show a zero-slope linear component, but fitting to only a portion of a single cycle will typically yield a nonzero slope. This is not overfitting, is not exactly underfitting (because the relevant structure is barely present in the data, as opposed to missed by an insufficiently powerful model), is not bias (the data are fit well), and is not even necessarily a problem (the local relationship may be what you are interested in). Yet, it does not reflect the larger structure of the data.

      We do not know of a standard term for this phenomenon, so instead of dragging the reader through this tangential argument, we have tried to offer a simpler motivation for using multiple targets:

      “Assessing the relationship between neural activity and the details of movement requires striking a balance between achieving repeatable behavior and evoking sufficient trial-to-trial variability to broadly sample movement space”.

      (4) Page 5: Caudal Forelimb Area should not be capitalized.

      Obviated with the change in area nomenclature.

      (5) Page 7: "of linearly independent degrees of freedom" - for a neuroscience audience, I think it is better to explicitly mention that the resulting PCs are uncorrelated.

      We agree that this section could benefit from clarification. We have attempted to provide additional nuance to indicate what the analysis was intended to test.

      “Despite the strong coupling between the proximal and distal joint angles, rich variation remained in the action of different joints over time. The presence of strong correlations across joints suggested that the kinematics may be well described by a smaller number of independent degrees of freedom than the total number of recorded angles. To assess the number of linearly independent (uncorrelated) degrees of freedom amongst the 24 joint angles and velocities, we used double-cross-validated PCA (Yu et al. 2009); Methods; Fig. 3D), finding intermediate dimensionalities of 7 (median for joint angles) and 10 (velocities; Fig. 3E). This is consistent with the idea that joint angles across the limb are coordinated instead of controlled independently, and that this coordination is flexible enough over time to enable accurately performing reaching and grasping to different targets.”

      (6) Page 7: In the Results, the authors should mention what indicator is being used, the imaging frame rate, and summarize briefly how cells were defined.

      Thank you for the suggestion, these details have been added to the relevant results section for clarity.

      “To do so, we recorded neural activity from neurons in layer 2/3 M1-fl extending into the immediately adjacent secondary motor cortex (M2), and the forelimb region of S1 (S1-fl) using two-photon calcium imaging of GCaMP6f-expressing neurons in layer 2/3 (185-230 μm deep, imaged at 31 Hz, cells extracted with Suite2p (Pachitariu et al 2017)).”

      (7) Page 7: "corrected at n=2" - n doesn't typically refer to the number of tests, so for clarity I would say "corrected for dual tests."

      Thank you for pointing this out, we have corrected the text and added additional explanation in the methods for our approach to determining statistical significance across the targets and locking events.

      “P-values obtained through the ZETA were then Bonferroni corrected for dual tests when measuring the number of cells modulated to a given event and corrected for six tests (2 targets and 3 events) when measuring the overall number of modulated cells.”

      (8) Page 7: In the Results, when the decoding is introduced, it would be helpful to have a few details without having to hunt through the Methods. For example, were things regularized, how was cross-validation handled, etc?

      Thank you for the suggestion, these details have been added to the relevant results section for clarity.

      A simple linear regression model related the single-trial joint angles at all time points to single-trial neural activity at the corresponding moments. The model was fit with ridge regression, the ridge penalty was determined via a heuristic (Karabatsos 2018), and performance was measured on held-out trials (80/20 train/test split, 50 folds).

      (9) Page 8: I think it is worth noting how much mouse reaching involves shoulder rotation as opposed to movement in other joints, as this seems very different from primates.

      Thank you for pointing this out. We think this is mostly a task difference: our mice were in a quadrupedal stance, whereas monkeys are typically asked to reach from a sitting position. We now mention this in the Results. 

      “Reaching evoked particularly large rotation of the shoulder, likely because the mice reached from a quadrupedal position to targets on either side of the snout.”

      (10) Page 8: Should provide quantification to clarify what is meant by "closely tracked."

      We have updated the text to indicate that this claim was meant to be qualitative, and to more clearly highlight that the interest here is the first demonstration of the ability to reconstruct valid forelimb postures from decoded joint angles in the mouse. Quantifying the reconstruction properly would require substantially more manual data labeling, and the successful decoding itself demonstrates indirectly that the reconstructions are good enough to obtain the results of interest.

      Additionally, we reconstructed the skeletal representation of the forelimb from the decoded joint angles and found that, as intended, the reconstructed postures had strong qualitative resemblance to the true postures, even of “minor” angles like cylindrical paw deformation or digit splay (Fig. 5C,G).

      (11) Page 8: "Overall, these results suggest that instantaneous movement-related signals are similarly distributed across CFA and fS1." - I know we are being succinct here, but this sentence sounds like a non sequitur in the context of this paragraph - perhaps include a conclusion from the results in this paragraph first, then summarize the whole section.

      Thank you for the suggestion, we have updated this text to more clearly conclude the results of this section.

      Overall, these results reveal that neural activity in M1-fl and S1-fl is closely related to the kinematic details of reach-to-grasp movements. The ability to decode substantial variance in proximal and distal joints suggests that this relationship extends to the entire forelimb and the similar performance obtained from each area suggests that this information is similarly distributed across M1-fl and S1-fl. 

      (12) Page 10: Mention of projections from fS1 does not explicitly specify their preferential targeting of the dorsal horn, which seems relevant.

      We appreciate the suggestion and have added this detail to the text.

      Rodent S1-fl is known to influence interneuron populations in the spinal cord through direct and indirect projections that predominantly target the dorsal horn (Ueno et al. 2018), thus these signals may also reflect S1-fl’s important role in modulating reflex circuits to coordinate sensory feedback with movement generation (Moreno-López et al. 2016; Moreno-Lopez et al. 2021; Seki et al. 2003).

      (13) Page 31: Labels on the figure indicating what blue and red stand for would be helpful.

      Thank you for the suggestion, labels have been added to indicate left and right trials for Figure 5 C/F and Figure 6A.

      (14) Page 32: Legend does not include panel D.

      Thank you for catching this, the corresponding caption has been added.

      Reviewer #2 (Recommendations for the authors):

      (1) The Introduction could perhaps set the central question in starker relief. What specifically do the authors mean by high- vs low-level control? As suggested by the cited studies, this has been a fraught issue in primate work for decades, and I think a finer-grained framing of alternative hypotheses would help set up the results. For example, would better performance at decoding joint angles than paw position be evidence for lower-level control? The clarity of the Introduction might also be improved if the facts and unknowns were broken down by species throughout.

      We have tried to further improve the focus of the Introduction on the central question, clarify what we mean, and make clearer in the review of the literature which species a finding comes from.

      The clarifying text from the introduction is quoted below:

      Extensive motor mapping experiments in rodents have revealed that activating different parts of the sensorimotor cortex evokes movements of different body parts or different kinds of movements of the same body part, as it does in primates (for review, see (Harrison and Murphy 2014)). Yet it is unclear how the topography of stimulation-evoked movements relates to the roles of these areas during volitional actions. Perturbations during behavioral tasks in mice involving forelimb lever or reaching movements have provided a coarse-level understanding of how these areas contribute during behavior. Inactivations and lesions of M1 and S1 have shown that M1 is required for the execution of dexterous reach-to-grasp movements (Guo et al. 2015; Sauerbrei et al. 2020; Galiñanes et al. 2018; Wang et al. 2017; Whishaw et al. 1991; Whishaw 2000) and that S1 is essential for adapting learned movements to external perturbations of a joystick (Mathis et al. 2017). However, spinal cord projections from mouse M1 and S1 primarily target spinal interneurons rather than directly synapsing onto motor neurons (Gu et al. 2017; Ueno et al. 2018; Wang et al. 2017), suggesting cortical activity might play a more modulatory role. Further, stimulation of brainstem nuclei alone can evoke naturalistic forelimb actions, including realistic reaching movements involving coordinated flexion and extension of the proximal and distal limb (Esposito et al. 2014; Ruder et al. 2021; Yang et al. 2023). Taken together, these results have raised the question of what role mouse M1 and S1 play in the control of goal-directed forelimb movements. 

      One route to answering this question involves characterizing the signals present in mouse M1 and S1 during movement. If mouse M1 and S1 were to control only high-level aspects of forelimb movements, activity should be dominated by ‘abstract’ signals like target location and reflect little trial-to-trial variability in reach kinematics. If instead M1 and S1 control low-level movement features then activity should correlate strongly with forelimb joint angle kinematics and their trial-to-trial variation when reaching to different targets. While the presence of high- or low-level signals in a cortical area does not necessarily imply that they are causally responsible for these aspects of movement, characterizing what signals are present serves as a first step toward determining how these areas relate to movement.

      (2) The kinematics and calcium traces appear to be highly stereotyped across trials. If the population encodes joint angles, would one expect to find correlations between the neural and kinematic residuals after subtraction of the time-varying means? Some additional analysis and/or discussion on this point would be helpful, especially as there are only two targets.

      This is a great idea. As suggested, we implemented regression models on the residuals for each target in the new Figure 5S3. Figure 5S3 A and B show the performance when decoding the residuals for right trials and C and D show performance for left trials. Decoding remained well above chance, despite shrinking down due to predicting this relatively small within-target variation. This analysis supports our claims from the main regression models in Figure 5 and 5S1-2, and also suggests that movements ipsilateral to the reaching limb (contralateral to the recording hemisphere) may be better encoded than movements contralateral to the reaching limb. We have added a reference to this additional residual analysis in the final paragraph of the decoding section of the Results section:

      “Finally, we tested whether the ability to decode these many joint angles was a direct consequence of inter-joint correlations, and might not be indicative of the presence of “real” information about some of these joints. To do so, we fit partial correlation models that removed correlations between proximal and distal joints, or removed correlations of the joint angles with a high-level parameter – the overall distance of the paw centroid to the spout. Despite substantially lowering the behavioral variance, in each case the residuals could still be decoded from neural activity (Fig 5S2A-D). Similar decoding performance for M1-fl and S1-fl was obtained from models fit to decode single-trial residuals separately for left and right trials (Fig 5S3A-D), indicating that trial-to-trial variations on each basic movement were decodable from these populations.”

      Along similar lines, binary classification is used to characterize cue-, lift-, and contact-responsive neurons. Is it possible to exploit trial-to-trial variation in the cue-lift and lift-contact latencies to extract the time-varying marginal effects of each event (e.g., using a GLM)?

      For the detection of single-cell modulations by different events, we have elected to retain our simple statistical test to determine modulation; in our experience, encoding models typically involve a surprising number of steps to get them to do what you actually intend. We leave more extensive encoding model-style analysis to future work, currently in progress.

      (3) The authors mention prior studies suggesting that the control of some forelimb tasks can be gradually transferred from the cortex to the subcortical centers. Have they performed the inactivation at different time points across learning, and if so, do they have evidence for a diminishing effect over time (e.g., blocking of both initiation and coordination early in training)? In addition, the effects of motor cortex inactivation are similar to, but slightly different from, effects shown in reaching tasks in prior studies. Some additional discussion on this point would be useful.

      Our inactivation experiments in this study were intended to coarsely demonstrate the involvement of mouse forelimb sensorimotor cortex in our task. We have not performed the inactivations over learning and leave such experiments to future work. 

      We agree that a little more clarity relating our results to previous ones was warranted. Previous studies (Guo et al. 2015 and Galinanes et al. 2018) have demonstrated inactivation impacts on similar tasks, but for thoroughness we sought to show the same for our task as it varied from the pellet and motorized water spout tasks in both training time and target configurations. Our results are strongly in line with those of Galinanes et al. 2018 which used a fairly similar water spout target configuration. In the inactivation experiments of that paper, 3 out of 13 animals with initiation-triggered inactivations were able to initiate reaching within a time window similar to control trials. Additionally, a proportion of trials across multiple mice proceeded with little perturbation from the inactivations. This is consistent with our observation that M1-fl inactivations may either abolish movement initiation or allow movement initiation but impair task completion on a trial-by-trial and animal-to-animal basis. Further work is required to determine what factors influence these differential responses to inactivation and to determine how these effects differ across task variations (i.e., pellet vs water spout). We have added a brief description of these nuances to the text for clarity. 

      “These inactivations blocked the execution of the reach to grasp sequence, preventing the animal from making contact with the spout during the 3-second laser stimulation period (Fig. 1F; 86.5% control trials with contact within 3 seconds of cue, 5.1% inactivation trials with contact, P < 10<sup>-191</sup>, Mann-Whitney U test, 2 mice, 495 stimulation trials). Interestingly, inactivation at the time of cue often did not prevent reach initiation (mouse 1: 54.7%, mouse 2: 34.2% of inactivation trials with lift within 3 seconds; 93.5%, 86.2% control trials). Yet the movement stalled once the paw and digits extended towards the spout, producing uncoordinated and unsuccessful reaching trajectories (Fig. 1I, two representative datasets). Taken together, these results support the involvement of M1-fl in the water-reaching task and suggest that the strength of inactivation effects may depend on specific task details like training time or target configuration (c.f. Galinanes et al. 2018).”

      Minor points

      (1) The rationale for the multiple comparisons procedure in identifying event-locked responses should be explained in more detail. If I understand correctly, the authors are not correcting for comparisons across ROIs, but instead control the family-wise error rate across brain regions and event types (dividing alpha by two or six). Why not instead control the false discovery rate across ROIs? 

      Thank you for pointing this out, it was confusing as written and we received a similar comment from Reviewer 1. We have fixed the wording now to make it clearer why we did this. We simply aimed to describe how many of the recorded neurons in each area were modulated by the task as a proxy for the engagement of these areas during the behavior, and to use this measure of modulation as a criterion for including the neuron in subsequent analysis. In other words, if the question had been “are any neurons in this area modulated by the task?” then correcting for the number of ROIs would be the correct method; but if the question is, “is this neuron probably modulated and therefore worth including in my decoder?” correcting for the number of ROIs will typically be much too conservative. Thus, we only sought to correct for the false discovery rate across events and targets for each ROI. We have added additional text in the methods to clarify these choices, below. Please also see response to (7) from Reviewer 1 above.

      “Note that we did not correct for the number of ROIs tested for two reasons. First, the goal of this testing was to serve as a criterion for inclusion in subsequent decoding analyses, not to determine whether any neurons in the area at all were modulated; and second, correcting for the number of ROIs would bias comparison between areas if different numbers of ROIs were recorded in one area vs. the other.”

      (2) It appears joint angles are treated as linear variables in the decoding analysis; is this correct? This seems reasonable as long as the range of motion is not too large, but the authors might briefly comment on the issue in the Methods. 

      Yes, all joint angles are treated as linear variables in the linear regression model. We observed empirically (as can be seen in Figure 3B and Figure 5B/F) that the joint angle variables were relatively constrained to specific ranges during the task, with no angles displaying substantial wrap-around during the reaching and grasping movements. It is true that use of nonlinear decoding would almost surely improve performance further. Future work could also compare decoding of joint angles with muscle forces, which correlate and which we made no effort to distinguish here. In this work, though, the demonstration of a substantial relationship between neural activity and kinematics already tells us that fine details of movement are present in the M1 and S1-fl populations, which is a critical fact to understand these areas and was not previously known. We now comment explicitly on this, as suggested.

      “Joint angle or velocity kinematics were linearly interpolated from their original 6.66 ms to 10 ms and smoothed with a Gaussian (15 ms s.d.). These angular variables were then treated linearly in decoding analyses as their ranges were relatively constrained during the reaching and grasping movements; although the true relationships are likely nonlinear, this serves as a sufficient approximation to demonstrate the presence of a relationship between neural activity and kinematics.”

      (3) Are the limb pose estimates mirrored along the mediolateral axis? Figures 1C and 2D appear to show reaches to the left spout on the animal's right.

      Thank you for pointing out the ambiguity in the display of these data. The reach trajectories were not mirrored along the mediolateral axis, but they are displayed from the perspective of the behavioral imaging cameras as shown in Figure 1A. Thus the right target reaches (ipsilateral to the animal’s reaching arm) are on the left side of the camera image and the left target reaches (contralateral to the animal’s reaching arm) are on the right side of the image. We have clarified this in the figure captions.

    1. Author response:

      The following is the authors’ response to the previous reviews

      General recommendations (from the Reviewing Editor):

      The reviewers agreed that addressing some specific concerns would improve the clarity of the paper and the strength of the conclusions. These points are listed below, and described in more detail in the reviewer-specific 'Recommendations for Authors':

      We thanks the editor and reviewers for the encouraging feedback and constructive comments. We provide our point-by-point response below.

      (1) The details of the new experiment including number of subjects and a description of the analysis should be provided in the main text.

      We now provide a detailed description of the methods (including the number of subjects; N = 30) and analyses for the new experiment. See our response to Reviewer 2 for more details.

      (2) It would be informative to see how the amplitude biases observed, agree with those found by Gordon et al. 1994.

      Addressed. Please see our response to Reviewer 1, comment 1.

      (3) Each of the models lead to different bias patterns. It would be very helpful to hear the author's interpretation, ideally with a mathematical explanation, of what leads to these distinct patterns.

      Addressed. Please see our response to Reviewer 1, comment 2.

      Reviewer #1 (Recommendations for the authors):

      (1) Most of my points have been addressed convincingly in this revision. The new experiment in which also biases in movement amplitude were determined is a welcome addition to the paper. However, I could not see the results of this study, as the authors did not include Fig. 4 in the manuscript, but repeated Fig. 3. That's unfortunate as I would have like to see the similarity between the biases in direction and amplitude. Moreover, I would have liked to see how the amplitude biases agree with those found by Gordon et al. EBR (1994) 99:112-130, and to which extent Gordon et al.'s explanation can explain the pattern.

      We apologize for including the incorrect figure in the previous version of our manuscript. We did make a correction and submitted a corrected version, but it appears that it didn’t make its way to you. The correct Figure 4 is now in the manuscript.

      The motor biases in amplitude (extent) observed in Experiment 4 (Author response image 1) are qualitatively similar to the pattern reported by Gordon et al. 1994. While the exact peaks do not match perfectly, both datasets show a two-peaked pattern.

      Gordon et al. (1994) attributed the bias in amplitude to direction-dependent variation in movement speed which, in their view, arise from anisotropies in limb inertia. Specifically, moving the upper arm along its quasiorthogonal direction (i.e., rotation about the elbow) requires lower effective inertia than moving parallel to the upper-arm axis. Given the arm posture in both datasets, the upper limb points toward ~135°/315°, with the orthogonal direction corresponding to ~45°/225°. The two-peaked speed profiles in both our data Author response image 1 and Gordon et al. are consistent with this prediction.

      Author response image 1.

      Gordon et al (1994) noted that, while the extent bias function should mirror the speed bias function, the motor planning system might proactively compensate for the speed bias. Indeed, while the extent and speed bias functions are roughly aligned in their study, the two are misaligned in our Experiment 4. For example, the speed function peaks around 45° which corresponds to a valley in the extent bias function. The difference between their data and ours could be due to a difference in the starting point configuration. However, their model predicts alignment of the speed and extent functions independent of starting point configuration. In contrast, the TR+TG model does predict our observed extent bias function and yields predictions about how this should change with different start point configurations. As such, while heterogeneity in movement speed may contribute to extent bias to some degree, we think the transformation bias and visual-target bias likely play a larger role in determining the amplitude bias observed extent bias at movement endpoint.

      We have added a discussion section about the bias function reported by Gordon et al. (1994) and their account in the manuscript (lines 482-493). We do not repeat it here, as the content largely overlaps with the response above.

      (2) One of the most important new insights from this study is that the three single-source models lead to different bias patterns, with 1, 2 or 4 peaks. However, what I miss in the paper is an intuitive explanation why they do so. Now, the models are described and their predictions are shown, but it remains unclear where these distinct patterns come from. As scientists, we want to understand things, so I would very much appreciate if the authors can provide such an intuitive explanation, for instance using a mathematical proof. That could also identify how general these patterns are, or if there are certain requirements for them to occur (such as a certain shape of the transformation bias).

      Note that the closed-form mathematical expression for the motor bias function is not straight forward. As such, the intuition comes primarily from inspection, that is, the model simulations themselves, what we show Figure 1 of the paper. Importantly, the model predictions are insensitive to the parameter values over a reasonable range. Thus, the number of peaks predicted by each model is a core distinguishing feature. We present in the Supplementary Results a formalized mathematical analysis to illustrate how different models produce different numbers of peaks in the movement-bias function.

      (3) I think it's a good idea to change the previous "Visual Bias" into a "Target Bias". This raises the question whether the "Prioprioceptive Bias" should not be changed into a "Hand Bias" or "Start Bias"?

      While we appreciate the reviewer’s point here, we prefer the term “Proprioceptive Bias” given that this term has been used in the literature and provides a contrast with sources of bias arising from vision. “Hand Bias” and "Start Bias” seem more ambiguous.

      L51: I think "would fall short" should be replaced by "would overshoot".

      L127: I think "biased toward the vertical axis" should be replaced by "biased away from the vertical axis". Figure 3 still contains the old terminology like T+V. Please replace by the new terminology. L255: Replace "Exp 1a" by "Exp 1b".

      L376: Replace 60 by 6.

      L831-2: I hope the summed LL was maximized, not minimized.

      Thanks for catching the typos. We have corrected all of them.

      Reviewer #2 (Recommendations for the authors):

      I think that Experiment 4 does not mention how many participants performed the study. (Only in the response to the reviewers I found this)

      We have added information regarding the number of participants in the Fig 4 (N=30).

      I am very happy that the authors added the biomechanical simulation into the paper. I am not convinced that this addressed my concerns exactly but it is an excellent addition and the authors have now adjusted the text appropriately.

      We appreciate the positive response to our additional assessment of biomechanical factors. We welcome any additional information on how we might fully address this issue.

      line 826: extend -> extent

      Corrected.

      Figure 4. I think that the authors have put the wrong figure here. I cannot see any data for extent. I would need to see this figure (or please correct me - but the caption doesn't match the figure and I don't see the results clearly. (I think the review might have the correct figure).

      We apologize for this mistake. We now provided the correct Figure 4 in the paper (also included in the first page of the response letter).

      I am missing the detailed description on when the direction error and distance error were calculated for exp 4 - and what exactly was used? How did the authors examine the values without correction? What time point was used? Did I miss the analysis section for this?

      Participants were instructed to make fast, straight movement without any corrections and were given up to 1 s to complete the movement. Hand position was recorded once the movement speed dropped below 1 cm/s. On 99.8% of trials, movement speed did not increase once this threshold was passed, indicating that the participants adhered to the instructions. On the remaining trials, we detected a secondary corrective movement (increase in speed >5 cm/s). On these trials, we used the position recorded when the movement speed initially dropped below 1 cm/s as the endpoint position. The pattern of results would be the same were we to exclude these trials.

      This information has been added to the Methods section (line 661-666).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1:

      SOM+ interneurons such as Martinotti cells target the apical tufts of pyramidals in the cortex. Since interneurons in general are strongly implicated in mediating rhythmic population activity over a range of timescales, it is quite appropriate to study the consequence of rhythmic inhibition provided by SOM+ interneurons for synaptic integration, including the phenomenon of dendritic spikes. However, using conclusions from a singular study (ref 22) to identify the beta band as the rhythm mediated by SOM+ is not very accurate. SOM+ interneurons have been implicated in regulating rhythms centered just below 30 Hz (refs 22, 21). It is a range that lies in the grey zone of the traditional definition of beta and gamma. However, it is significantly higher than the 16 Hz rhythms explored in this study. It thus remains unknown how a 25-30 Hz rhythmic inhibition (that has an experimentally suggested role for dendrite targeting SOM+ INs) in apical tufts regulates dendritic spikes.

      We agree with the reviewer that the rhythms arising from SOM+ interneurons can extend their frequencies higher than the 16 Hz analyzed in this study. To address this, we have conducted a new set of simulations where we delivered distal dendritic inhibition across a range of frequencies, from 0.5 to 80 Hz (see new Results section “Frequency specific effects of rhythmic inhibition on neuronal integration”). These results revealed, surprisingly, that at 30 Hz their ability to entrain Ca<sup>2+</sup> and NMDA spikes degrades (but not Na<sup>+</sup> spikes). This suggests that beta rhythms in the 20-30 Hz range are operating at the highest frequency for which dendritically targeting inhibition will be effective. The implications are covered in the Discussion section “Interaction with microcircuitry”. They are:

      “Particularly in the visual cortex, SOM interneurons can generate a rhythm in the 25-30 Hz range [22]. We found this to be at the upper end of the frequency range for dendritic inhibitory rhythms to be effective in modulating NMDA and Ca<sup>2+</sup> spikes. If this rhythm solely recruited SOM interneurons, its effectiveness would be marginal. Potentially compensating for this, recent work has found that PV interneurons also participate in beta/low-gamma [23, 24] (but see [21, 22]). In our model, on its own when beta rhythmic inhibition was delivered perisomatically we found that it was less able to entrain spiking and had an overall hyperpolarizing effect. However, if delivered in conjunction with the distal dendritic inhibition arising from SOM interneurons, this may strengthen entrainment.”

      Distal dendritic inhibition has been previously shown to be more effective in controlling dendritic spikes. However, given the slow timescale of dendritic spikes, it can be hypothesized that high-frequency rhythmic inhibition would be ineffective in entraining the dendritic spikes either in distal or proximal location, as demonstrated by 4H and 5F, and vice versa. A computational study can take this further by exploring the robustness of this hypothesis. By sticking to a single-frequency definition of what constitutes Gamma (64 Hz) and Beta (16 Hz) inhibition, the current exploration does support the core hypothesis. However, given the temporal dynamics of dendritic spikes, it is valuable to learn, for example, the upper bound of "Beta" range (13-30Hz) inhibition that fails to phasically modulate them. In addition to the reason stated in the earlier paragraph, Alpha band activity (8-12 Hz), has been implicated (e.g. van Kerkoerle, 2014) in signaling of inter-areal feedback to the superficial layer in the cortex, potentially targeting apical tufts of pyramidals from multiple layers and resulting in alpha-range rhythmic inhibition. To make the findings significant, it might therefore be more pertinent to understand the consequences of ~10Hz rhythmic inhibition (in addition to the ~25-30 Hz Beta/Gamma) in the apical tufts for phasic modulation of dendritic spikes.

      We added an additional set of simulations that address this in the Results section ‘Frequency specific effects of rhythmic inhibition on neuronal integration’. In general, we found that dendritic and perisomatic inhibitory rhythms at lower frequencies could entrain AP generation, but with less functional specialization. This is explored in our Discussion section ‘Interneuron specializations and rhythm timescales’.

      The differential effect of Gamma and Beta range inhibition on basal and apical excitatory clusters is not convincing from the information provided. The basal cluster appears to overlap with perisomatic inhibitory synapses. The description in the methods does not have enough information to negate the visual perception (ln 979-81). With this understanding, it is not surprising that the correlation between excitation and APs is high (during the trough of gamma) for basal and not apical excitation. A more comparable scenario would be a more distal location of the basal excitatory cluster.

      While we stated in the original manuscript that we were contrasting ‘basal’ vs. ‘apical’ clustered inputs, this terminology did not reflect our intent with these analyses. We meant to contrast proximal vs. distal dendritic clustered synaptic inputs, which the reviewer correctly noted is confounded in the apical vs. basal comparison. We have rewritten these results, their discussion, and corresponding figure, to clearly state that we are contrasting proximal vs. distal synaptic input.

      Reviewer #2:

      The weaknesses are probably in some of the parameterizations of inhibitory synaptic dynamics. A unitary peak conductance of 1nS is very high for inhibitory synapses. This high value could invariably skew some of the network-level predictions. The authors could obtain specific parameters from the Neocortical Collaboration Portal (https://bbp.epfl.ch/nmcportal/microcircuit.html), which is an incredible resource for cortical neurons and synapses.

      We appreciate the valuable resource mentioned by the reviewer and will consult it when constructing future models. Regarding the present one, our choice of peak conductance was based on previous studies, namely:

      Egger R, Narayanan RT, Guest JM, Bast A, Udvary D, Messore LF, Das S, de Kock CPJ, Oberlaender M (2020) Cortical output is gated by horizontally projecting neurons in the deep layers. Neuron 105, 122-137.e128.

      and

      Xiang Z, Huguenard JR, Prince DA (2002) Synaptic inhibition of pyramidal cells evoked by different interneuronal subtypes in layer v of rat visual cortex. J Neurophysiol 88, 740-750.

      The study by Egger et al. used an inhibitory peak conductance of 1 nS and was simulating circuitry very similar to ours. We validated these synapses in pilot simulations that sought to characterize the resulting IPSPs and IPSCs, and whose results can be seen in Table 1 of our methods. These synapses exhibited IPSCs whose peak amplitudes ranged over values (~24162 pA) that agreed with the experimental literature, such as Xiang et al.

      Given this, we feel our parameterization of inhibitory synapses does not warrant any changes.

      Reviewer #3:

      What disappointed me a bit was the lack of a concise summary of what we learned beyond the fact that beta and gamma act differently on dendritic integration. The individual paragraphs of the discussion often are 80% summary of existing theories and only a single vague statement about how the results in this study relate. I think a summarizing schematic or similar would help immensely.

      We agree with the reviewer that a summary schematic would help the reader. This has been added to the manuscript as Figure 11. It demonstrates the principal findings of the paper and is referenced in the opening paragraph of the discussion section.

      Orthogonal to that, there were some points where the authors could have offered more depth on specific features. For example, the authors summarized that their "results suggest that the timescales of these rhythms align with the specialized impacts of SOM and PV interneurons on neuronal integration". Here they could go deeper and try to explain why SOM impact is specialized at slower time scales. (I think their results provide enough for a speculative outlook.)

      This discussion has been expanded under the section “Interneuron specializations and rhythm timescales”. The added text is:

      “So, while our results suggest that spatial targeting of SOM and PV interneurons aligns with the timescales of their network-level rhythms, it could also be that their timing and subcellular localization interact to produce specialized neuron-level functions [85]. For instance, NMDA and Ca<sup>2+</sup> spikes in the distal dendrites last for ~50 ms, making the slower beta rhythm more appropriate for bidirectionally controlling them. Both can be described as dynamical systems with distinct phases with differing sensitivity to inhibition. Ca<sup>2+</sup> spikes are dynamical events comprised of an initiation, plateau, and termination phase. Inhibition delivered during the plateau phase shortens their duration [86]. If the beta rhythm is comprised of cycling between periods of elevated excitation (increased NMDA spike generation) followed by elevated inhibition, then Ca<sup>2+</sup> spike initiation will tend to occur during the excitatory phase, and its plateau during the subsequent inhibitory phase. A plateau during the inhibitory phase will more quickly enter termination. This is bidirectional control. On the other hand, slower rhythms (e.g. 1 Hz) initiate Ca<sup>2+</sup> spikes during the excitatory phase that plateau and enter termination autonomously, before the inhibitory phase is reached. The same principle holds for NMDA spikes [87]. As a result, rhythms in the range from 15-30 Hz are optimal for synchronizing the onsets and offsets of dendritic spikes across a population of neurons.

      The integrative effects of gamma (>40 Hz) are also specialized. Low frequency inhibitory rhythms delivered to the soma tended to shift the membrane potential higher or lower with the rhythm’s phase, effectively bringing it closer or farther from AP generation but not changing the neuron’s sensitivity to fast synaptic inputs. In the gamma frequency range, this is reversed, with the mean membrane potential not varying with rhythm phase but with a shifting bias to positive or negative membrane potential fluctuations. In addition, the trough phase of gamma lowers the threshold for AP generation, while slower rhythms like beta only raise the threshold. Consequently, the timing of gamma is ideal for increasing the sensitivity of the neuron to rapid excitation. This agrees with the observation that gamma oscillations accompany rapid excitation-inhibition balancing [88].”

      We also extended our discussion section ‘Relevance to coding’ to explore how beta and gamma rhythms can support sparse vs. dense population coding, respectively. It reads:

      “One interpretation of rhythms arising from local inhibitory feedback is that they maintain the balance between excitation and inhibition. This can be thought of as a normalization operation that maintains activity within a set range. Normalization can be achieved either through a subtractive effect that raises the threshold for initiating an action potential, or a multiplicative effect that lowers the slope of the relationship between excitation and action potential firing rate. When considered at the population level, these normalization effects impact coding in different ways. Subtractive normalization increases sparsity by dropping out neurons whose excitation is below the raised threshold. Multiplicative normalization, however, encourages dense codes by scaling down firing rates and compressing the range of firing rates. This study found that while both perisomatic and distal dendritic inhibition produced subtractive effects, only perisomatic had a multiplicative effect. Tying this to beta and gamma, beta rhythms may encourage sparse population codes while gamma allows for dense.”

      Beyond that, the authors invite the community to reappraise the role of gamma and beta in coding. This idea seems to be hindered by the fact that I cannot find a mention of a release of the model used in this work. The base pyramidal cell model is of course available from the original study, but it would be helpful for follow-up work to release the complete setup including excitatory and inhibitory synapses and their activation in the different simulation paradigms used. As well as code related to that.

      We have added a Code and Data Availability section that addresses this. It reads: “Simulation code is deposited at ModelDB athttps://modeldb.science/2019883 . The raw simulation data are available from DBH upon request. Analysis code is posted as a github repo at https://github.com/dbheadley/InhibOnDendComp.”

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The Drosophila wing disc is an epithelial tissue, the study of which has provided many insights into the genetic regulation of organ patterning and growth. One fundamental aspect of wing development is the positioning of the wing primordia, which occurs at the confluence of two developmental boundaries, the anterior-posterior and the dorsal-ventral. The dorsal-ventral boundary is determined by the domain of expression of the gene apterous, which is set early in the development of the wing disc. For this reason, the regulation of apterous expression is a fundamental aspect of wing formation.

      In this manuscript, the authors used state-of-the-art genomic engineering and a bottom-up approach to analyze the contribution of a 463 base pair fragment of apterous regulatory DNA. They find compelling evidence about the inner structure of this regulatory DNA and the upstream transcription factors that likely bind to this DNA to regulate apterous early expression in the Drosophila wing disc.

      Strengths:

      This manuscript has several strengths concerning both the experimental techniques used to address the problem of gene regulation and the relevance of the subject. To identify the mode of operation of the 463 bp enhancer, the authors use a balanced combination of different experimental approaches. First, they use bioinformatic analysis (sequence conservation and identification of transcription factors binding sites) to identify individual modules within the 463 bp enhancer. Second, they identify the functional modules through genetic analysis by generating Drosophila strains with individual deletions. Each deletion is characterized by looking at the resulting adult phenotype and also by monitoring apterous expression in the mutant wing discs. They then use a clever method to interfere in a more dynamic manner with the function of the enhancer, by directing the expression of catalytically inactive Cas9 to specific regions of this DNA. Finally, they recur to a more classical genetic approach to uncover the relevance of candidate transcription factors, some of them previously known and others suggested by the bioinformatic analysis of the 463 bp sequence. This workflow is clearly reflected in the manuscript, and constitutes a great example of how to proceed experimentally in the analysis of regulatory DNA.

      We thank the reviewer for these positive comments on the manuscript.

      Weaknesses:

      There are several caveats with the data that might be constructed as weaknesses, some of them are intrinsic to this detailed analysis or to the experimental difficulties of dealing with the wing disc in its earliest stages, and others are more conceptual and are offered here in case the authors may wish to consider them.

      (1) The primordium of the wing region of the wing imaginal disc is defined by the expression of the gen vestigial, which is regulated by inputs coming from the dorsal-ventral boundary (Notch and wg) and from the anterior-posterior boundary (Dpp). Having such a principal role in wing primordium specification and expansion, I am surprised that this manuscript does not mention this gene in the main text and only contains indirect references to it. I consider that the manuscript would have benefited a lot by including vestigial in the analysis, at least as a marker of early wing primordium. This might allow us to visualize directly the positioning of the primordium in the apterous mutants generated in this study, adding more verisimilitude to the interpretations that place this domain based on indirect evidence.

      Vg does indeed play a critical role on the formation of the wing disc, and it is an ideal marker for the identification of the wing pouch. In the updated version of the article, we have now followed the expression of vg in some of the OR463 mutants via immunostaining of the Vg protein (Supplementary Figure 6). Cells within posterior wing outgrowths in Δm1flies were invariably positive for Vg. This result further supports our previous identification of these cells as pouch cells. In those mutants in which no cross-over between DV and AP was observed, vg expression was severely reduced or absent, indicating that the wing pouch had not been specified. We thank the reviewer for this experimental idea, which we believe strengthens the final manuscript.

      We have added to the text:

      “To identify the nature of the posterior outgrowths, we performed anti-Vestigal (Vg) antibody staining of Δm1 mutants (Supplementary Figure 6). Vg is a key regulator of wing specifications and also participates in wing growth and patterning (Baena-Lopez & García-Bellido, 2006; Kim et al., 1996; Zecca & Struhl, 2007a). In those discs, in which the stripe was extended and the P compartment was enlarged, Vg was detected throughout the outgrowth, supporting the wing pouch identity of this region (Supplementary Figure 6B). Hemizygous Δm3 mutants presented a highly reduced anti-Vg signal, which suggests that no wing pouch is specified in these mutants (Supplementary Figure 6C).”

      (2) The authors place some emphasis on the idea that their work addresses possible coordination between setting the D/V boundary and the A/P boundary:

      Abstract: "Thus, the correct establishment of ap expression pattern with respect to en must be tightly controlled", "...challenging the mechanism by which apE miss-regulation leads to AP defects." "Detailed mutational analyses using CRISPR/Cas revealed a role of apE in positioning the DV boundary with respect to the AP boundary"

      Introduction: "However, little is known about how the expression pattern of ap is set up with respect that of en. In other words, how is the DV boundary positioned with respect to the AP boundary?"

      "How such interaction between ap and the AP specification program arises is unknown."

      Results: "Some of these phenotypes are reminiscent of those reported for apBlot (Whittle, 1979) and point towards a yet undescribed crosstalk between ap early expression and the AP specification program."

      At the same time, they express the notion, with which this reviewer agrees, that all defects observed in A/P patterning arising as a result of apterous miss-regulation are due to the fact that in their mutants, apterous expression is lost mainly in the posterior dorsal compartment, bringing novel confrontations between the A/P and the D/V boundaries.

      To me, the key point is why the expression of apterous in different mutants of the OR463 enhancer affects only the posterior compartment. This should be discussed because it is far from obvious that apterous expression has different regulatory requirements in the anterior and posterior compartments.

      We agree with the reviewer that the differential effect of the mutations on the expression of ap in the A and P compartment is a key factor underlying our explanation of how the phenotypes arise. To clarify this point, we have now extended our first discussion point. Moreover, we have included some other references of differential enhancer regulation in different wing disc compartments. In addition, we have discussed whether this effect has to do with the different regulation of the enhancer in the A and P compartment or due to regulation of downstream effectors.

      Added paragraph:

      “Although apE is active throughout the dorsal compartment, its disruption leads to a preferential loss of ap expression in posterior cells. The asymmetric effect of apE perturbation on the anterior and posterior compartments suggests that apE transcriptional control is not equivalent across the A/P axis. Compartment-dependent differences in enhancer regulation have also been documented in other developmental contexts; for example, the Distal-less DMX-R element is interpreted through distinct cofactor combinations (Sloppy paired anteriorly and Engrailed posteriorly) (Gebelein et al., 2004), and specific mutations within DMX-R preferentially disrupt enhancer function in anterior versus posterior cells. It is possible that apE is more sensitive to misregulation due to differential transcriptional regulation across compartments. Nevertheless, we cannot exclude the possibility that the posterior bias we observe arises not from enhancer logic per se, but from intrinsic differences in tissue architecture or the dynamics of boundary positioning during wing disc development.”

      (3) The description of gene expression in the wing disc of novel apterous mutants is only carried out in late third instar discs (Figs. 2, 3, 5, and 7). This is understandable given the technical difficulties of dealing with early discs, as those shown in the analysis of candidate apterous regulatory transcription factors (Fig. 4F, Fig. 6 C-D). However, because the effects of the mutants on apterous expression are expected to occur much earlier than the time of expression analysis, this fact should be discussed.

      We agree with the reviewer regarding the limitations of our analysis whenever we analyzed third instar larvae to assess the expression of the OE463 enhancer. We have included a statement in which this is mentioned in the discussion:

      “It is important to acknowledge that all expression analyses were conducted in third-instar discs, a stage that follows the initial establishment of ap expression. Earlier effects are therefore inferred rather than directly observed, as imaging and staging of early discs present significant technical challenges due to their small size and fragility. A direct observation of the early wing disc across mutant conditions would likely help to clarify the role of the discovered factors during early ap expression.”

      Reviewer #2 (Public Review):

      In their manuscript, "Transcriptional control of compartmental boundary positioning during Drosophila wing development," Aguilar and colleagues do an exceptional job of exploring how tissue axes are established across Drosophila development. The authors perform a series of functional perturbations using mutational analyses at the native locus of apterous (ap), and perform tissue-specific enhancer disruption via dCas9 expression. This innovative approach allowed them to explore the spatio-temporal requirements of an apterous enhancer. Combining these techniques allowed the authors to explore the molecular basis of apterous expression, connecting the genotypes to the phenotypical effects of enhancer perturbations. To me, this paper was a beautiful example of what can be done using modern drosophila genetics to understand classic questions in developmental biology and transcriptional regulation.

      In sum, this was a rigorous paper bridging scales from the molecular to phenotypes, with new insight into how enhancers control compartmental boundary positioning during Drosophila wing development.

      We would like to thank the reviewer for its positive and encouraging comments, as well as for the careful review of the manuscript and figures. We have adapted most of the suggestions in the new manuscript.

      Reviewer #3 (Public Review):

      In this manuscript, authors use the Drosophila wing as a model system and combine state-ofthe-art genetic engineering to identify and validate the molecular players mediating the activity of one of the cis-regulatory enhancers of the apterous gene involved in the regulation of its expression domain in the dorsal compartment of the wing primordium during larval development.

      (1) The authors raise two very important questions in the Introduction: (1) who is locating the relative position of the AP and DV boundaries in the developing wing, and (2) who is responsible for the maintenance of the apterous expression domain late in larval development. None of these two questions have been responded to and, indeed, the summary of the work (as stated in the conclusions of the last paragraph of the Introduction) does not resolve any of these questions.

      We believe the results presented, together with those added during the revision, shed some on the positioning of the boundary. We proposed that the combined integration of four TFs by the OR463 enhancer is fundamental for the correct positioning. Additionally, we proposed a model on how these positioning problems result in the phenotypes observed (Supplementary figure 7, now also shown in Figure 2D). Our results indicate that ap expression in the PD quadrant is particularly sensitive to mutations in the enhancer, which we have now further elaborated on in the first part of the discussion. Together, we believe that our results do tackle the first problem posed in the introduction, while not completely solving them. As for the second question, we have tried to remove any suggestions that this article tries to explain later regulation of apterous. Probably this misunderstanding arises from a sentence in the introduction which has now been deleted. The means of the maintenance of ap expression in later stages has been partially explored previously (See Bieli et al 2015) and it is subject of our current studies.

      (2) The authors have identified two different regions whose deletions give very interesting phenotypes in the adult wing (AP identify change & outgrowths, and loss of wing), and have bioinformatically identified and functionally verified 4 TFs that mediate the activity of these regions by their capacity to phenocopy the wing phenotype. While identification of the 2 TFs acting on the m1 is incremental with respect to previous work on the identification of the enhancer responsible for the early expression of Ap, identification of Antp and Grn does not explain the loss of function phenotype of the m3 enhancer. Does any of these results shed any light on the first two Qs? Do these results explain the compartment boundary position in the wing as stated in the title? Expression of lacZ reporter assays is fundamental to demonstrate their model of Figure 8. The reduction of the PD compartment is difficult to understand by the sole reduction in ap expression in this region (which has not been demonstrated).

      We agree that the identification of Antp and Grn does not by itself explain the loss-of-function phenotype of the m3 enhancer. However, these transcription factors represent the best current candidates for direct regulators for this enhancer. We have clarified in the text that Antp and Grn may not act as instructive inputs but rather play a permissive role in enabling ap expression through m3. Importantly, the dCas9-mediated perturbation experiments directly demonstrate that targeted manipulation of apE in this region is sufficient to produce the characteristic duplications, providing functional evidence that apE activity underlies the observed phenotypes. In addition, lacZ reporter assays confirm that apE expression is indeed affected in all cases where the experimental setup permitted detection. Together, these results validate that the observed morphological phenotypes stem from perturbation of apE activity and support the proposed model for enhancer regulation and its role in compartment boundary maintenance.

      (3) The authors state in one of the sections "Spatio-temporal analysis of apE via dCas9 ". No temporal manipulation of gene activity is shown. The authors should combine GAL4/UAs with the Gal80ts to demonstrate the temporal requirements of Antp/Grn and Pnt/Hth as depicted in their model of Figure 8.

      We agree with the reviewer that the temporal dimension was not explored in the first version of the manuscript (aside of the temporal constrains of en-Gal4 driver). As suggested by the reviewer, we have now used a tub-Gal80ts allele to temporally control the enhancer perturbation and delimit its window of activity. The results are included in two new panels in the figure 3 (H and H’). The new data agrees with the notion that apE enhancer is important up to L2 stages but dispensable later in development. We have added the following paragraph to the text:

      “To define the developmental time window during which the apE enhancer remains sensitive to repression, we combined the temperature-sensitive tub-Gal80<sup>ts</sup> system with temporally controlled expression of dCas9. Animals carrying the en-Gal4, tub-Gal80<sup>ts</sup>, UAS-dCas9 and U6-OR463gRNA(4x) transgenes were maintained at 18 °C to suppress dCas9 expression. Independent sets of embryos were then shifted to 29 °C at successive developmental intervals ranging from 0 to 168 h after egg laying (AEL), so that dCas9 induction occurred at distinct time points in development (Figure 3H). Under these conditions, dCas9 transcription was induced only after the temperature shift, while the gRNAs were expressed constitutively. Wing phenotypes were quantified in adult progeny as a readout of apE enhancer perturbation. When dCas9 was expressed from embryonic or early larval stages (0–48 h AEL), nearly all wings (70–90%) displayed severe ap-like phenotypes, including posterior compartment duplication and loss of anterior–posterior boundary integrity. Shifting animals later (48–72 h AEL) still produced a majority (~66%) of abnormal wings, whereas induction after 72 h AEL resulted in progressively weaker effects and complete loss of phenotypes by 96 h AEL (Figure 3H’).

      These results delineate the developmental period during which apE activity is required for proper wing patterning. Perturbation during the first half of the second larval instar (≤ 96 h at 18 °C) was sufficient to elicit strong ap-like transformations, consistent with the enhancer being functionally required during early larval stages and becoming dispensable thereafter. The temporal decline in phenotype penetrance thus reflects the progressive loss of apE sensitivity to dCas9-mediated repression, providing a precise estimate of when its activity is no longer required for wing morphogenesis.”

      (4) The authors have not managed to explain the AP phenotype. Thus, this work opens many unresolved questions and does not resolve the title, which is a big overstatement. Thus, strengths (technically excellent), weakness (there is not much to learn about wing development and apterous regulation from these results besides the incremental identification of 4 additional TFs mediating the regulation of ap expression by their ability to phenocopy regulatory mutations of the apterous gene).

      As mentioned in response to reviewer 1, we have indeed no concrete explanation  for why the P compartment seems more sensitive to mutations. We have now further discussed this point (see below paragraph, now included in  the discussion). As for how the adult phenotypes arise from the mutant wing discs, we have a good idea (see Supplementary figure 7 and Figure 2). 

      We are pleased to hear that the reviewer considers our article technically valuable. Therefore, we have reformulated the title such as the technical merits play a bigger role in it:

      ”in situ mutational screening and CRISPR interference demonstrate that the apterous Early enhancer is required for developmental boundary positioning”

      Paragraph added to the discussion:

      " Although apE is active throughout the dorsal compartment, its disruption leads to a preferential loss of ap expression in posterior cells. The asymmetric effect of apE perturbation on the anterior and posterior compartments suggests that apE transcriptional control is not equivalent across the A/P axis. Compartment-dependent differences in enhancer regulation have also been documented in other developmental contexts; for example, the Distal-less DMX-R element is interpreted through distinct cofactor combinations (Sloppy paired anteriorly and Engrailed posteriorly) (Gebelein et al., 2004), and specific mutations within DMX-R preferentially disrupt enhancer function in anterior versus posterior cells. It is possible that apE is more sensitive to misregulation due to differential transcriptional regulation across compartments. Nevertheless, we cannot exclude the possibility that the posterior bias we observe arises not from enhancer logic per se, but from intrinsic differences in tissue architecture or the dynamics of boundary positioning during wing disc development.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Formatting of references should be checked throughout the manuscript

      Reviewer #2 (Recommendations For The Authors):

      Here, I note a few points that would help clarify the manuscript and connect it with a broader community.

      Figure 1: it could help the reader to add the landing site genetic scheme to the main figure.

      In a first draft that was exactly the original configuration, but after comparing both versions we determined that the presence of the landing site removes a bit of the focus of the phenotypes.

      Figure 1: what species were used for the conservation alignment? Further details would be nice to add here.

      We have now added a section of bioinformatical analysis, which was missing in the original manuscript:

      Sequence conservation of the OR463 fragment within the ap upstream intergenic region was analysed across different dipteran species using the “Cons 124 Insects” multiple-alignment track of the D. melanogaster dm6 genome on the UCSC Genome Browser (Kent et al., 2002, https://genome.ucsc.edu). Conservation scores were obtained from the phastCons (Siepel et al., 2005) and used to delineate conserved and less conserved blocks within OR463. Conserved transcription factor binding sites were predicted with MotEvo (Arnold et al., 2011), which defined four conserved modules (m1–m4) and six inter-modules (N1–N6). Additional motif analysis was performed using the JASPAR CORE Insecta database and the Target Explorer tool to cross-validate conserved binding-site predictions and refine motif assignments within the enhancer.

      From Figure 2: I would consider moving the model or portions of it to a main figure. These models, while descriptive, really help make the manuscript more approachable. Note that eLife does not have forced figure requirements.

      We have adapted the reviewer’s suggestion and we are very grateful for it. We think the figure has greatly improved. The final figure now highlights a small part of the model, which is still included in the Supplementary Figure.

      Figure 5: This figure is fantastic, and the results are particularly important. I would recommend increasing the weight of the arrows from D to E, making it more obvious. Did the authors consider any temperature or other perturbations to look at robustness? They mention "robustness" a few times, and this could be an excellent system to explore a bit further. For panels F and G, it would be nice to have a bit of biochemistry here to test the spacing requirements' effects on the distances (but it's great phenotypical data, regardless).

      We have chosen a darker grey to highlight the lines. 

      We appreciate the reviewer’s suggestions. With respect to robustness assays, such as temperature perturbations, we agree that the apE enhancer would be a suitable system for such experiments. However, these analyses would move the study beyond its current scope, which is focused on defining the regulatory logic of boundary positioning through mutational dissection and CRISPRi. We therefore prefer not to expand the work in this direction here, but we note that this would be an interesting avenue for future investigation.

      Similarly, biochemical assays probing spacing requirements would provide additional mechanistic insight but would represent a separate line of work. In this manuscript, we aimed to establish the functional consequences of motif spacing using in vivo genetic and phenotypic analyses, which we believe sufficiently support our conclusions.

      Thank you for the insight.

      Discussion: To the point "most point mutations or short deletions in enhancer regions have little effect on gene expression" I would push the authors to discuss their work in relation to Fuqua et al., (Nature 2020) and Kvon et al., (Cell 2020). Their work is consistent with enhancers being sensitive to mutations, and this warrants further discussion because it could be important for the transcription field.

      Hox genes as pioneer factors, I would recommend citing Loker et al., (Curr Biol 2021), as an example of Hox genes functioning as a pioneer factor.

      We thank the reviewer for this suggestion. We have now added a short paragraph in the Discussion noting how our observations may relate to the mutational patterns described in Fuqua et al. (2020) and Kvon et al. (2020), while keeping the interpretation tentative. The text now says:

      “Recent large-scale enhancer mutagenesis studies have shown that the mutational consequences within enhancers can vary widely. In some cases, many nucleotide positions appear tolerant to single-base changes and only a small subset of mutations produce clear functional effects (Kvon et al., 2020). In other enhancers, regulatory information is distributed more densely, and mutations at multiple positions can alter output (Fuqua et al., 2020). Together, these studies illustrate that enhancer sensitivity is not uniform but depends on enhancer-specific features such as motif organization, cooperativity, and redundancy. Within this broader landscape, the apE enhancer appears to represent a particularly sensitive case.”

      We also included a citation to Loker et al. (2021) in connection with the possible pioneer-like contribution of HOX input to apE.

      We would like to thank all reviewers for their effort.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      I read the paper by Parrotta et al with great interest. The authors are asking an interesting and important question regarding pain perception, which is derived from predictive processing accounts of brain function. They ask: If the brain indeed integrates information coming from within the body (interoceptive information) to comprise predictions about the expected incoming input and how to respond to it, could we provide false interoceptive information to modulate its predictions, and subsequently alter the perception of such input? To test this question, they use pain as the input and the sounds of heartbeats (falsified or accurate) as the interoceptive signal.

      Strengths:

      I found the question well-established, interesting, and important, with important implications and contributions for several fields, including neuroscience of prediction-perception, pain research, placebo research, and health psychology. The paper is well-written, the methods are adequate, and the findings largely support the hypothesis of the authors. The authors carried out a control experiment to rule out an alternative explanation of their finding, which was important.

      Weaknesses:

      I will list here one theoretical weakness or concern I had, and several methodological weaknesses.

      The theoretical concern regards what I see as a misalignment between a hypothesis and a result, which could influence our understanding of the manipulation of heartbeats, and its meaning: The authors indicate from prior literature and find in their own findings, that when preparing for an aversive incoming stimulus, heartbeats *decrease*. However, in their findings, manipulating the heartbeats that participants hear to be slower than their own prior to receiving a painful stimulus had *no effect* on participants' actual heartbeats, nor on their pain perceptions. What authors did find is that when listening to heartbeats that are *increased* in frequency - that was when their own heartbeats decreased (meaning they expected an aversive stimulus) and their pain perceptions increased.

      This is quite complex - but here is my concern: If the assumption is that the brain is collecting evidence from both outside and inside the body to prepare for an upcoming stimulus, and we know that *slowing down* of heartbeats predicts an aversive stimulus, why is it that participants responded in a change in pain perception and physiological response when listened to *increased heartbeats* and not decreased? My interpretation is that the manipulation did not fool the interoceptive signals that the brain collects, but rather the more conscious experience of participants, which may then have been translated to fear/preparation for the incoming stimulus. As the authors indicate in the discussion (lines 704-705), participants do not *know* that decreased heartbeats indicate upcoming aversive stimulus, and I would even argue the opposite - the common knowledge or intuitive response is to increase alertness when we hear increased heartbeats, like in horror films or similar scenarios. Therefore, the unfortunate conclusion is that what the authors assume is a manipulation of interoception - to me seems like a manipulation of participants' alertness or conscious experience of possible danger. I hope the (important) distinction between the two is clear enough because I find this issue of utmost importance for the point the paper is trying to make. If to summarize in one sentence - if it is decreased heartbeats that lead the brain to predict an approaching aversive input, and we assume the manipulation is altering the brain's interoceptive data collection, why isn't it responding to the decreased signal? --> My conclusion is, that this is not in fact a manipulation of interoception, unfortunately

      We thank the reviewer for their comment, which gives us the opportunity to clarify what we believe is a theoretical misunderstanding that we have not sufficiently made clear in the previous version of the manuscript. The reviewer suggests that a decreased heart rate itself might act as an internal cue for a forthcoming aversive stimulus, and questions why our manipulation of slower heartbeats then did not produce measurable effects.

      The central point is this: decreased heart rate is not a signal the brain uses to predict a threat, but is a consequence of the brain having already predicted the threat. This distinction is crucial. The well-known anticipatory decrease of heartrate serves an allostatic function: preparing the body in advance so that physiological responses to the actual stressor (such as an increase in sympathetic activation) do not overshoot. In other words, the deceleration is an output of the predictive model, not an input from which predictions are inferred. It would be maladaptive for the brain to predict threat through a decrease in heartrate, as this would then call for a further decrease, creating a potential runaway cycle.

      Instead, increased heart rate is a salient and evolutionarily conserved cue for arousal, threat, and pain. This association is reinforced both culturally - for example, through the use of accelerating heartbeats in films and media to signal urgency, as R1 mentions - and physiologically, as elevated heart rates reliably occur in response to actual (not anticipated) stressors. Decreased heartrates, in contrast, are reliably associated with the absence of stressors, for example during relaxation and before (and during) sleep. Thus, across various everyday experiences, increased (instead of decreased) heartrates are robustly associated with actual stressors, and there is no a priori reason to assume that the brain would treat decelerating heartrates as cue for threat. As we argued in previous work, “the relationship between the increase in cardiac activity and the anticipation of a threat may have emerged from participants’ first-hand experience of increased heart rates to actual, not anticipated, pain” (Parrotta et al., 2024). The changes in heart rate and pain perception that we hypothesize (and observe) are therefore fully in line with the prior literature on the anticipatory compensatory heartrate response (Bradley et al., 2008, 2005; Colloca et al., 2006; Lykken et al., 1972; Taggart et al., 1976; Tracy et al., 2017; Skora et al., 2022), as well as with Embodied Predictive Coding models (Barrett & Simmons, 2015; Pezzulo, 2014; Seth, 2013; Seth et al., 2012), which assume that our body is regulated through embodied simulations that anticipate likely bodily responses to upcoming events, thereby enabling anticipatory or allostatic regulation of physiological states (Barrett, 2017).

      We now add further explanation to this point to the Discussion (lines 740-758) and Introduction (lines 145-148; 154-156) of our manuscript to make this important point clearer.

      Barrett, L. F., & Simmons, W. K. (2015). Interoceptive predictions in the brain. Nature reviews neuroscience, 16(7), 419-429.

      Barrett, L. F. (2017). The theory of constructed emotion: An active inference account of interoception and categorization. Social cognitive and affective neuroscience, 12(1), 1-23.

      Bradley, M. M., Moulder, B., & Lang, P. J. (2005). When good things go bad: The reflex physiology of defense. Psychological science, 16(6), 468-473.

      Bradley, M. M., Silakowski, T., & Lang, P. J. (2008). Fear of pain and defensive activation. PAIN®, 137(1), 156-163.

      Colloca, L., Petrovic, P., Wager, T. D., Ingvar, M., & Benedetti, F. (2010). How the number of learning trials affects placebo and nocebo responses. Pain®, 151(2), 430-439.

      Lykken, D., Macindoe, I., & Tellegen, A. (1972). Preception: Autonomic response to shock as a function of predictability in time and locus. Psychophysiology, 9(3), 318-333.

      Taggart, P., Hedworth-Whitty, R., Carruthers, M., & Gordon, P. D. (1976). Observations on electrocardiogram and plasma catecholamines during dental procedures: The forgotten vagus. British Medical Journal, 2(6039), 787-789.

      Tracy, L. M., Gibson, S. J., Georgiou-Karistianis, N., & Giummarra, M. J. (2017). Effects of explicit cueing and ambiguity on the anticipation and experience of a painful thermal stimulus. PloS One, 12(8), e0183650.

      Parrotta, E., Bach, P., Perrucci, M. G., Costantini, M., & Ferri, F. (2024). Heart is deceitful above all things: Threat expectancy induces the illusory perception of increased heartrate. Cognition, 245, 105719.

      Pezzulo, G. (2014). Why do you fear the bogeyman? An embodied predictive coding model of perceptual inference. Cognitive, Affective & Behavioral Neuroscience, 14(3), 902-911.

      Seth, A., Suzuki, K., & Critchley, H. (2012). An Interoceptive Predictive Coding Model of Conscious Presence. Frontiers in Psychology, 2. https://www.frontiersin.org/articles/10.3389/fpsyg.2011.00395

      Seth, A. K. (2013). Interoceptive inference, emotion, and the embodied self. Trends in Cognitive Sciences, 17(11), 565-573.

      Skora, L. I., Livermore, J. J. A., & Roelofs, K. (2022). The functional role of cardiac activity in perception and action. Neuroscience & Biobehavioral Reviews, 104655.

      I will add that the control experiment - with an exteroceptive signal (knocking of wood) manipulated in a similar manner - could be seen as evidence of the fact that heartbeats are regarded as an interoceptive signal, and it is an important control experiment, however, to me it seems that what it is showing is the importance of human-relevant signals to pain prediction/perception, and not directly proves that it is considered interoceptive. For example, it could be experienced as a social cue of human anxiety/fear etc, and induce alertness.

      The reviewer asks us to consider whether our measured changes in pain response happen not because the brain treats the heartrate feedback in Experiment 1 as interoceptive stimulus, but because heartbeat sounds could have signalled threat on a more abstract, perhaps metacognitive or affective, level, in contrast to the less visceral control sounds in Experiment 2. We deem this highly unlikely for several reasons.

      First, as we point out in our response to Reviewer 3 (Point 3), if this were the case, the different sounds in both experiments should have induced overall (between-experiment) differences in pain perception and heart rate, induced by the (supposedly) generally more threatening heart beat sounds. However, when we added such comparisons, no such between-experiment differences were obtained (See Results Experiment 2, and Supplementary Materials, Cross-experiment analysis between-subjects model). Instead, we only find a significant interaction between experiment and feedback (faster, slower). Thus, it is not the heartbeat sounds per se that induce the measured changes to pain perception, but the modulation of their rate, and that identical changes to the rate of non-heartrate sounds produce no such effects. In other words, pain perception is sensitive to a change in heart rate feedback, as we predicted, instead of the overall presence of heartbeat sounds (as one would need to predict if heart beat sounds had more generally induced threat or stress).

      Second, one may suspect that it is precisely the acceleration of heartrate feedback that could act as cue to arousal, while accelerated exteroceptive feedback would not. However, if this were the case, one would need to predict a general heart rate increase with accelerated feedback, as this is the general physiological marker of increasing alertness and arousal (e.g. Tousignant-Laflamme et al., 2005; Terkelsen et al., 2005; for a review, see Forte et al., 2022). However, the data shows the opposite, with real heartrates decreasing when the heartrate feedback increases. This result is again fully in line with the predicted interoceptive consequences of accelerated heartrate feedback, which mandates an immediate autonomic regulation, especially when preparing for an anticipated stressor.

      Third, our view is further supported by neurophysiological evidence showing that heartbeat sounds, particularly under the belief they reflect one’s own body, are not processed merely as generic aversive or “human-relevant” signals. For instance, Vicentin et al. (2024) showed that simulated faster heartbeat sounds elicited stronger EEG alpha-band suppression, indicative of increased cortical activation  over frontocentral and right frontal areas, compatible with the localization of brain regions contributing to interoceptive processes (Kleint et al., 2015). Importantly, Kleint et al. also demonstrated via fMRI that heartbeat sounds, compared to acoustically matched tones, selectively activate bilateral anterior insula and frontal operculum, key hubs of the interoceptive network. This suggests that the semantic identity of the sound as a heartbeat is sufficient to elicit internal body representations, despite its exteroceptive nature. Further evidence comes from van Elk et al. (2014), who found that heartbeat sounds suppress the auditory N1 component, a neural marker of sensory attenuation typically associated with self-generated or predicted stimuli. The authors interpret this as evidence that the brain treats heartbeat sounds as internally predicted bodily signals, supporting interoceptive predictive coding accounts in which exteroceptive cues (i.e., auditory cardiac feedback) are integrated with visceral information to generate coherent internal body representations.

      Finally, it is worth noting that the manipulation of heartrate feedback in our study elicited measurable compensatory changes in participants’ actual heart rate. This is striking compared to our previous work (Parrotta et al., 2024), wherein we used a highly similar design as here, combined with a very strong threat manipulation. Specifically, we presented participants with highly salient threat cues (knives directed at an anatomical depiction of a heart), which predicted forthcoming pain with 100% validity (compared to flowers that did predict the absence of pain with 100%). In other words, these cues perfectly predicted actual pain, through highly visceral stimuli. Nevertheless, we found no measurable decrease in actual heartrate. From an abstract threat perspective, it is therefore striking that the much weaker manipulation of slightly increased or decreased heartrates we used here would induce such a change. The difference therefore suggests that what caused the response here is not due to an abstract feeling of threat, but because the brain indeed treated the increased heartrate feedback as an interoceptive signal for (stressor-induced) sympathetic activation, which would then be immediately down-regulated.

      Together, we hope you agree that these considerations make a strong case against a non-specific, arousal or alertness-related explanation of our data. We now make this point clearer in the new paragraph of the Discussion (Accounting for general unspecific contributionslines 796-830), and have added the relevant between experiment comparisons to the Results of Experiment 2.

      Forte, G., Troisi, G., Pazzaglia, M., Pascalis, V. D., & Casagrande, M. (2022). Heart rate variability and pain: a systematic review. Brain sciences, 12(2), 153.

      Vicentin, S., Guglielmi, S., Stramucci, G., Bisiacchi, P., & Cainelli, E. (2024). Listen to the beat: behavioral and neurophysiological correlates of slow and fast heartbeat sounds. International Journal of Psychophysiology, 206, 112447.

      Kleint, N. I., Wittchen, H. U., & Lueken, U. (2015). Probing the interoceptive network by listening to heartbeats: an fMRI study. PloS one, 10(7), e0133164.

      Parrotta, E., Bach, P., Perrucci, M. G., Costantini, M., & Ferri, F. (2024). Heart is deceitful above all things: Threat expectancy induces the illusory perception of increased heartrate. Cognition, 245, 105719.

      Terkelsen, A. J., Mølgaard, H., Hansen, J., Andersen, O. K., & Jensen, T. S. (2005). Acute pain increases heart rate: differential mechanisms during rest and mental stress. Autonomic Neuroscience, 121(1-2), 101-109.

      Tousignant-Laflamme, Y., Rainville, P., & Marchand, S. (2005). Establishing a link between heart rate and pain in healthy subjects: a gender effect. The journal of pain, 6(6), 341-347.

      van Elk, M., Lenggenhager, B., Heydrich, L., & Blanke, O. (2014). Suppression of the auditory N1-component for heartbeat-related sounds reflects interoceptive predictive coding. Biological psychology, 99, 172-182.

      Several additional, more methodological weaknesses include the very small number of trials per condition - the methods mention 18 test trials per participant for the 3 conditions, with varying pain intensities, which are later averaged (and whether this is appropriate is a different issue). This means 6 trials per condition, and only 2 trials per condition and pain intensity. I thought that this number could be increased, though it is not a huge concern of the paper. It is, however, needed to show some statistics about the distribution of responses, given the very small trial number (see recommendations for authors). The sample size is also rather small, on the verge of "just right" to meet the required sample size according to the authors' calculations.

      We provide detailed responses to these points in the “Recommendations for The Authors” section, where each of these issues is addressed point by point in response to the specific questions raised.

      Finally, and just as important, the data exists to analyze participants' physiological responses (ECG) after receiving the painful stimulus - this could support the authors' claims about the change in both subjective and objective responses to pain. It could also strengthen the physiological evidence, which is rather weak in terms of its effect. Nevertheless, this is missing from the paper.

      This is indeed an interesting point, and we agree that analyzing physiological responses such as ECG following the painful stimulus could offer additional insights into the objective correlates of pain. However, it is important to clarify that the experiment was not designed to investigate post-stimulus physiological responses. Our primary focus was on the anticipatory processes leading up to the pain event. Notably, in the time window immediately following the stimulus - when one might typically expect to observe physiological changes such as an increase in heart rate - participants were asked to provide subjective ratings of their nociceptive experience. It is therefore not a “clean” interval that would lend itself for measurement, especially as a substantial body of evidence indicates that one’s heart rate is strongly modulated by higher-order cognitive processes, including attentional control, executive functioning, decision-making and action itself (e.g., Forte et al., 2021a; Forte et al., 2021b; Luque-Casado et al., 2016).

      This limitation is particularly important as the induced change in pain ratings by our heart rate manipulation is substantially smaller than the changes in heart rate induced by actual pain (e.g., Loggia et al., 2011). To confirm this for our study, we simply estimated how much change in heart rate is produced by a change in actual stimulus intensity in the initial no feedback phase of our experiment. There, we find that a change between stimulus intensities 2 and 4 induces a NPS change of 32.95 and a heart rate acceleration response of 1.19 (difference in heart rate response relative to baseline, Colloca et al., 2006), d = .52, p < .001. The change of NPS induced by our implicit heart rate manipulation, however, is only a seventh of this (4.81 on the NPS). This means that the expected effect size of heart rate acceleration produced by our manipulation would only be d = .17. A power analysis, using GPower, reveals that a sample size of n = 266 would be required to detect such an effect, if it exists. Thus, while we agree that this is an exciting hypothesis to be tested, it requires a specifically designed study, and a much larger sample than was possible here.

      Colloca, L., Benedetti, F., & Pollo, A. (2006). Repeatability of autonomic responses to pain anticipation and pain stimulation. European Journal of Pain, 10(7), 659-665.

      Forte, G., Morelli, M., & Casagrande, M. (2021a). Heart rate variability and decision-making: Autonomic responses in making decisions. Brain sciences, 11(2), 243.

      Forte, G., Favieri, F., Oliha, E. O., Marotta, A., & Casagrande, M. (2021b). Anxiety and attentional processes: the role of resting heart rate variability. Brain sciences, 11(4), 480.

      Loggia, M. L., Juneau, M., & Bushnell, M. C. (2011). Autonomic responses to heat pain: Heart rate, skin conductance, and their relation to verbal ratings and stimulus intensity. PAIN®, 152(3), 592-598.

      Luque-Casado, A., Perales, J. C., Cárdenas, D., & Sanabria, D. (2016). Heart rate variability and cognitive processing: The autonomic response to task demands. Biological psychology, 113, 83-90

      I have several additional recommendations regarding data analysis (using an ANOVA rather than multiple t-tests, using raw normalized data rather than change scores, questioning the averaging across 3 pain intensities) - which I will detail in the "recommendations for authors" section.

      We provide detailed responses to these points in the “Recommendations for The Authors” section, where each of these issues is addressed point by point in response to the specific questions raised.

      Conclusion:

      To conclude, the authors have shown in their findings that predictions about an upcoming aversive (pain) stimulus - and its subsequent subjective perception - can be altered not only by external expectations, or manipulating the pain cue, as was done in studies so far, but also by manipulating a cue that has fundamental importance to human physiological status, namely heartbeats. Whether this is a manipulation of actual interoception as sensed by the brain is - in my view - left to be proven.

      Still, the paper has important implications in several fields of science ranging from neuroscience prediction-perception research, to pain and placebo research, and may have implications for clinical disorders, as the authors propose. Furthermore, it may lead - either the authors or someone else - to further test this interesting question of manipulation of interoception in a different or more controlled manner.

      I salute the authors for coming up with this interesting question and encourage them to continue and explore ways to study it and related follow-up questions.

      We sincerely thank the reviewer for the thoughtful and encouraging feedback. We hope our responses to your points below convince you a bit more that what we are measuring does indeed capture interoceptive processes, but we of course fully acknowledge that additional measures - for example from brain imaging (or computational modelling, see Reviewer 3) - could further support our interpretation, and highlights in the Limitations and Future directions section.

      Reviewer #2 (Public Review):

      In this manuscript, Parrotta et al. tested whether it is possible to modulate pain perception and heart rate by providing false HR acoustic feedback before administering electrical cutaneous shocks. To this end, they performed two experiments. The first experiment tested whether false HR acoustic feedback alters pain perception and the cardiac anticipatory response. The second experiment tested whether the same perceptual and physiological changes are observed when participants are exposed to a non-interoceptive feedback. The main results of the first experiment showed a modulatory effect for faster HR acoustic feedback on pain intensity, unpleasantness, and cardiac anticipatory response compared to a control (acoustic feedback congruent to the participant's actual HR). However, the results of the second experiment also showed an increase in pain ratings for the faster non-interoceptive acoustic feedback compared to the control condition, with no differences in pain unpleasantness or cardiac response.

      The main strengths of the manuscript are the clarity with which it was written, and its solid theoretical and conceptual framework. The researchers make an in-depth review of predictive processing models to account for the complex experience of pain, and how these models are updated by perceptual and active inference. They follow with an account of how pain expectations modulate physiological responses and draw attention to the fact that most previous studies focus on exteroceptive cues. At this point, they make the link between pain experience and heart rate changes, and introduce their own previous work showing that people may illusorily perceive a higher cardiac frequency when expecting painful stimulation, even though anticipating pain typically goes along with a decrease in HR. From here, they hypothesize that false HR acoustic feedback evokes more intense and unpleasant pain perception, although the actual HR actually decreases due to the orienting cardiac response. Furthermore, they also test the hypothesis that an exteroceptive cue will lead to no (or less) changes in those variables. The discussion of their results is also well-rooted in the existing bibliography, and for the most part, provides a credible account of the findings.

      Thank you for the clear and thoughtful review. We appreciate your positive comments on the manuscript’s clarity, theoretical framework, and interpretation of results.

      The main weaknesses of the manuscript lies in a few choices in methodology and data analysis that hinder the interpretation of the results and the conclusions as they stand.

      The first peculiar choice is the convoluted definition of the outcomes. Specifically, pain intensity and unpleasantness are first normalized and then transformed into variation rates (sic) or deltas, which makes the interpretation of the results unnecessarily complicated. This is also linked to the definitions of the smallest effect of interest (SESOI) in terms of these outcomes, which is crucial to determining the sample size and gauging the differences between conditions. However, the choice of SESOI is not properly justified, and strangely, it changes from the first experiment to the second.

      We thank the reviewer for this important observation. In the revised manuscript, we have made substantial changes and clarifications to address both aspects of this concern: (1) the definition of outcome variables and their normalization, and (2) the definition of the SESOI.

      First, As explained in our response to Reviewer #1, we have revised the analyses and removed the difference-based change scores from the main results, addressing concerns about interpretability. However, we retained the normalization procedure: all variables (heart rate, pain intensity, unpleasantness) are normalized relative to the no-feedback baseline using a standard proportional change formula (X−bX)/bX(X - bX)/bX(X−bX)/bX, where X is the feedback-phase mean and bX is the no-feedback baseline. This is a widely used normalization procedure (e.g., Bartolo et al., 2013; Cecchini et al., 2020). This method controls for interindividual variability by expressing responses relative to each participant’s own baseline. The resulting normalized values are then used directly in all analyses, and not further transformed into deltas.

      To address potential concerns about this baseline correction approach and its interpretability, we also conducted a new set of supplementary analyses (now reported in the supplementary materials) that include the no-feedback condition explicitly in the models, rather than treating it as a baseline for normalization. These models confirm that our main effects are not driven by the choice of normalization and hold even when no-feedback is analyzed as an independent condition. The new analyses and results are now reported in the Supplementary Materials.

      Second, concerning the SESOI values and their justification: The difference in SESOI values between Experiment 1 and Experiment 2 reflects the outcome of sensitivity analyses conducted for each dataset separately, rather than a post-hoc reinterpretation of our results. Specifically, we followed current methodological recommendations (Anderson, Kelley & Maxwell, 2017; Albers & Lakens, 2017; Lakens, 2022), which advise against estimating statistical power based on previously published effect sizes, especially when working with novel paradigms or when effect sizes in the literature may be inflated or imprecise. Instead, we used the sensitivity analysis function in G*Power (Version 3.1) to determine the smallest effect size our design was capable of detecting with high statistical power (90%), given the actual sample size, test type, and alpha level used in each experiment. This is a prospective, design-based estimation rather than a post-hoc analysis of observed effects. The slight differences in SESOI are due to more participants falling below our exclusions criteria in Experiment 2, leading to slightly larger effect sizes that can be detected (d = 0.62 vs d = 0.57). Importantly, both experiments remain adequately powered to detect effects of a size commonly reported in the literature on top-down pain modulation. For instance, Iodice et al. (2019) reported effects of approximately d = 0.7, which is well above the minimum detectable thresholds of our designs.

      We have now clarified the logic in the Participant section of Experiment 1 (193-218).

      Anderson, S. F., Kelley, K., & Maxwell, S. E. (2017). Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty. Psychological Science, 28(11), 1547-1562.

      Bartolo, M., Serrao, M., Gamgebeli, Z., Alpaidze, M., Perrotta, A., Padua, L., Pierelli, F., Nappi, G., & Sandrini, G. (2013). Modulation of the human nociceptive flexion reflex by pleasant and unpleasant odors. PAIN®, 154(10), 2054-2059.

      Cecchini, M. P., Riello, M., Sandri, A., Zanini, A., Fiorio, M., & Tinazzi, M. (2020). Smell and taste dissociations in the modulation of tonic pain perception induced by a capsaicin cream application. European Journal of Pain, 24(10), 1946-1955.

      Lakens, D. (2022). Sample size justification. Collabra: psychology, 8(1), 33267.

      Albers, C., & Lakens, D. (2018). When power analyses based on pilot data are biased: Inaccurate effect size estimators and follow-up bias. Journal of experimental social psychology, 74, 187-195.

      Furthermore, the researchers propose the comparison of faster vs. slower delta HR acoustic feedback throughout the manuscript when the natural comparison is the incongruent vs. the congruent feedback.

      We very much disagree that the natural comparison is congruent vs incongruent feedback. First, please note that congruency simply refers to whether the heartrate feedback was congruent with (i.e., matched) the participant’s heartrate measurements in the no feedback trials, or whether it was incongruent, and was therefore either faster or slower than this baseline frequency. As such, simply comparing congruent with incongruent feedback could only indicate that pain ratings change when the feedback does not match the real heart rate, irrespective of whether it is faster or slower. Such a test can therefore only reveal potential general effects of surprise or salience, when the feedback heartrate does not match the real one.

      We therefore assume that the reviewer specifically refers to the comparison of congruent vs incongruent faster feedback. However, this is not a good test either, as this comparison is, by necessity, confounded with the factor of surprise described above. In other words, if a difference would be found, it would not be clear if it emerges because, as we assume, that faster feedback is represented as an interoceptive signal for threat, or simply because participants are surprised about heartrate feedback that diverges from their real heartrate. Note that even a non-significant result in the analogous comparison of congruent vs incongruent slower feedback would not be able to resolve this confound, as in null hypothesis testing the absence of a significant effect does, per definition, not indicate that there is no effect - only that it could not be detected here.

      Instead, the only possible test of our hypothesis is the one we have designed our experiment around and focussed on with our central t-test: the comparison of incongruent faster with incongruent slower feedback. This keeps any possible effects of surprise/salience from generally altered feedback constant and allows us to test our specific hypothesis: that real heart rates will decrease and pain ratings will increase when receiving false interoceptive feedback about increased compared to decreasing heartrates. Note that this test of faster vs slower feedback is also statistically the most appropriate, as it collapses our prediction onto a single and highest-powered hypothesis test: As faster and slower heartrate feedback are assumed to induce effects in the opposite direction, the effect size of their difference is, per definition, double than the averaged effect size for the two separate tests of faster vs congruent feedback and slower vs congruent feedback.

      That being said, we also included comparisons with the congruent condition in our revised analysis, in line with the reviewer’s suggestion and previous studies. These analyses help explore potential asymmetries in the effect of false feedback. While faster feedback (both interoceptive and exteroceptive) significantly modulated pain relative to congruent feedback, the slower feedback did not, consistent with previous literature showing stronger effects for arousal-increasing cues (e.g., Valins, 1966; Iodice et al., 2019). To address this point, in the revised manuscript we have added a paragraph to the Data Analysis section of Experiment 1 (lines 405-437) to make this logic clearer.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      Iodice, P., Porciello, G., Bufalari, I., Barca, L., & Pezzulo, G. (2019). An interoceptive illusion of effort induced by false heart-rate feedback. Proceedings of the National Academy of Sciences, 116(28), 13897-13902.

      This could be influenced by the fact that the faster HR exteroceptive cue in experiment 2 also shows a significant modulatory effect on pain intensity compared to congruent HR feedback, which puts into question the hypothesized differences between interoceptive vs. exteroceptive cues. These results could also be influenced by the specific choice of exteroceptive cue: the researchers imply that the main driver of the effect is the nature of the cue (interoceptive vs. exteroceptive) and not its frequency. However, they attempt to generalize their findings using knocking wood sounds to all possible sounds, but it is possible that some features of these sounds (e.g., auditory roughness or loomingness) could be the drivers behind the observed effects.

      We appreciate this thoughtful comment. We agree that low-level auditory features can potentially introduce confounds in the experimental design, and we acknowledge the importance of distinguishing these factors from the higher-order distinction that is central to our study: whether the sound is perceived as interoceptive (originating from within the body) or exteroceptive (perceived as external). To this end, the knocking sound was chosen not for its specific acoustic profile, but because it lacked bodily relevance, thus allowing us to test whether the same temporal manipulations (faster, congruent, slower) would have different effects depending on whether the cue was interpreted as reflecting an internal bodily state or not. In this context, the exteroceptive cue served as a conceptual contrast rather than an exhaustive control for all auditory dimensions.

      Several aspects of our data make it unlikely that the observed effects are driven by unspecific acoustic characteristics of the sounds used in the exteroceptive and interoceptive experiments (see also our responses to Reviewer 1 and Reviewer 3 who raised similar points).

      First, if the knocking sound had inherent acoustic features that strongly influenced perception or physiological responses, we would expect it to have produced consistent effects across all feedback conditions (Faster, Slower, Congruent), regardless of the interpretive context. This would have manifested as an overall difference between experiments in the between-subjects analyses and in the supplementary mixed-effects models that included Experiment as a fixed factor. Yet, we observed no such main effects in any of our variables. Instead, significant differences emerged only in specific theoretically predicted comparisons (e.g., Faster vs. Slower), and critically, these effects depended on the cue type (interoceptive vs. exteroceptive), suggesting that perceived bodily relevance, rather than a specific acoustic property, was the critical modulator. In other words, any alternative explanation based on acoustic features would need to be able to explain why these acoustic properties would induce not an overall change in heart rate and pain perception (i.e., similarly across slower, faster, and congruent feedback), but the brain’s response to changes in the rate of this feedback – increasing pain ratings and decreasing heartrates for faster relative to slower feedback. We hope you agree that a simple effect of acoustic features would not predict such a sensitivity to the rate with which the sound was played.

      Please refer to our responses to Reviewers 1 and 2 for further aspects of the data, arguing strongly against other features associated with the sounds (e.g., alertness, arousal) could be responsible for the results, as the data pattern again goes in the opposite direction than that predicted by such accounts (e.g., faster heartrate feedback decreased real heartrate, instead of increasing them, as would be expected if accelerated heartrate feedback increased arousal).

      Finally, to further support this interpretation, we refer to neurophysiological evidence showing that heartbeat sounds are not processed as generic auditory signals, but as internal, bodily relevant cues especially when believed to reflect one’s own physiological state. For instance, fMRI research (Kleint et al., 2015) shows that heartbeat sounds engage key interoceptive regions such as the anterior insula and frontal operculum more than acoustically matched control tones. EEG data (Vicentin et al., 2024) showed that faster heartbeat sounds produce stronger alpha suppression over frontocentral areas, suggesting enhanced processing in networks associated with interoceptive attention. Moreover, van Elk et al. (2014) found that heartbeat sounds attenuate the auditory N1 response, a neural signature typically linked to self-generated or predicted bodily signals. These findings consistently demonstrate that heartbeats sounds are processed as interoceptive and self-generated signals, which is in line with our rationale that the critical factor at play concern whether it is semantically perceived as reflecting one’s own bodily state, rather than the physical properties of the sound.

      We now explicitly discuss these issues in the revised Discussion section (lines 740-758).

      Kleint, N. I., Wittchen, H. U., & Lueken, U. (2015). Probing the interoceptive network by listening to heartbeats: an fMRI study. PloS one, 10(7), e0133164.

      van Elk, M., Lenggenhager, B., Heydrich, L., & Blanke, O. (2014). Suppression of the auditory N1-component for heartbeat-related sounds reflects interoceptive predictive coding. Biological psychology, 99, 172-182.

      Vicentin, S., Guglielmi, S., Stramucci, G., Bisiacchi, P., & Cainelli, E. (2024). Listen to the beat: behavioral and neurophysiological correlates of slow and fast heartbeat sounds. International Journal of Psychophysiology, 206, 112447.

      Finally, it is noteworthy that the researchers divided the study into two experiments when it would have been optimal to test all the conditions with the same subjects in a randomized order in a single cross-over experiment to reduce between-subject variability. Taking this into consideration, I believe that the conclusions are only partially supported by the evidence. Despite of the outcome transformations, a clear effect of faster HR acoustic feedback can be observed in the first experiment, which is larger than the proposed exteroceptive counterpart. This work could be of broad interest to pain researchers, particularly those working on predictive coding of pain.

      We appreciate the reviewer’s suggestion regarding a within-subject crossover design. While such a design indeed offers increased statistical power by reducing interindividual variability (Charness, Gneezy, & Kuhn, 2012), we intentionally opted for a between-subjects design due to theoretical and methodological considerations specific to studies involving deceptive feedback. Most importantly, carryover effects are a major concern in deception paradigms. Participants exposed to one type of feedback initially (e.g., interoceptive), and then the other (exteroceptive) would be more likely to develop suspicion or adaptive strategies that would alter their responses. Such expectancy effects could contaminate results in a crossover design, particularly when participants realize that feedback is manipulated. In line with this idea, past studies on false cardiac feedback (e.g., Valins, 1966; Pennebaker & Lightner, 1980) often employed between-subjects or blocked designs to mitigate this risk.

      Pennebaker, J. W., & Lightner, J. M. (1980). Competition of internal and external information in an exercise setting. Journal of personality and social psychology, 39(1), 165.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      Reviewer #3 (Public Review):

      In their manuscript titled "Exposure to false cardiac feedback alters pain perception and anticipatory cardiac frequency", Parrotta and colleagues describe an experimental study on the interplay between false heart rate feedback and pain experience in healthy, adult humans. The experimental design is derived from Bayesian perspectives on interoceptive inference. In Experiment 1 (N=34), participants rated the intensity and unpleasantness of an electrical pulse presented to their middle fingers. Participants received auditory cardiac feedback prior to the electrical pulse. This feedback was congruent with the participant's heart rate or manipulated to have a higher or lower frequency than the participant's true heart rate (incongruent high/ low feedback). The authors find heightened ratings of pain intensity and unpleasantness as well as a decreased heart rate in participants who were exposed to the incongruent-high cardiac feedback. Experiment 2 (N=29) is equivalent to Experiment 1 with the exception that non-interoceptive auditory feedback was presented. Here, mean pain intensity and unpleasantness ratings were unaffected by feedback frequency.

      Strengths:

      The authors present interesting experimental data that was derived from modern theoretical accounts of interoceptive inference and pain processing.

      (1) The motivation for the study is well-explained and rooted within the current literature, whereas pain is the result of a multimodal, inferential process. The separation of nociceptive stimulation and pain experience is explained clearly and stringently throughout the text.

      (2) The idea of manipulating pain-related expectations via an internal, instead of an external cue, is very innovative.

      (3) An appropriate control experiment was implemented, where an external (non-physiological) auditory cue with parallel frequency to the cardiac cue was presented.

      (4) The chosen statistical methods are appropriate, albeit averaging may limit the opportunity for mechanistic insight, see weaknesses section.

      (5) The behavioral data, showing increased unpleasantness and intensity ratings after exposure to incongruent-high cardiac feedback, but not exteroceptive high-frequency auditory feedback, is backed up by ECG data. Here, the decrease in heart rate during the incongruent-high condition speaks towards a specific, expectation-induced physiological effect that can be seen as resulting from interoceptive inference.

      We thank the reviewer for their positive feedback. We are glad that the study’s theoretical foundation, innovative design, appropriate control conditions, and convergence of behavioral and physiological data were well received.

      Weaknesses:

      Additional analyses and/ or more extensive discussion are needed to address these limitations:

      (1) I would like to know more about potential learning effects during the study. Is there a significant change in ∆ intensity and ∆ unpleasantness over time; e.g. in early trials compared to later trials? It would be helpful to exclude the alternative explanation that over time, participants learned to interpret the exteroceptive cue more in line with the cardiac cue, and the effect is driven by a lack of learning about the slightly less familiar cue (the exteroceptive cue) in early trials. In other words, the heartbeat-like auditory feedback might be "overlearned", compared to the less naturalistic tone, and more exposure to the less naturalistic cue might rule out any differences between them w.r.t. pain unpleasantness ratings.

      We thank the reviewer for raising this important point. Please note that the repetitions in our task were relatively limited (6 trials per condition), which limits the potential influence of such differential learning effects between experiments. To address this concern, we performed an additional analysis, reported in the Supplementary Materials, using a Linear Mixed-Effects Model approach. This method allowed us to include "Trial" (the rank order of each trial) as a variable to account for potential time-on-task effects such as learning, adaptation, or fatigue (e.g., Möckel et al., 2015). All feedback conditions (no-feedback, congruent, faster, slower) and all stimulus intensity levels were included.

      Specifically, we tested the following models:

      Likert Pain Unpleasantness Ratings ~ Experiment × Feedback × StimInt × Trial + (StimInt + Trial | Subject)

      Numeric Pain Scale of Intensity Ratings ~ Experiment × Feedback × StimInt × Trial + (StimInt + Trial | Subject)

      In both models, no significant interactions involving Trial × Experiment or Trial × Feedback × Experiment were found. Instead, we just find generally larger effects in early trials compared to later ones (Main effect of Trial within each Experiment), similar to other cognitive illusions where repeated exposure diminishes effects. Thus, although some unspecific changes over time may have occurred (e.g., due to general task exposure), these changes did not differ systematically across experimental conditions (interoceptive vs. exteroceptive) or feedback types. However, we are fully aware that the absence of significant higher-order interactions does not conclusively rule out the possibility of learning-related effects. It is possible that our models lacked the statistical power to detect more subtle or complex time-dependent modulations, particularly if such effects differ in magnitude or direction across feedback conditions.

      We report the full description of these analyses and results in the Supplementary materials 1. Cross-experiment analysis (between-subjects model).

      (2) The origin of the difference in Cohen's d (Exp. 1: .57, Exp. 2: .62) and subsequently sample size in the sensitivity analyses remains unclear, it would be helpful to clarify where these values are coming from (are they related to the effects reported in the results? If so, they should be marked as post-hoc analyses).

      Following recommendations (Anderson, Kelley & Maxwell, 2017; Albers &  Lakens, 2017), we do not report theoretical power based on previously reported effect sizes as this neglects uncertainty around effect size measurements, especially for new effects for which no reliable expected effect size estimates can be derived across the literature. Instead, the power analysis is based on a sensitivity analysis, conducted in G*Power (Version 3.1). Importantly, these are not post-hoc analyses, as they are not based on observed effect sizes in our study, but derived a priori. Sensitivity analyses estimate effect sizes that our design is well-powered (90%) to detect (i.e. given target power, sample size, type of test), for the crucial comparison between faster and slower feedback in both experiments (Lakens, 2022). Following recommendations, we also report the smallest effect size this test can in principle detect in our study (SESOI, Lakens, 2022). This yields effect sizes of d = .57 in Experiment 1 and d = .62 in Experiment 2 at 90% power and SESOIs of d = .34 and .37, respectively. Note that values are slightly higher in Experiment 2, as more participants were excluded based on our exclusion criteria. Importantly, detectable effect sizes in both experiments are smaller than reported effect sizes for comparable top-down effects on pain measurements of d = .7 (Iodice et al., 2019).  We have now added more information to the power analysis sections to make this clearer (lines 208-217).

      Albers, C., & Lakens, D. (2018). When power analyses based on pilot data are biased: Inaccurate effect size estimators and follow-up bias. Journal of experimental social psychology, 74, 187-195.

      Anderson, S. F., Kelley, K., & Maxwell, S. E. (2017). Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty. Psychological Science, 28(11), 1547-1562.

      Lakens, D. (2022). Sample size justification. Collabra: psychology, 8(1), 33267.

      (3) As an alternative explanation, it is conceivable that the cardiac cue may have just increased unspecific arousal or attention to a larger extent than the exteroceptive cue. It would be helpful to discuss the role of these rather unspecific mechanisms, and how it may have differed between experiments.

      We thank the reviewer for raising this important point. We agree that, in principle, unspecific mechanisms such as increased arousal or attention driven by cardiac feedback could be an alternative explanation for the observed effects. However, several aspects of our data indicate that this is unlikely:

      (1) No main effect of Experiment on pain ratings:

      If the cardiac feedback had simply increased arousal or attention in a general (non-specific) way, we would expect a main effect of Experiment (i.e., interoceptive vs exteroceptive condition) on pain intensity or unpleasantness ratings, regardless of feedback frequency. However, such a main effect was never observed when we compared between experiments (see between-experiment t-tests in results, and in supplementary analyses). Instead, effects were specific to the manipulation of feedback frequency.

      (2) Heart rate as an arousal measure:

      Heart rate (HR) is a classical physiological index of arousal. If there had been an unspecific increase in arousal in the interoceptive condition, we would expect a main effect of Experiment on HR. However, no such main effect was found. Instead, our HR analyses revealed a significant interaction between feedback and experiment, suggesting that HR changes depended specifically on the feedback manipulation rather than reflecting a general arousal increase.

      (3) Arousal predicts faster, not slower, heart rates

      In Experiment 1, faster interoceptive cardiac feedback led to a slowdown in heartrates both when compared to slower feedback and to congruent cardiac feedback. This is in line with the predicted compensatory response to faster heart rates. In contrast, if faster feedback would have only generally increased arousal, heart rates should have increased instead of decreased, as indicated by several prior studies (Tousignant-Laflamme et al., 2005; Terkelsen et al., 2005; for a review, see Forte et al., 2022), predicting the opposite pattern of responses than was found in Experiment 1.

      Taken together, these findings indicate that the effects observed are unlikely to be driven by unspecific arousal or attention mechanisms, but rather are consistent with feedback-specific modulations, in line with our interoceptive inference framework.

      We have now integrated these considerations in the revised discussion (lines 796-830), and added the relevant between-experiment comparisons to the Results of Experiment 2 and the supplementary analysis.

      Terkelsen, A. J., Mølgaard, H., Hansen, J., Andersen, O. K., & Jensen, T. S. (2005). Acute pain increases heart rate: differential mechanisms during rest and mental stress. Autonomic Neuroscience, 121(1-2), 101-109.

      Tousignant-Laflamme, Y., Rainville, P., & Marchand, S. (2005). Establishing a link between heart rate and pain in healthy subjects: a gender effect. The journal of pain, 6(6), 341-347.

      Forte, G., Troisi, G., Pazzaglia, M., Pascalis, V. D., & Casagrande, M. (2022). Heart rate variability and pain: a systematic review. Brain sciences, 12(2), 153.

      (4) The hypothesis (increased pain intensity with incongruent-high cardiac feedback) should be motivated by some additional literature.

      We thank the reviewer for this helpful suggestion. Please note that the current phenomenon was tested in this experiment for the first time. Therefore, there is no specific prior study that motivated our hypotheses; they were driven theoretically, and derived from our model of interoceptive integration of pain and cardiac perception. The idea that accelerated cardiac feedback (relative to decelerated feedback) will increase pain perception and reduce heart rates is grounded on Embodied Predictive coding frameworks. Accordingly, expectations and signals from different sensory modalities (sensory, proprioceptive, interoceptive) are integrated both to efficiently infer crucial homeostatic and physiological variables, such as hunger, thirst, and, in this case, pain, and regulate the body’s own autonomic responses based on these inferences.

      Within this framework, the concept of an interoceptive schema (Tschantz et al., 2022; Iodice et al., 2019; Parrotta et al., 2024; Schoeller et al., 2022) offers the basis for understanding interoceptive illusions, wherein inferred levels of interoceptive states (i.e., pain) deviate from the actual physiological state. Cardiac signals conveyed by the feedback manipulation act as a misleading prior, shaping the internal generative model of pain. Specifically, an increased heart rate may signal a state of threat, establishing a prior expectation of heightened pain. Building on predictive models of interoception, we predict that this cardiac prior is integrated with interoceptive (i.e., actual nociceptive signal) and exteroceptive inputs (i.e., auditory feedback input), leading to a subjective experience of increased pain even when there is no corresponding increase in the nociceptive input.

      This idea is not completely new, but it is based on our previous findings of an interoceptive cardiac illusion driven by misleading priors about anticipated threat (i.e., pain). Specifically, in Parrotta et al. (2024), we tested whether a common false belief that heart rate increases in response to threat lead to an illusory perception of accelerated cardiac activity when anticipating pain. In two experiments, we asked participants to monitor and report their heartbeat while their ECG was recorded. Participants performed these tasks while visual cues reliably predicted a forthcoming harmless (low-intensity) vs. threatening (high-intensity) cutaneous electrical stimulus. We showed that anticipating a painful vs. harmless stimulus causes participants to report an increased cardiac frequency, which does not reflect their real cardiac response, but the common (false) belief that heart rates would accelerate under threat, reflecting the hypothesised integration of prior expectations and interoceptive inputs when estimating cardiac activity.

      Here we tested the counterpart of such a cardiac illusion. We reasoned that if cardiac interoception is shaped by expectations about pain, then the inverse should also be true: manipulating beliefs about cardiac activity (via cardiac feedback) in the context of pain anticipation should influence the perception of pain. Specifically, we hypothesized that presenting accelerated cardiac feedback would act as a misleading prior, leading to an illusory increase in pain experience, even in the absence of an actual change in nociceptive input.

      Moreover, next to the references already provided in the last version of the manuscript, there is ample prior research that provides more general support for such relationships. Specifically, studies have shown that providing mismatched cardiac feedback in contexts where cardiovascular changes are typically expected (i.e. sexual arousal, Rupp & Wallen, 2008; Valins, 1996; physical exercise, Iodice et al., 2019) can enhance the perception of interoceptive states associated with those experiences. Furthermore, findings that false cardiac feedback can influence emotional experience suggest that it is the conscious perception of physiological arousal, combined with the cognitive interpretation of the stimulus, that plays a key role in shaping emotional responses (Crucian et al., 2000).

      This point is now addressed in the revised Introduction, wherein additional references have been integrated (lines 157-170).

      Crucian, G. P., Hughes, J. D., Barrett, A. M., Williamson, D. J. G., Bauer, R. M., Bowers, D., & Heilman, K. M. (2000). Emotional and physiological responses to false feedback. Cortex, 36(5), 623-647.

      Iodice, P., Porciello, G., Bufalari, I., Barca, L., & Pezzulo, G. (2019). An interoceptive illusion of effort induced by false heart-rate feedback. Proceedings of the National Academy of Sciences, 116(28), 13897-13902.

      Parrotta, E., Bach, P., Perrucci, M. G., Costantini, M., & Ferri, F. (2024). Heart is deceitful above all things: Threat expectancy induces the illusory perception of increased heartrate. Cognition, 245, 105719.

      Rupp, H. A., & Wallen, K. (2008). Sex differences in response to visual sexual stimuli: A review. Archives of sexual behavior, 37(2), 206-218.

      Schoeller, F., Horowitz, A., Maes, P., Jain, A., Reggente, N., Moore, L. C., Trousselard, M., Klein, A., Barca, L., & Pezzulo, G. (2022). Interoceptive technologies for clinical neuroscience.

      Tschantz, A., Barca, L., Maisto, D., Buckley, C. L., Seth, A. K., & Pezzulo, G. (2022). Simulating homeostatic, allostatic and goal-directed forms of interoceptive control using active inference. Biological Psychology, 169, 108266.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      (5) The discussion section does not address the study's limitations in a sufficient manner. For example, I would expect a more thorough discussion on the lack of correlation between participant ratings and self-reported bodily awareness and reactivity, as assessed with the BPQ.

      We thank the reviewer for this valuable observation. In response, we have revised the Discussion section to explicitly acknowledge and elaborate on the lack of significant correlations between participants’ pain ratings and their self-reported bodily awareness and reactivity as assessed with the BPQ.

      We now clarify that the inclusion of this questionnaire was exploratory. While it would be theoretically interesting to observe a relationship between subjective pain modulation and individual differences in interoceptive awareness, detecting robust correlations between within-subject experimental effects and between-subjects trait measures such as the BPQ typically requires much larger sample sizes (often exceeding N = 200) due to the inherently low reliability of such cross-level associations (see Hedge, Powell & Sumner, 2018; the “reliability paradox”). As such, the absence of a significant correlation in our study does not undermine the conclusions we draw from our main findings. Future studies with larger samples will be needed to systematically address this question. We now acknowledge this point explicitly in the revised manuscript (lines 501-504; 832-851).

      Hedge, C., Powell, G., & Sumner, P. (2018). The reliability paradox: Why robust cognitive tasks do not produce reliable individual differences. Behavior Research Methods, 50(3), 1166-1186. https://doi.org/10.3758/s13428-017-0935-1

      (a) Some short, additional information on why the authors chose to focus on body awareness and supradiaphragmatic reactivity subscales would be helpful.

      We chose to focus on the body awareness and supradiaphragmatic reactivity subscales because these aspects are closely tied to emotional and physiological processing, particularly in the context of interoception. Body awareness plays a critical role in how individuals perceive and interpret bodily signals, which in turn affects emotional regulation and self-awareness. Supradiaphragmatic reactivity refers specifically to organs located or occurring above the diaphragm (i.e., the muscle that separates the chest cavity from the abdomen), which includes the heart, compared to subdiaphragmatic reactivity subscales further down. Our decision to include these subscales is further motivated by recent research, including the work by Petzschner et al. (2021), which demonstrates that the focus of attention can modulate the heartbeat-evoked potential (HEP), and that this modulation is predicted by participants’ responses on the supradiaphragmatic reactivity subscales. Thus, this subscale, and the more general body awareness scale, allows us to explore the interplay between bodily awareness, physiological reactivity, and emotional processing in our study. We now clarify this point in the revised version of the Methods - Body Perception Questionnaire (lines 384-393).

      (6) The analyses presented in this version of the manuscript allow only limited mechanistic conclusions - a computational model of participants' behavior would be a very strong addition to the paper. While this may be out of the scope of the article, it would be helpful for the reader to discuss the limitations of the presented analyses and outline avenues towards a more mechanistic understanding and analysis of the data. The computational model in [7] might contain some starting ideas.

      Thank you for your valuable feedback. We agree that a computational model would enhance the mechanistic understanding of our findings. While this is beyond the current scope, we now discuss the limitations of our analysis in the Limitations and Future directions section (lines 852-863). Specifically, we acknowledge that future studies could use computational models to better understand the interactions between physiological, cognitive, and perceptual factors.

      Some additional topics were not considered in the first version of the manuscript:

      (1) The possible advantages of a computational model of task behavior should be discussed.

      We agree that a computational model of task behavior could provide several advantages. By formalizing principles of predictive processing and active inference, such a model could generate quantitative predictions about how heart rate (HR) and feedback interact, providing a more precise understanding of their respective contributions to pain modulation. However, this is a first demonstration of a theoretically predicted phenomenon, and computationally modelling it is currently outside the scope of the article. We would be excited to explore this in the future. We have added a brief discussion of these potential advantages in the revised manuscript and suggest that future work could integrate computational modelling to further deepen our understanding of these processes (lines 852-890).

      (2) Across both experiments, there was a slightly larger number of female participants. Research suggests significant sex-related differences in pain processing [1,2]. It would be interesting to see what role this may have played in this data.

      Thank you for your insightful comment. While we acknowledge that sex-related differences in pain processing are well-documented in the literature, we do not have enough participants in our sample to test this in a well-powered way. As such, exploring the role of sex differences in pain perception will need to be addressed in future studies with more balanced samples. It would be interesting if more sensitive individuals, with a more precise representation of pain, also show smaller effects on pain perception. We have noted this point in the revised manuscript (lines 845-851) and suggest that future research could specifically investigate how sex differences might influence the modulation of pain and physiological responses in similar experimental contexts.

      (3) There are a few very relevant papers that come to mind which may be of interest. These sources might be particularly useful when discussing the roadmap towards a mechanistic understanding of the inferential processes underlying the task responses [3,4] and their clinical implications.

      Thank you for highlighting these relevant papers. We appreciate your suggestion and have now cited them in the Limitations and Future directions paragraph (lines 852-863).

      (4) In this version of the paper, we only see plots that illustrate ∆ scores, averaged across pain intensities - to better understand participant responses and the relationship with stimulus intensity, it would be helpful to see a more descriptive plot of task behavior (e.g. stimulus intensity and raw pain ratings)

      To directly address the reviewer’s request, we now provide additional descriptive plots in the supplementary material of the revised manuscript, showing raw pain ratings across different stimulus intensities and feedback conditions. These plots offer a clearer view of participant behavior without averaging across pain levels, helping to better illustrate the relationship between stimulus intensity and reported pain.

      Mogil, J. S. (2020). Qualitative sex differences in pain processing: emerging evidence of a biased literature. Nature Reviews Neuroscience, 21(7), 353-365. https://www.nature.com/articles/s41583-020-0310-6

      Sorge, R. E., & Strath, L. J. (2018). Sex differences in pain responses. Current Opinion in Physiology, 6, 75-81. https://www.sciencedirect.com/science/article/abs/pii/S2468867318300786?via%3Dihub

      Unal, O., Eren, O. C., Alkan, G., Petzschner, F. H., Yao, Y., & Stephan, K. E. (2021). Inference on homeostatic belief precision. Biological Psychology, 165, 108190.

      Allen, M., Levy, A., Parr, T., & Friston, K. J. (2022). In the body's eye: the computational anatomy of interoceptive inference. PLoS Computational Biology, 18(9), e1010490.

      Stephan, K. E., Manjaly, Z. M., Mathys, C. D., Weber, L. A., Paliwal, S., Gard, T., ... & Petzschner, F. H. (2016). Allostatic self-efficacy: A metacognitive theory of dyshomeostasis-induced fatigue and depression. Frontiers in human neuroscience, 10, 550.

      Friston, K. J., Stephan, K. E., Montague, R., & Dolan, R. J. (2014). Computational psychiatry: the brain as a phantastic organ. The Lancet Psychiatry, 1(2), 148-158.

      Eckert, A. L., Pabst, K., & Endres, D. M. (2022). A Bayesian model for chronic pain. Frontiers in Pain Research, 3, 966034.

      We thank the reviewer for highlighting these relevant references which have now been integrated in the revised version of the manuscript.

      Recommendations For The Authors: 

      Reviewer #1 (Recommendations For The Authors):

      At the time I was reviewing this paper, I could not think of a detailed experiment that would answer my biggest concern: Is this a manipulation of the brain's interoceptive data integration, or rather a manipulation of participants' alertness which indirectly influences their pain prediction?

      One incomplete idea that came to mind was delivering this signal in a more "covert" manner (though I am not sure it will suffice), or perhaps correlating the effect size of a participant with their interoceptive abilities, as measured in a different task or through a questionnaire.... Another potential idea is to tell participants that  this is someone else's HR that they hear and see if that changes the results (though requires further thought). I leave it to the authors to think further, and perhaps this is to be answered in a different paper - but if so, I am sorry to say that I do not think the claims can remain as they are now, and the paper will need a revision of its arguments, unfortunately. I urge the authors to ask further questions if my point about the concern was not made clear enough for them to address or contemplate it.

      We thank the reviewer for raising this important point. As detailed in our previous response, this point invites an important clarification regarding the role of cardiac deceleration in threat processing. Rather than serving as an interoceptive input from which the brain infers the likelihood of a forthcoming aversive event, heart rate deceleration is better described as an output of an already ongoing predictive process, as it reflects an allostatic adjustment of the bodily state aimed at minimizing the impact of the predicted perturbation (e.g., pain) and preventing sympathetic overshoot. It would be maladaptive for the brain to use a decelerating heart rate as evidence of impending threat, since this would paradoxically trigger further parasympathetic activation, initiating a potentially destabilizing feedback loop. Conversely, increased heart rate represents an evolutionarily conserved cue for arousal, threat, and pain. Our results therefore align with the idea that the brain treats externally manipulated increases in cardiac signals as congruent with anticipated sympathetic activation, prompting a compensatory autonomic and perceptual response consistent with embodied predictive processing frameworks (e.g., Barrett & Simmons, 2015; Seth, 2013).

      We would also like to re-iterate that our results cannot be explained by general differences induced by the different heart rate sounds relative to the exteroceptive (see also our detailed comments to your point above, and our response to a similar point from Reviewer 3), for three main reasons.

      (1) No main effect of Experiment on pain ratings:

      If the cardiac feedback had simply increased arousal or attention in a general (non-specific) way, we would expect a main effect of Experiment (i.e., interoceptive vs exteroceptive condition) on pain intensity or unpleasantness ratings, regardless of feedback frequency. However, such a main effect was never observed. Instead, effects were specific to the manipulation of feedback frequency.

      (2) Heart rate as an arousal measure:

      Heart rate (HR) is a classical physiological index of arousal. If there had been an unspecific increase in arousal in the interoceptive condition, we would expect a main effect of Experiment on HR. However, no such main effect was found. Instead, our HR analyses revealed a significant interaction between feedback and experiment, suggesting that HR changes depended specifically on the feedback manipulation rather than reflecting a general arousal increase.

      (3) Arousal predicts faster, not slower, heart rates

      In Experiment 1, faster interoceptive cardiac feedback led to a slowdown in heartrates both when compared to slower feedback and to congruent cardiac feedback. This is in line with the predicted compensatory response to faster heart rates. In contrast, if faster feedback would have only generally increased arousal, heart rates should have increased instead of decreased, as indicated by several prior studies (for a review, see Forte et al., 2022), predicting the opposite pattern of responses than was found in Experiment 1.

      Taken together, these findings indicate that the effects observed are unlikely to be driven by unspecific arousal or attention mechanisms, but rather are consistent with feedback-specific modulations, in line with our interoceptive inference framework. We now integrate these considerations in the general discussion (lines 796-830).

      Barrett, L. F., & Simmons, W. K. (2015). Interoceptive predictions in the brain. Nature reviews neuroscience, 16(7), 419-429.

      Forte, G., Troisi, G., Pazzaglia, M., Pascalis, V. D., & Casagrande, M. (2022). Heart rate variability and pain: a systematic review. Brain sciences, 12(2), 153.

      Seth, A. K. (2013). Interoceptive inference, emotion, and the embodied self. Trends in Cognitive Sciences, 17(11), 565-573.

      Additional recommendations:

      Major (in order of importance):

      (1) Number of trials per participant, per condition: as I mentioned, having only 6 trials for each condition is very little. The minimum requirement to accept so few trials would be to show data about the distribution of participants' responses to these trials, both per pain intensity (which was later averaged across - another issue discussed later), and across pain intensities, and see that it allows averaging across and that it is not incredibly variable such that the mean is unreliable.

      We appreciate the reviewer’s concern regarding the limited number of trials per condition. This choice was driven by both theoretical and methodological considerations.

      First, as is common in body illusion paradigms (e.g., the Rubber Hand Illusion, Botvinick & Cohen, 1998; the Full Body Illusion, Ehrsson, 2007; the Cardio-visual full body illusion, Pratviel et al., 2022) only a few trials are typically employed due to the immediate effects these manipulations elicit. Repetition can reduce the strength of the illusion through habituation, increased awareness, or loss of believability.

      Second, the experiment was already quite long (1.5h to 2h per participant) and cognitively demanding. It would not have been feasible to expand it further without compromising data quality due to fatigue, attentional decline, or participant disengagement.

      Third, the need for a large number of trials is more relevant when using implicit measures such as response times or physiological indices, which are typically indirectly related to the psychological constructs of interest. In contrast, explicit ratings are often more sensitive and less noisy, and thus require fewer repetitions to yield reliable effects (e.g., Corneille et al., 2024).

      Importantly, we also addressed your concern analytically. We ran therefore linear mixed-effects model analyses across all dependent variables (See Supplementary materials), with Trial (i.e., the rank order of each trial) included as a predictor to account for potential time-on-task effects such as learning, adaptation, or fatigue (e.g., Möckel et al., 2015). These models captured trial-by-trial variability and allowed us to test for systematic changes in heart rate (HR) and pain ratings including interactions with feedback conditions (e.g., Klieg et al., 2011; Baayen et al., 2010; Ambrosini et al., 2019). The consistent effects of Trial suggest that repetition dampens the illusion, reinforcing our decision to limit the number of exposures.

      In the interoceptive experiment, these analyses revealed a significant Feedback × Trial interaction (F(3, 711.19) = 6.16, p < .001), indicating that the effect of feedback on HR was not constant over time. As we suspected, and in line with other illusion-like effects, the difference between Faster and Slower feedback, which was significant early on (estimate = 1.68 bpm, p = .0007), decreased by mid-session (estimate = 0.69 bpm, p = .0048), and was no longer significant in later trials (estimate = 0.30 bpm, p = .4775). At the end of the session, HR values in the Faster and Slower conditions even numerically converged (Faster: M = 74.4, Slower: M = 74.1), and the non-significant contrast confirms that the difference had effectively vanished (for further details about slope estimation, see Supplementary material).

      The same pattern emerged for pain-unpleasantness ratings. A significant Feedback × Trial interaction (F (3, 675.33) = 3.44, p = .0165) revealed that the difference between Faster and Slower feedback was strongest at the beginning of the session and progressively weakened. Specifically, Faster feedback produced higher unpleasantness than Slower in early trials (estimate= -0.28, p = .0058) and mid-session (estimate = - 0.19, p = .0001), but this contrast was no longer significant in the final trials, wherein all the differences between active feedback conditions vanished (all ps > .55).

      Finally, similar results were yielded for pain intensity ratings. A significant Feedback × Trial interaction (F (3, 669.15) = 9.86, p < .001) showed that the Faster vs Slower difference was greatest at the start of the session and progressively vanished over trials. In early trials Faster feedback exceeded Slower (estimate=-8.33, p = .0001); by mid-session this gap had shrunk to 4.48 points (p < .0001); and in the final trials it was no longer significant (all ps > .94).

      Taken together, our results show that the illusion induced by Faster relative to slower feedback fades with repetition; adding further trials would likely have masked this key effect, confirming the methodological choice to restrict each condition to fewer exposures. To conclude, given that this is the first study to investigate an illusion of pain using heartbeat-based manipulation, we intentionally limited repeated exposures to preserve the integrity of the illusion. The use of mixed models as complementary analyses strengthens the reliability of our conclusions within these necessary design constraints. We now clarify this point in the Procedure paragraph (lines 328-335)

      Ambrosini, E., Peressotti, F., Gennari, M., Benavides-Varela, S., & Montefinese, M. (2023). Aging-related effects on the controlled retrieval of semantic information. Psychology and Aging, 38(3), 219.

      Baayen, R. H., & Milin, P. (2010). Analyzing reaction times. International Journal of Psychological Research, 3(2), 12-28.

      Botvinick, M., & Cohen, J. (1998). Rubber hands ‘feel’touch that eyes see. Nature, 391(6669), 756-756.

      Corneille, O., & Gawronski, B. (2024). Self-reports are better measurement instruments than implicit measures. Nature Reviews Psychology, 3(12), 835–846.

      Ehrsson, H. H. (2007). The experimental induction of out-of-body experiences. Science, 317(5841), 1048-1048.

      Kliegl, R., Wei, P., Dambacher, M., Yan, M., & Zhou, X. (2011). Experimental effects and individual differences in linear mixed models: Estimating the relation of spatial, object, and attraction effects in visual attention. Frontiers in Psychology, 1, 238. https://doi.org/10.3389/fpsyg.2010.00238

      Möckel, T., Beste, C., & Wascher, E. (2015). The effects of time on task in response selection-an ERP study of mental fatigue. Scientific reports, 5(1), 10113.

      Pratviel, Y., Bouni, A., Deschodt-Arsac, V., Larrue, F., & Arsac, L. M. (2022). Avatar embodiment in VR: Are there individual susceptibilities to visuo-tactile or cardio-visual stimulations?. Frontiers in Virtual Reality, 3, 954808.

      (2) Using different pain intensities: what was the purpose of training participants on correctly identifying pain intensities? You state that the aim of having 5 intensities is to cause ambiguity. What is the purpose of making sure participants accurately identify the intensities? Also, why then only 3 intensities were used in the test phase? The rationale for these is lacking.

      We thank the reviewer for raising these important points regarding the use of different pain intensities. The purpose of using five levels during the calibration and training phases was to introduce variability and increase ambiguity in the participants’ sensory experience. This variability aimed to reduce predictability and prevent participants from forming fixed expectations about stimulus intensity, thereby enhancing the plausibility of the illusion. It also helped prevent habituation to a single intensity and made the manipulation subtler and more credible. We had no specific theoretical hypotheses about this manipulation. Regarding the accuracy training, although the paradigm introduced ambiguity, it was important to ensure that participants developed a stable and consistent internal representation of the pain scale. This step was essential to control for individual differences in sensory discrimination and to ensure that illusion effects were not confounded by participants’ inability to reliably distinguish between intensities.

      As for the use of only three pain intensities in the test phase, the rationale was to focus on a manageable subset that still covered a meaningful range of the stimulus spectrum. This approach followed the same logic as Iodice et al. (2019, PNAS), who used five (rather than all seven) intensity levels during their experimental session. Specifically, they excluded the extreme levels (45 W and 125 W) used during baseline, to avoid floor and ceiling effects and to ensure that each test intensity could be paired with both a “slower” and a “faster” feedback from an adjacent level. This would not have been possible at the extremes of the intensity range, where no adjacent level exists in one direction. We adopted the same strategy to preserve the internal consistency and plausibility of our feedback manipulation.

      We further clarified these points in the revised manuscript (lines 336-342).

      Iodice, P., Porciello, G., Bufalari, I., Barca, L., & Pezzulo, G. (2019). An interoceptive illusion of effort induced by false heart-rate feedback. Proceedings of the National Academy of Sciences, 116(28), 13897-13902.

      (3) Averaging across pain intensities: this is, in my opinion, not the best approach as by matching a participant's specific responses to a pain stimulus before and after the manipulation, you can more closely identify changes resulting from the manipulation. Nevertheless, the minimal requirement to do so is to show data of distributions of pain intensities so we know they did not differ between conditions per participant, and in general - as you indicate they were randomly distributed.

      We thank the reviewer for this thoughtful comment. The decision to average across pain intensities in our main analyses was driven by the specific aim of the study: we did not intend to determine at which exact intensity level the illusion was most effective, and the limited number of trials makes such an analysis difficult. Rather, we introduced variability in nociceptive input to increase ambiguity and reduce predictability in the participants’ sensory experience. This variability was critical for enhancing the plausibility of the illusion by preventing participants from forming fixed expectations about stimulus strength. Additionally, using a range of intensities helped to minimize habituation effects and made the feedback manipulation subtler and more credible.

      That said, we appreciate the reviewer’s point that matching specific responses before and after the manipulation at each intensity level could provide further insights into how the illusion operates across varying levels of nociceptive input. We therefore conducted supplementary analyses using linear mixed-effects models in which all three stimulus intensities were included as a continuous fixed factor. This allowed us to examine whether the effects of feedback were intensity-specific or generalized across different levels of stimulation

      These analyses revealed that, in both the interoceptive and exteroceptive experiments, the effect of feedback on pain ratings was significantly modulated by stimulus intensity, as indicated by a Feedback × Stimulus Intensity interaction (Interoceptive: unpleasantness F(3, 672.32)=3.90, p=.0088; intensity ratings F(3, 667.07)=3.46, p=.016. Exteroceptive: unpleasantness F(3, 569.16)=8.21, p<.0001; intensity ratings F(3, 570.65)=3.00, p=.0301). The interaction term confirmed that the impact of feedback varied with stimulus strength, yet the pattern that emerged in each study diverged markedly.

      In the interoceptive experiment, the accelerated-heartbeat feedback (Faster) systematically heightened pain relative to the decelerated version (Slower) at every level of noxious input: for low-intensity trials Faster exceeded Slower by 0.22 ± 0.08 points on the unpleasantness scale (t = 2.84, p = .0094) and by 3.87 ± 1.69 units on the numeric intensity scale (t = 2.29, p = .0448); at the medium intensity the corresponding differences were 0.19 ± 0.05 (t = -4.02, p = .0001) and 4.52 ± 1.06 (t = 4.28, p < .0001); and even at the highest intensity, Faster still surpassed Slower by 0.17 ± 0.08 on unpleasantness (t = 2.21, p = .0326) and by 5.16 ± 1.67 on intensity (t = 3.09, p = .0032). This uniform Faster > Slower pattern indicates that the interoceptive manipulation amplifies perceived pain in a stimulus-independent fashion.

      The exteroceptive control experiment told a different story: the Faster-Slower contrast reached significance only at the most noxious setting (unpleasantness: estimate = 0.24 ± 0.07, t = -3.24, p = .0019; intensity: estimate = - 5.14 ± 1.82, t = 2.83, p = .0072) and was absent at the medium level (intensity , p=0.29; unpleasantness,  p=0.45), while at the lowest level Slower actually produced numerically higher unpleasantness (2.56 versus 2.40) and intensity ratings (44.7 versus 42.2).

      Thus, although both studies show that feedback effects depend on the actual nociceptive level of the stimulus, the results suggest that the faster vs. slower interoceptive feedback manipulation delivers a robust and intensity-invariant enhancement of pain, whereas the exteroceptive cue exerts a sporadic influence that surfaces solely under maximal stimulation.

      These new results are now included in the Supplementary Materials, where we report the detailed analyses for both the Interoceptive and Exteroceptive experiments on the Likert unpleasantness ratings and the numeric pain intensity ratings.

      (4) Sample size: It seems that the sample size was determined after the experiment was conducted, as the required N is identical to the actual N. I would be transparent about that, and say that retrospective sample size analyses support the ability of your sample size to support your claims. In general, a larger sample size than is required is always recommended, and if you were to run another study, I suggest you increase the sample size.

      As also addressed in our responses to your later comments (see our detailed reply regarding the justification of SESOI and power analyses), the power analyses reported here were not post-hoc power analyses based on obtained results. In line with current recommendations (Anderson, Kelley & Maxwell, 2017; Albers & Lakens, 2018), we did not base our analyses on previously reported effect sizes, as these can carry considerable uncertainty, particularly for novel effects where robust estimates are lacking. Instead, we used sensitivity analyses, conducted using the sensitivity analysis function in G*Power (Version 3.1). Sensitivity analyses allow us to report effect sizes that our design was adequately powered (90%) to detect, given the actual sample size, desired power level, and the statistical test used in each experiment (Lakens, 2022). Following further guidance (Lakens, 2022), we also report the smallest effect size of interest (SESOI) that these tests could reliably detect.

      This approach indicated that our design was powered to detect effect sizes of d = 0.57 in Experiment 1 and d = 0.62 in Experiment 2, with corresponding SESOIs of d = 0.34 and d = 0.37, respectively. The slightly higher value in Experiment 2 reflects the greater number of participants excluded (from an equal number originally tested) based on pre-specified criteria. Importantly, both experiments were well-powered to detect effects smaller than those typically reported in similar top-down pain modulation studies, where effect sizes around d = 0.7 have been observed (Iodice et al., 2019).

      We have now clarified this rationale in the revised manuscript, Experiment 1- Methods - Participants (lines 208-217).

      Albers, C., & Lakens, D. (2018). When power analyses based on pilot data are biased: Inaccurate effect size estimators and follow-up bias. Journal of experimental social psychology, 74, 187-195.

      Anderson, S. F., Kelley, K., & Maxwell, S. E. (2017). Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty. Psychological Science, 28(11), 1547-1562. https://doi.org/10.1177/0956797617723724

      Lakens, D. (2022). Sample size justification. Collabra: psychology, 8(1), 33267.

      (5) Analysis: the use of change scores instead of the actual scores is not recommended, as it is a loss of data, but could have been ignored if it didn't have a significant effect on the analyses conducted. Instead of conducting an RM-ANOVA of conditions (faster, slower, normal heartbeats) across participants, finding significant interaction, and then moving on to specific post-hoc paired comparisons between conditions, the authors begin with the change score but then move on to conduct the said paired comparisons without ever anchoring these analyses in an appropriate larger ANOVA. I strongly recommend the use of an ANOVA but if not, the authors would have to correct for multiple comparisons at the minimum.

      We thank the reviewer for their comment regarding the use of change scores. These were originally derived from the difference between the slower and faster feedback conditions relative to the congruent condition. In line with the reviewer’s recommendation, we have now removed these difference-based change scores from the main analysis. The results remain identical. Please note that we have retained the normalization procedure, relative to each participant’s initial baseline in the no feedback trials, as it is widely used in the interoceptive and pain literature (e.g., Bartolo et al., 2013; Cecchini et al., 2020; Riello et al., 2019). This approach helps to control for interindividual variability and baseline differences by expressing each participant’s response relative to their no-feedback baseline. As before, normalization was applied across all dependent variables (heart rate, pain intensity, and pain unpleasantness).

      To address the reviewer’s concern about statistical validity, we now first report a 1-factor repeated-measures ANOVA (Greenhouse-Geisser corrected) for each dependent variable, with feedback condition (slower, congruent, faster) as the within-subject factor.

      These show in each case a significant main effect, which we then follow with planned paired-sample t-tests comparing:

      Faster vs. slower feedback (our main hypothesis, as these manipulations are expected to produce largest, most powerful, test of our hypothesis, see response to Reviewer 3),

      Faster vs. congruent and slower vs. congruent (to test for potential asymmetries, as suggested  by previous false heart rate feedback studies).

      The rationale of these analyses is further discussed in the Data Analysis of Experiment 1 (lines 405-437).

      Although we report the omnibus one-factor RM-ANOVAs to satisfy conventional expectations, we note that such tests are not statistically necessary, nor even optimal, when the research question is fully captured by a priori, theory-driven contrasts. Extensive methodological work shows that, in this situation, going straight to planned contrasts maximises power without inflating Type I error and avoids the logical circularity of first testing an effect one does not predict (e.g., Rosenthal & Rosnow, 1985). In other words, an omnibus F is warranted only when one wishes to protect against unspecified patterns of differences. Here our hypotheses were precise (Faster ≠ Slower; potential asymmetry relative to Congruent), so the planned paired comparisons would have sufficed statistically. We therefore include the RM-ANOVAs solely for readers who expect to see them, but our inferential conclusions rest on the theoretically motivated contrasts.

      Rosenthal, R., & Rosnow, R. L. (1985). Contrast analysis. New York: Cambridge.

      (6) Correlations: were there correlations between subjects' own heartbeats (which are considered a predictive cue) and pain perceptions? This is critical to show that the two are in fact related.

      We thank the reviewer for this thoughtful suggestion. While we agree that testing for a correlation between anticipatory heart rate responses and subjective pain ratings is theoretically relevant. However, we have not conducted this analysis in the current manuscript, as our study was not designed or powered to reliably detect such individual differences. As noted by Hedge, Powell, and Sumner (2018), robust within-subject experimental designs tend to minimize between-subject variability in order to detect clear experimental effects. This reduction in variance at the between-subject level limits the reliability of correlational analyses involving trait-like or individual response patterns. This issue, known as the reliability paradox, highlights that measures showing robust within-subject effects may not show stable individual differences, and therefore correlations with other individual-level variables (like subjective ratings used here) require much larger samples to produce interpretable results than available here (and commonly used in the literature), typically more than 200 participants. For these reasons, we believe that running such an analysis in our current dataset would not yield informative results and could be misleading.

      We now explicitly acknowledge this point in the revised version of the manuscript (Limitations and future directions, lines 832-851) and suggest that future studies specifically designed to examine individual variability in anticipatory physiological responses and pain perception would be better suited to address this question.

      Hedge, C., Powell, G., & Sumner, P. (2018). The reliability paradox: Why robust cognitive tasks do not produce reliable individual differences. Behavior Research Methods, 50(3), 1166-1186. https://doi.org/10.3758/s13428-017-0935-1

      (7) The direct comparison between studies is great! and finally the use of ANOVA - but why without the appropriate post-hoc tests to support the bold claims in lines 542-544? This is needed. Same for 556-558.

      We apologize if our writing was not clear here, but the result of the ANOVAs fully warrants the claims in 542-544 (now lines 616-618) and 556-558 (now lines 601-603).

      In a 2x2 design, the interaction term is mathematically identical to comparing the difference induced by Factor 1 at one level of Factor 2 with the same difference induced at the other level of Factor 2. In our 2x2 analysis with the factors Experiment (Cardiac feedback, Exteroceptive feedback - between participants) and Feedback Frequency (faster, slower - within participants), the interaction therefore directly tests whether the effect of Feedback frequency differs statistically (i.e., is larger or smaller) in the participants in the interoceptive and exteroceptive experiments. Thus, the conclusion that “faster feedback affected the perceptual bias more strongly in the Experiment 1 than in Experiment 2” captures the outcome of the significant interaction exactly. Indeed, this test would be statistically equivalent (and would produce identical p values) to a simple between-group t-test between each participant’s difference between the faster and slower feedback in the interoceptive group and the analogous differences between the faster and slower feedback in the exteroceptive group, as illustrated in standard examples of factorial analysis (see, e.g., Maxwell, Delaney and Kelley, 2018).

      Please note that, for the above reason, mathematically the conclusion of larger effects in one experiment than the other is licensed by the significant interaction even without follow-up t-tests. However, if the reader would like to see these tests, they are simply the main analysis results reported in each of the two experiment sections, where significant (t-test) differences between faster and slower feedback were induced with interoceptive cues (Experiment 1) but not exteroceptive cues (Experiment 2). Reporting them in the between-experiment comparison section again would therefore be redundant.

      To avoid this lack of clarity, we have now re-written the results section of each experiment. First, as noted above, we now precede our main hypothesis test - the crucial t-test comparing heartrate and pain ratings after faster vs slower feedback - with an ANOVA including all three levels (faster, congruent, slower feedback). Moreover, we removed the separate between-experiment comparison section. Instead, in the Result section of the exteroceptive Experiment 2, we now directly compare the (absent or reversed) effects of faster vs slower feedback directly, with a between-groups t-test, with the present effects in the interoceptive Experiment 1. This shows conclusively, and hopefully more clearly, that the effects in both experiments differ. We hope that this makes the logic of our analyses clearer.

      Maxwell, S. E., Delaney, H. D., & Kelley, K. (2017). Designing experiments and analyzing data: A model comparison perspective. Routledge.

      (8) The discussion is missing a limitation paragraph.

      Thank you for the suggestion. We have now added a dedicated limitations paragraph in the Discussion section (lines 832-890).

      Additional recommendations:

      Minor (chronological order):

      (1) Sample size calculations for both experiments: what was the effect size based on? A citation or further information is needed. Also, clarify why the effect size differed between the two experiments.

      Please see above

      (2) "Participants were asked to either not drink coffee or smoke cigarettes" - either is implying that one of the two was asked. I suspect it is redundant as both were not permitted.

      The intention was to restrict both behaviors, so we have corrected the sentence to clarify that participants were asked not to drink coffee or smoke cigarettes before the session.

      (3) Normalization of ECG - what exactly was normalized, namely what measure of the ECG?

      The normalized measure was the heart rate, expressed in beats per minute (bpm). We now clarify this in the Data Analysis section of Experiment 1 (Measures of the heart rate recorded with the ECG (beats per minute) in the feedback phase were normalized)

      (4) Line 360: "Mean Δ pain unpleasantness ratings were analysed analogously" - this is unclear, if already described in methods then should be removed here, if not - should be further explained here.

      Thank you for your observation. We are no longer using change scores.

      (5) Lines 418-420: "Consequently, perceptual and cardiac modulations associated with the feedback manipulation should be reduced over the exposure to the faster exteroceptive sound." - why reduced and not unchanged? I didn't follow the logic.

      We chose the term “reduced” rather than “unchanged” to remain cautious in our interpretation. Statistically, the absence of a significant effect in one experiment does not necessarily mean that no effect is present; it simply means we did not detect one. For this reason, we avoided using language that would suggest complete absence of modulation. It also more closely matches the results of the between experiment comparisons that we report in the Result section of Experiment 2, which can in principle only show that the effect in Experiment 2 was smaller than that of Experiment 1, not that it was absent. Even the TOST analysis that we utilize to show the absence of an effect can only show that any effect that is present is smaller than we could reasonably expect to detect with our experimental design, not its complete absence.

      Also, on a theoretical level, pain is a complex, multidimensional experience influenced not only by sensory input but also by cognitive, emotional, social and expectancy factors. For this reason, we considered it important to remain open to the possibility that other mechanisms beyond the misleading cardiac prior induced by the feedback might have contributed to the observed effects. If such other influences had contributed to the induced differences between faster and slower feedback in Experiment 1, some remainder of this difference could have been observed in Experiment 2 as well.

      Thus, for both statistical and theoretical reasons, we were careful to predict a reduction of the crucial difference, not its complete elimination. However, to warrant the possibility that effects could be completely eliminated we now write that “perceptual and cardiac modulations associated with the feedback manipulation should be reduced or eliminated with exteroceptive feedback”

      (6) Study 2 generation of feedback - was this again tailored per participants (25% above and beyond their own HR at baseline + gradually increasing or decreasing), or identical for everyone?

      Yes, in Study 2, the generation of feedback was tailored to each participant, mirroring the procedure or Experiment 1. Specifically, the feedback was set to be 25% above or below their baseline heart rate, with the feedback gradually increasing or decreasing. This individualized approach ensured that each participant experienced feedback relative to their own baseline heart rate. We now clarify this in the Methods section (lines 306-318).

      (7) I did not follow why we need the TOST and how to interpret its results.

      We thank the reviewer for raising this important point. In classical null hypothesis significance testing (NHST), a non-significant p-value (e.g., p > .05) only indicates that we failed to find a statistically significant difference, not that there is no difference. It therefore does not allow us to conclude that two conditions are equivalent – only that we cannot confidently say they are different. In our case, to support the claim that exteroceptive feedback does not induce perceptual or physiological changes (unlike interoceptive feedback), we needed a method to test for the absence of a meaningful effect, not just the absence of a statistically detectable one.

      The TOST (Two One-Sided Tests) procedure reverses the logic of NHST by testing whether the observed effect falls within a predefined equivalence interval, called the smallest effect size of interest (SESOI) that is in principle measurable with our design parameters (e.g., type of test, number of participants). This approach is necessary when the goal is not to detect a difference, but rather to demonstrate that an observed effect is so small that it can be considered negligible – or at the least smaller than we could in principle expect to observe in the given experiment. We used the TOST procedure in Experiment 2 to test for statistical equivalence between the effects of faster and slower exteroceptive feedback on pain ratings and heart rate.

      We hope that the clearer explanation now provided in data analysis of Experiment 2 section (lines 5589-563) fully addresses the reviewer’s concern.

      (8) Lines 492-3: authors say TOST significant, while p value = 0.065

      We thank the reviewer for spotting this inconsistency. The discrepancy was due to a typographical error in the initial manuscript. During the revision of the paper, we rechecked and fully recomputed all TOST analyses, and the results have now been corrected throughout the manuscript to accurately reflect the statistical outcomes. In particular, for the comparison of heart rate between faster and slower exteroceptive feedback in Experiment 2, the corrected TOST analysis now shows a significant equivalence, with the observed effect size being d = -0.19 (90% CI [-0.36, -0.03]) and both one-sided tests yielding p = .025 and p < .001. These updated results are reported in the revised Results section.

      Reviewer #2 (Recommendations For The Authors):

      I would suggest the authors revise their definition of pain in the introduction, since it is not always a protective experience. The new IASP definition specifically takes this into consideration.

      We thank the reviewer for this suggestion. We have updated the definition of pain in the Introduction (lines 2-4) to align with the most recent IASP definition (2020), which characterizes pain as “an unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage” (lines 51-53).

      The work on exteroceptive cues does not necessarily neglect the role of interoceptive sources of information, although it is true that it has been comparatively less studied. I suggest rephrasing this sentence to reflect this.

      We thank the reviewer for pointing out this important nuance. We agree that studies employing exteroceptive cues to modulate pain perception do not necessarily neglect the role of interoceptive sources, even though these are not always the primary focus of investigation. Our intention was not to imply a strict dichotomy, but rather to highlight that interoceptive mechanisms have been comparatively under-investigated. We have revised the sentence in the Introduction accordingly to better reflect this perspective (Introduction, lines 110-112, “Although interoceptive processes may have contributed to the observed effects, these studies did not specifically target interoceptive sources of information within the inferential process.”).

      The last paragraph of the introduction (lines 158-164) contains generalizations beyond what can be supported by the data and the results, about the generation of predictive processes and the origins of these predictions. The statements regarding the understanding of pain-related pathologies in terms of chronic aberrant predictions in the context of this study are also unwarranted.

      We have deleted this paragraph now.

      I could not find the study registration (at least in clinicaltrials.gov). This is curious considering that the hypothesis and the experimental design seem in principle well thought out, and a study pre-registration improves the credibility of the research (Nosek et al., 2018). I also find the choice for the smallest effect of interest (SESOI) odd. Besides the unnecessary variable transformations (more on that later), there is no justification for why that particular SESOI was chosen, or why it changes between experiments (Dienes, 2021; King, 2011), which makes the choice look arbitrary. The SESOI is a fundamental component of a priori power analysis (Lakens, 2022), and without rationale and preregistration, it is impossible to tell whether this is a case of SPARKing or not (Sasaki & Yamada, 2023).

      We acknowledge that the study was not preregistered. Although our hypotheses and design were developed a priori and informed by established theoretical frameworks, the lack of formal preregistration is a limitation.

      The SESOI values for Experiments 1 and 2 were derived from sensitivity analyses based on the fixed design parameters (type of test, number of participants, alpha level) of our study, not from any post-hoc interpretation based on observed results - they can therefore not be a case of SPARKing. Following current recommendations (Anderson, Kelley & Maxwell, 2017; Albers & Lakens, 2017; Lakens, 2022), we avoided basing power estimates on published effect sizes, as no such values exist for in novel paradigms, and are typically inflated due to publication and other biases. Instead, sensitivity analyses (using G*Power, v 3.1) allows us to calculate, prospectively, the smallest effect each design could detect with 90 % power, given the actual sample size, test type, and α level. Because more participants were excluded in Experiment 2, this design can detect slightly larger effects (d = 0.62) than Experiment 1 (d = 0.57). Please note that both studies therefore remain well-powered to capture effects of the magnitude typically reported in previous research using feedback manipulations to explore interoceptive illusions (e.g., Iodice et al., 2019, d ≈ 0.7).

      We have added this clarification to the Participants section of Experiment 1 (Lines 208-217).

      Anderson, S. F., Kelley, K., & Maxwell, S. E. (2017). Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty. Psychological Science, 28(11), 1547-1562.

      Lakens, D. (2022). Sample size justification. Collabra: psychology, 8(1), 33267.

      Albers, C., & Lakens, D. (2018). When power analyses based on pilot data are biased: Inaccurate effect size estimators and follow-up bias. Journal of experimental social psychology, 74, 187-195.

      In the Apparatus subsection, it is stated that the intensity of the electrical stimuli was fixed at 2 ms. I believe the authors refer to the duration of the stimulus, not its intensity.

      You are right, thank you for pointing that out. The text should refer to the duration of the electrical stimulus, not its intensity. We have corrected this wording in the revised manuscript to avoid confusion.

      It would be interesting to report (in graphical form) the stimulation intensities corresponding to the calibration procedure for the five different pain levels identified for all subjects.

      That's a good suggestion. We have included a supplementary figure showing the stimulation intensities corresponding to the five individually calibrated pain levels across all participants (Supplementary Figure 11.)

      It is questionable that researchers state that "pain and unpleasantness should be rated independently" but then the first level of the Likert scale for unpleasantness is "1=no pain". This is particularly relevant since simulation (and specifically electrical stimulation) can be unpleasant but non-painful at the same time. Since the experiments were already performed, the researchers should at least explain this choice.

      Thank you for raising this point. You are right in that the label of “no pain” in the pain unpleasantness scale was not ideal, and we now acknowledge this in the text (lines 886-890). Please note that this was always the second rating that participants gave (after pain intensity), and the strongest results come from this first rating.

      Discussion.

      I did not find in the manuscript the rationale for varying the frequency of the heart rate by 25% (instead of any other arbitrary quantity).

      We thank the Reviewer for this observation, which prompted us to clarify the rationale behind our choice of a ±25% manipulation of heart rate feedback. False feedback paradigms have historically relied on a variety of approaches to modulate perceived cardiac signals. Some studies have adopted non-individualised values, using fixed frequencies (e.g., 60 or 110 bpm) to evoke states of calm or arousal, independently of participants’ actual physiology (Valins, 1966; Shahidi & Baluch, 1991; Crucian et al., 2000; Tajadura-Jiménez et al., 2008). Others have used the participant’s real-time heart rate as a basis, introducing accelerations or decelerations without applying a specific percentage transformation (e.g., Iodice et al., 2019). More recently, a growing body of work has employed percentage-based alterations of the instantaneous heart rate, offering a controlled and participant-specific manipulation. These include studies using −20% (Azevedo et al., 2017), ±30% (Dey et al., 2018), and even ±50% (Gray et al., 2007).

      These different methodologies - non-individualised, absolute, or proportionally scaled - have all been shown to effectively modulate subjective and physiological responses. They suggest that the impact of false feedback does not depend on a single fixed method, but rather on the plausibility and salience of the manipulation within the context of the task. We chose to apply a ±25% variation because it falls well within the most commonly used range and strikes a balance between producing a detectable effect and maintaining the illusion of physiological realism. The magnitude is conceptually justified as being large enough to shape interoceptive and emotional experience (as shown by Azevedo and Dey), yet small enough to avoid implausible or disruptive alterations, such as those approaching ±50%. We have now clarified this rationale in the revised Procedure paragraph of Experiment 1 (lines 306-318).

      T. Azevedo, R., Bennett, N., Bilicki, A., Hooper, J., Markopoulou, F., & Tsakiris, M. (2017). The calming effect of a new wearable device during the anticipation of public speech. Scientific reports, 7(1), 2285.

      Crucian, G. P., Hughes, J. D., Barrett, A. M., Williamson, D. J. G., Bauer, R. M., Bowers, D., & Heilman, K. M. (2000). Emotional and physiological responses to false feedback. Cortex, 36(5), 623-647.

      Dey, A., Chen, H., Billinghurst, M., & Lindeman, R. W. (2018, October). Effects of manipulating physiological feedback in immersive virtual environments. In Proceedings of the 2018 Annual Symposium on Computer-Human Interaction in Play (pp. 101-111).

      Gray, M. A., Harrison, N. A., Wiens, S., & Critchley, H. D. (2007). Modulation of emotional appraisal by false physiological feedback during fMRI. PLoS one, 2(6), e546.

      Shahidi, S., & Baluch, B. (1991). False heart-rate feedback, social anxiety and self-attribution of embarrassment. Psychological reports, 69(3), 1024-1026.

      Tajadura-Jiménez, A., Väljamäe, A., & Västfjäll, D. (2008). Self-representation in mediated environments: the experience of emotions modulated by auditory-vibrotactile heartbeat. CyberPsychology & Behavior, 11(1), 33-38.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      The researchers state that pain ratings collected in the feedback phase were normalized to the no-feedback phase to control for inter-individual variability in pain perception, as established by previous research. They cite three studies involving smell and taste, of which the last two contain the same normalization presented in this study. However, unlike these studies, the outcomes here require no normalization whatsoever, because there should be no (or very little) inter-individual variability in pain intensity ratings. Indeed, pain intensity ratings in this study are anchored to 30, 50, and 70 / 100 as a condition of the experimental design. The researchers go to extreme lengths to ensure this is the case, by adjusting stimulation intensities until at least 75% of stimulation intensities are correctly matched to their pain ratings counterpart in the pre-experiment procedure. In other words, inter-individual variability in this study is in stimulation intensities, and not pain intensity ratings. Even if it could be argued that pain unpleasantness and heart rate still need to account for inter-individual variability, the best way to do this is by using the baseline (no-feedback) measures as covariates in a mixed linear model. Another advantage of this approach is that all the effects can be described in terms of the original scales and are readily understandable, and post hoc tests between levels can be corrected for multiple comparisons. On the contrary, the familywise error rate for the comparisons between conditions in the current analysis is larger than 5% (since there is a "main" paired t-test and additional "simple" tests).

      We disagree that there is little to no variability in the no feedback phase. Participants were tested in their ability to distinguish intensities in an initial pre-experiment calibration phase. In the no feedback phase, participants rated the pain stimuli in the full experimental context.

      In the pre-experiment calibration phase, participants were tested only once in their ability to match five electrical‐stimulation levels to the 0-100 NPS scale, before any feedback manipulation started. During this pre-experiment calibration we required that each level was classified correctly on ≥ 75 % of the four repetitions; “correct” meant falling within ± 5 NPS units of the target anchor (e.g., a response of 25–35 was accepted for the 30/100 anchor). This procedure served one purpose only: to make sure that every participant entered the main experiment with three unambiguously distinguishable stimulation levels (30 / 50 / 70). We integrated this point in the revised manuscript lines 263-270.

      Once the real task began, the context changed: shocks are unpredictable, attention is drawn to the heartbeat, and participants must judge both intensity and unpleasantness. In this full experimental setting the no-feedback block indeed shows considerable variability, even for the pain intensity ratings. Participants mean rating on the NPS scale was 46.4, with a standard deviation of 11.9 - thus participants vary quite strongly in their mean ratings (range 14.5 to 70). Moreover, while all participants show a positive correlation between actual intensities and their ratings (i.e., they rate the higher intensities as more intense than the lower ones), they vary in how much of the scale they use, with differences between reported highest and lowest intensities ranging between 8 and 91, for the participants showing the smallest and largest differences, respectively.

      Thus, while we simplified the analysis to remove the difference scoring relative to the congruent trials and now use these congruent trials as an additional condition in the analysis, we retained the normalisation procedure to account for the in-fact-existing between-participant variability, and ensure consistency with prior research (Bartolo et al., 2013; Cecchini et al., 2020; Riello et al., 2019) and our a priori analysis plan.

      However, to ensure we fully address your point here (and the other reviewers’ points about potential additional factors affecting the effects, like trial number and stimulus intensity), we also report an additional linear mixed-effects model analysis without normalization. It includes every feedback level as condition (No-Feedback, Congruent, Slower, Faster), plus additional predictors for actual stimulus intensity and trial rank within the experiment (as suggested by the other reviewers). This confirms that all relevant results remain intact once baseline and congruent trials are explicitly included in the model.

      In brief, cross‐experiment analyses demonstrated that the Faster vs Slower contrast was markedly larger when the feedback was interoceptive than when it was exteroceptive. This held for heart-rate deceleration (b = 0.94 bpm, p = .005), for increases in unpleasantness (b = -0.16 Likert units, p = .015), and in pain-intensity ratings (b = -3.27 NPS points, p = .037).

      These findings were then further confirmed by within-experiment analyses. Within the interoceptive experiment, the mixed-model on raw scores replicated every original effect: heart rate was lower after Faster than Slower feedback (estimate = –0.69 bpm, p = .005); unpleasantness was higher after Faster than Slower feedback (estimate = 0.19, p < .001); pain-intensity rose after Faster versus Slower (estimate=-4.285, p < .001). In the exteroceptive experiment, however, none of these Faster–Slower contrasts reached significance for heart rate (all ps > .33), unpleasantness (all ps > .43) or intensity (all ps > .10).  Because these effects remain significant even with No-Feedback and Congruent trials explicitly included in the model and vanish under exteroceptive control, the supplementary, non-normalised analyses confirm that the faster vs. slower interoceptive feedback uniquely lowers anticipatory heart rate while amplifying both intensity and unpleasantness of pain, independent of data transformation or reference conditions.  Please see Supplementary analyses for further details.

      Bartolo, M., Serrao, M., Gamgebeli, Z., Alpaidze, M., Perrotta, A., Padua, L., Pierelli, F., Nappi, G., & Sandrini, G. (2013). Modulation of the human nociceptive flexion reflex by pleasant and unpleasant odors. PAIN®, 154(10), 2054-2059.

      Cecchini, M. P., Riello, M., Sandri, A., Zanini, A., Fiorio, M., & Tinazzi, M. (2020). Smell and taste dissociations in the modulation of tonic pain perception induced by a capsaicin cream application. European Journal of Pain, 24(10), 1946-1955.

      Riello, M., Cecchini, M. P., Zanini, A., Di Chiappari, M., Tinazzi, M., & Fiorio, M. (2019). Perception of phasic pain is modulated by smell and taste. European Journal of Pain, 23(10), 1790-1800.

      I could initially not find a rationale for bringing upfront the comparison between faster vs. slower HR acoustic feedback when in principle the intuitive comparisons would be faster vs. congruent and slower vs. congruent feedback. This is even more relevant considering that in the proposed main comparison, the congruent feedback does not play a role: since Δ outcomes are calculated as (faster - congruent) and (slower - congruent), a paired t-test between Δ faster and Δ slower outcomes equals (faster - congruent) - (slower - congruent) = (faster - slower). I later realized that the statistical comparison (paired t-test) of pain intensity ratings of faster vs. slower acoustic feedback is significant in experiment 1 but not in experiment 2, which in principle would support the argument that interoceptive, but not exteroceptive, feedback modulates pain perception. However, the "simple" t-tests show that faster feedback modulates pain perception in both experiments, although the effect is larger in experiment 1 (interoceptive feedback) compared to experiment 2 (exteroceptive feedback).

      The comparison between faster and slower feedback is indeed crucial, and we regret not having made this clearer in the first version of the manuscript. As noted in our response to your point in the public review, this comparison is both statistically most powerful, and theoretically the most appropriate, as it controls for any influence of salience or surprise when heart rates deviate (in either direction) from what is expected. It therefore provides a clean measure of how much accelerated heartrate affects pain perception and physiological response, relative to an equal change in the opposite direction. However, as noted above, in the new version of the manuscript we have now removed the analysis via difference scores, and directly compared all three relevant conditions (faster, congruent, slower), first via an ANOVA and then with follow-up planned t-tests.

      Please refer to our previous response for further details (i.e., Furthermore, the researchers propose the comparison of faster vs. slower delta HR acoustic feedback throughout the manuscript when the natural comparison is the incongruent vs. the congruent feedback [..]).

      The design of experiment two involves the selection of knocking wood sounds to act as exteroceptive acoustic feedback. Since the purpose is to test whether sound affects pain intensity ratings, unpleasantness, and heart rate, it would have made sense to choose sounds that would be more likely to elicit such changes, e.g. Taffou et al. (2021), Chen & Wang (2022), Zhou et al. (2022), Tajadura-Jiménez et al. (2010). Whereas I acknowledge that there is a difference in effect sizes between experiment 1 and experiment 2 for the faster acoustic feedback, I am not fully convinced that this difference is due to the nature of the feedback (interoceptive vs. exteroceptive), since a similar difference could arguably be obtained by exteroceptive sound with looming or rough qualities. Since the experiment was already carried out and this hypothesis cannot be tested, I suggest that the researchers moderate the inferences made in the Discussion regarding these results.

      Please refer to our previous response for a previous detailed answer to this point in the Public Review (i.e., This could be influenced by the fact that the faster HR exteroceptive cue in experiment 2 also shows a significant modulatory effect [..]). As we describe there, we see little grounds to suspect such a non-specific influence of acoustic parameters, as it is specifically the sensitivity to the change in heart rate (faster vs slower) that is affected by our between-experiment manipulation, not the overall response to the different exteroceptive or interoceptive sounds. Moreover, the specific change induced by the faster interoceptive feedback - a heartrate deceleration - is not consistent with a change in arousal or alertness (which would have predicted an increase in heartrate with increasing arousal). See also Discussion-Accounting for general unspecific contributions.

      Additionally, the fact that no significant effects were found for unpleasantness ratings or heart rate (absence of evidence) should not be taken as proof that faster exteroceptive feedback does not induce an effect on these outcomes (evidence of absence). In this case, it could be that there is actually no effect on these variables, or that the experiment was not sufficiently powered to detect those effects. This would depend on the SESOIs for these variables, which as stated before, was not properly justified.

      We very much agree that the absence of significant effects should not be interpreted as definitive evidence of absence. Indeed, we were careful not to overinterpret the null findings for heart rate and unpleasantness ratings, and we conducted additional analyses to clarify their interpretation. First, the TOST analysis shows that any effects in Experiment 2 are (significantly) smaller than the smallest effect size that can possibly be detected in our experiment, given the experimental parameters (number of participants, type of test, alpha level). Second, and more importantly, we run between-experiments comparisons (see Results Experiment 2, and Supplementary materials, Cross-experiment analysis between-subjects model) of the crucial difference in the changes induced by faster and slower feedback. This showed that the differences were larger with interoceptive (Experiment 1) than exteroceptive cues (Experiment 2). Thus, even if a smaller than is in principle detectable effect is induced by the exteroceptive cues in Experiment 2, it is smaller than with interoceptive cues in Experiment 1.

      To ensure we fully address this point, we have now simplified our main analysis (main manuscript), replicated it with a different analysis (Supplementary material), we motivate more clearly (Methods Experiment 1), why the comparison between faster and slower feedback is crucial, and we make clearer that the difference between these conditions is larger in Experiment 1 than Experiment 2 (Results Experiment 2). Moreover, we went through the manuscript and ensured that our wording does not over-interpret the absence of effects in Experiment 2, as an absence of a difference.

      The section "Additional comparison analysis between experiments" encompasses in a way all possible comparisons between levels of the different factors in both experiments. My original suggestion regarding the use of a mixed linear model with covariates is still valid for this case. This analysis also brings into question another aspect of the experimental design: what is the rationale for dividing the study into two experiments, considering that variability and confounding factors would have been much better controlled in a single experimental session that includes all conditions?

      We thank the reviewer for their comment. We would like to note, first, that the between-experiment analyses did not encompass all possible comparisons between levels, as it just included faster and slower feedback for the within-experiment comparison Instead, they focus on the specific interaction between faster and slower feedback on the one hand, and interoceptive vs exteroceptive cues on the other. This interaction essentially compares, for each dependent measure (HR, pain unpleasantness, pain intensity), the difference between faster and slower feedback in Experiment 1 with that the same difference in Experiment 2 (and would produce identical p values to a between-experiment t-test). The significant interactions therefore indicate larger effects of interoceptive cues than exteroceptive ones for each of the measures. To make this clearer, we have now exchanged the analysis with between-experiment t-tests of the difference between faster and slower feedback for each measure (Results Experiment 2), producing identical results. Moreover, as suggested, we also now report linear mixed model analyses (see Supplementary Materials), which provide a comprehensive comparison across experiments.

      Regarding the experimental design, we appreciate the reviewer’s suggestion regarding a within-subject crossover design. While such an approach indeed offers greater statistical power by reducing interindividual variability (Charness, Gneezy, & Kuhn, 2012), we intentionally chose a between-subjects design due to theoretical and methodological considerations specific to deceptive feedback paradigms. First, carryover effects are a major concern in deception studies. Participants exposed to one type of feedback could develop suspicion or adaptive strategies that would alter their responses in subsequent conditions (Martin & Sayette, 1993). Expectancy effects could thus contaminate results in a crossover design, particularly when feedback manipulation becomes apparent. In line with this idea, past studies on false cardiac feedback (e.g., Valins, 1966; Pennebaker & Lightner, 1980) often employed between-subjects or blocked designs to maintain the ecological validity of the illusion.

      Charness, G., Gneezy, U., & Kuhn, M. A. (2012). Experimental methods: Between-subject and within-subject design. Journal of economic behavior & organization, 81(1), 1-8.

      Martin, C. S., & Sayette, M. A. (1993). Experimental design in alcohol administration research: limitations and alternatives in the manipulation of dosage-set. Journal of studies on alcohol, 54(6), 750-761.

      Pennebaker, J. W., & Lightner, J. M. (1980). Competition of internal and external information in an exercise setting. Journal of personality and social psychology, 39(1), 165.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      References

      Chen ZS, Wang J. Pain, from perception to action: A computational perspective. iScience. 2022 Dec 1;26(1):105707. doi: 10.1016/j.isci.2022.105707.

      Dienes Z. Obtaining Evidence for No Effect. Collabra: Psychology 2021 Jan 4; 7 (1): 28202. doi: 10.1525/collabra.28202

      King MT. A point of minimal important difference (MID): a critique of terminology and methods. Expert Rev Pharmacoecon Outcomes Res. 2011 Apr;11(2):171-84. doi: 10.1586/erp.11.9.

      Lakens D. Sample Size Justification. Collabra: Psychology 2022 Jan 5; 8 (1): 33267. doi: 10.1525/collabra.33267

      Nosek BA, Ebersole CR, DeHaven AC, Mellor DT. The preregistration revolution. Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2600-2606. doi: 10.1073/pnas.1708274114.

      Sasaki K, Yamada Y. SPARKing: Sample-size planning after the results are known. Front Hum Neurosci. 2023 Feb 22;17:912338. doi: 10.3389/fnhum.2023.912338.

      Taffou M, Suied C, Viaud-Delmon I. Auditory roughness elicits defense reactions. Sci Rep. 2021 Jan 13;11(1):956. doi: 10.1038/s41598-020-79767-0.

      Tajadura-Jiménez A, Väljamäe A, Asutay E, Västfjäll D. Embodied auditory perception: The emotional impact of approaching and receding sound sources. Emotion. 2010, 10(2), 216-229.https://doi.org/10.1037/a0018422

      Zhou W, Ye C, Wang H, Mao Y, Zhang W, Liu A, Yang CL, Li T, Hayashi L, Zhao W, Chen L, Liu Y, Tao W, Zhang Z. Sound induces analgesia through corticothalamic circuits. Science. 2022 Jul 8;377(6602):198-204. doi: 10.1126/science.abn4663.

      Reviewer #3 (Recommendations For The Authors):

      The manuscript would benefit from some spelling- and grammar checking.

      Done

      Discussion:

      The discussion section is rather lengthy and would benefit from some re-structuring, editing, and sub-section headers.

      In response, we have restructured and edited the Discussion section to improve clarity and flow.

      I personally had a difficult time understanding how the data relates to the rubber hand illusion (l.623-630). I would recommend revising or deleting this section.

      We thank the reviewer for this valuable feedback. We have revised the paragraph and made the parallel clearer (lines 731-739).

      Other areas are a bit short and might benefit from some elaboration, such as clinical implications. Since they were mentioned in the abstract, I had expected a bit more thorough discussion here (l. 718).

      Thank you for this suggestion. We have expanded the discussion to more thoroughly address the clinical implications of our interoceptive pain illusion (See Limitations and Future Directions paragraph).

      Further, clarification is needed for the following:

      I would like some more details on participant instructions; in particular, the potential difference in instruction between Exp. 1 and 2, if any. In Exp. 1, it says: (l. 280) "Crucially, they were also informed that over the 60 seconds preceding the administration of the shock, they were exposed to acoustic feedback, which was equivalent to their ongoing heart rate". Was there a similar instruction for Exp. 2? If yes, it would suggest a more specific effect of cardiac auditory feedback; if no, the ramifications of this difference in instructions should be more thoroughly discussed.

      Thank you for this suggestion. We have clarified this point in the Procedure of Experiment 2 (548-550).

    1. Author response:

      We thank the editors and all reviewers for the detailed evaluation of the work and the overall positive remarks, as well as the constructive feedback to improve our manuscript. Based on the integrated comments of the reviewers and advice of the reviewing editor, we will suitably address all comments raised by the reviewers, and we outline our revision plan below:

      Interpretation of findings

      ● We will carefully reframe our interpretation of the data regarding the role of the pallium in the coupled saccade-tail turning events, and clearly state that we have not established a causal role, which requires additional perturbation experiments.

      ● We will also acknowledge the confounding interpretation that the pallial activities recorded may also represent or include arousal state signals.

      Streamlining the presentation

      ● In the introduction, we will better contextualize our study with additional discussions on (i) the advantageous use of zebrafish to study chemosensation, factoring in differences in the spread of chemical cues in water vs. air, and (ii) the disruption of eye-body coordination and underlying neural circuits.

      ● We will streamline the presentation of data in Fig. 1 by keeping the overall responses of the larvae to each chemical across concentrations in the main figure, while moving suitable additional details to a supplementary figure.

      ● Similarly, for each of the subsequent main figures, wherever suitable we will select an illustrative, core set of panels to retain in the main figure, and move other more detailed plots to supplementary figures.

      ● We will incorporate additional references and discussions of the past literature, including relating our findings to (i) chemosensation/multisensory integration in Drosophila, (ii) thermosensation-driven and navigational behavior in larval zebrafish, and (iii) fleeing or escape behavior in zebrafish and other species.

      ● We will clarify our animal subject inclusion criteria, that all larval subjects with sufficiently high-quality, stable imaging were included (i.e., we only excluded larvae because of insufficient quality of imaging, but not other factors).

      ● For applicable plots, adding suitable additional details to the plots or legends (e.g., clarification of measures, specifying numbers of cells).

      Data analysis and statistics

      We will perform additional data analysis, by making comparisons with statistics performedon fish subject-level, and include confident intervals wherever applicable.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews: 

      Reviewer #1 (Public Review): 

      Summary:

      The manuscript submitted by Langenbacher et al., entitled " Rtf1-dependent transcriptional pausing regulates cardiogenesis", describes very interesting and highly impactful observations about the function of Rtf-1 in cardiac development. Over the last few years, the Chen lab has published novel insights into the genes involved in cardiac morphogenesis. Here, they used the mouse model, the zebrafish model, cellular assays, single cell transcription, chemical inhibition, and pathway analysis to provide a comprehensive view of Rtf1 in RNAPII (Pol2) transcription pausing during cardiac development. They also conducted knockdown-rescue experiments to dissect the functions of Rtf1 domains. 

      Strengths:

      The most interesting discovery is the connection between Rtf1 and CDK9 in regulating Pol2 pausing as an essential step in normal heart development. The design and execution of these experiments also demonstrate a thorough approach to revealing a previously underappreciated role of Pol2 transcription pausing in cardiac development. This study also highlights the potential amelioration of related cardiac deficiencies using small molecule inhibitors against cyclin dependent kinases, many of which are already clinically approved, while many other specific inhibitors are at various preclinical stages of development for the treatment of other human diseases. Thus, this work is impactful and highly significant. 

      We thank the reviewer for appreciating our work.

      Reviewer #2 (Public Review): 

      Summary: 

      Langenbacher at el. examine the requirement of Rtf1, a component of the PAF1C, which regulates transcriptional pausing in cardiac development. The authors first confirm their previous morphant study with newly generated rtf1 mutant alleles, which recapitulate the defects in cardiac progenitor and diUerentiation gene expression observed previously in morphants. They then examine the conservation of Rtf1 in mouse embryos and embryonic stem cell-derived cardiomyocytes. Conditional loss of Rtf1 in mesodermal lineages and depletion in murine ESCs demonstrates a failure to turn on cardiac progenitor and diUerentiation marker genes, supporting conservation of Rtf1 in promoting cardiac development. The authors subsequently employ bulk RNA-seq on flow-sorted hand2:GFP+ cells and multiomic single-cell RNA-seq on whole Rtf1-depleted embryos at the 10-12 stage. These experiments corroborate that genes associated with cardiac and muscle development are lost. Furthermore, the diUerentiation trajectories suggest that the expression of genes associated with cardiac maturation is not initiated.  Structure-function analysis supports that the Plus3 domain is necessary for its function in promoting cardiac progenitor formation. ChIP-seq for RNA Pol II on 1012 somite stage embryos suggests that Rtf1 is required for proper promoter pausing. This defect can partially be rescued through use of a pharmacological inhibitor for Cdk9, which inhibits elongation, can partially restore elongation in rtf1 mutants.  

      Strengths: 

      Many aspects of the data are strong, which support the basic conclusions of the authors that Rtf1 is required for transcriptional pausing and has a conserved requirement in vertebrate cardiac development. Areas of strength include the genetic data supporting the conserved requirement for Rtf1 in promoting cardiac development, the complementary bulk and single-cell RNA-sequencing approaches providing some insight into the gene expression changes of the cardiac progenitors, the structure-function analysis supporting the requirement of the Plus3 domain, and the pharmacological epistasis combined with the RNA Pol II ChIP-seq, supporting the mechanism implicating Cdk9 in the Rtf1 dependent mechanism of RNA Pol II pausing. 

      We thank the reviewer for the summary and for recognizing many strengths of our work. 

      Weaknesses: 

      While most of the basic conclusions are supported by the data, there are a number of analyses that are confusing as to why they chose to perform the experiments the way they did and some places where the interpretations presently do not support the interpretations. One of the conclusions is that the phenotype aUects the maturation of the cardiomyocytes and they are arresting in an immature state. However, this seems to be mostly derived from picking a few candidates from the single cell data in Fig. 6. If that were the case, wouldn't the expectation be to observe relatively normal expression of earlier marker genes required for specification, such as Nkx2.5 and Gata5/6? The in situ expression analysis from fish and mice (Fig. 2 and Fig. 3) and bulk RNA-seq (Fig. 5) seems to suggest that there are pretty early specification and diUerentiation defects. While some genes associated with cardiac development are not changed, many of these are not specific to cardiomyocyte progenitors and expressed broadly throughout the ALPM. Similarly, it is not clear why a consistent set of cardiac progenitor genes (for instance mef2ca, nkx2.5, and tbx20) was analyzed for all the experiments, in particular with the single cell analysis. 

      A major conclusion of our study is that Rtf1 deficiency impairs myocardial lineage differentiation from mesoderm, as suggested by the reviewer. Thus, the main goal of this study is to understand how Rtf1 drives cardiac differentiation from the LPM, rather than the maturation of cardiomyocytes.  Multiple lines of evidence support this conclusion:

      (a) In situ hybridization showed that Rtf1 mutant embryos do not have nkx2.5+ cardiac progenitor cells and subsequently fail to produce cardiomyocytes (Figs. 2, 3).

      (b) RT-PCR analysis showed that knockdown of Rtf1 in mouse embryonic stem cells causes a dramatic reduction of cardiac gene expression and production of significantly fewer beating patches (Fig.4).

      (c) Bulk RNA sequencing revealed significant downregulation of cardiac lineage genes, including nkx2.5 (Fig. 5).

      (d) Single cell RNA sequencing clearly showed that lateral plate mesoderm (LPM) cells are significantly more abundant in Rtf1 morphant,s whereas cardiac progenitors are less abundant (Fig. 6 and Fig.6 Supplement 1-5). 

      When feasible, we used cardiac lineage restricted markers in our assays. Nkx2.5 and tbx5a are not highlighted in the single cell analysis because their expression in our sc-seq dataset was too low to examine in the clustering/trajectory analysis.  In this revised manuscript, we provide violin plots showing the low expression levels of these genes in single cells from Rtf1 deficient embryos (Figure 6 Supplement 5).

      The point of the multiomic analysis is confusing. RNA- and ATAC-seq were apparently done at the same time. Yet, the focus of the analysis that is presented is on a small part of the RNA-seq data. This data set could have been more thoroughly analyzed, particularly in light of how chromatin changes may be associated with the transcriptional pausing. This seems to be a lost opportunity. Additionally, how the single cell data is covered in Supplemental Fig. 2 and 3 is confusing. There is no indication of what the diUerent clusters are in the Figure or the legend. 

      In this study, we performed single cell multiome analysis and used both scRNAseq and scATACseq datasets to generate reliable clustering.  The scRNAseq analysis reveals how Rtf1 deficiency impacts cardiac differentiation from mesoderm, which inspired us to investigate the underlying mechanism and led to the discovery of defects in Rtf1-dependent transcriptional pause release.

      We agree with the reviewer that deep examination of Rtf1-dependent chromatin changes would provide additional insights into how Rtf1 influences early development and careful examination of the scATACseq dataset is certainly a good future direction.  

      In this revised manuscript, we have revised Fig.6 Supplement 1 to include the predicted cell types and provide an additional excel file showing the annotation of all 39 clusters (Supplementary Table 2). 

      While the effect of Rtf1 loss on cardiomyocyte markers is certainly dramatic, it is not clear how well the mutant fish have been analyzed and how specific the eUect is to this population. It is interpreted that the eUects on cardiomyocytes are not due to "transfating" of other cell fates, yet supplemental Fig. 4 shows numerous eUects on potentially adjacent cell populations. Minimally, additional data needs to be provided showing the live fish at these stages and marker analysis to support these statements. In some images, it is not clear the embryos are the same stage (one can see pigmentation in the eyes of controls that is not in the mutants/morphants), causing some concern about developmental delay in the mutants. 

      Single cell RNA sequencing showed an increased abundance of LPM cells and a reduced abundance of cardiac progenitors in Rtf1 morphants (Fig. 6 and Fig.6 Supplement 1-5). The reclustering of anterior lateral plate mesoderm (ALPM) cells and their derivatives further showed that cells representing undifferentiated ALPM were increased whereas cells representing all three ALPM derivatives were reduced. These findings indicate a defect in ALPM differentiation. 

      The reviewer questioned whether we examined stage-matched embryos. In our assay, Rtf1 mutant embryos were collected from crosses of Rtf1 heterozygotes. Each clutch from these crosses consists of ¼ embryos showing rtf1 mutant phenotypes and ¾ embryos showing wild type phenotypes which were used as control. Mutants and their wild type siblings were fixed or analyzed at the same time.

      The reviewer questioned the specificity of the Rtf1 deficient cardiac phenotype and pointed out that Rtf1 mutant embryos do not have pigment cells around the eye.  Rtf1 is a ubiquitously expressed transcriptional regulator.  Previous studies in zebrafish have shown that Rtf1 deficiency significantly impacts embryonic development. Rtf1 deficiency causes severe defects in cardiac lineage and neural crest cell development; consequently, Rtf1 deficient embryos do not have cardiomyocytes and pigmentation (Langenbacher et al., 2011, Akanuma et al., 2007, and Jurynec et al., 2019).  We now provide an image showing a 2-day-old Rtf1 mutant embryo and their wild type sibling to illustrate the cardiac, neural crest, and somitogenesis defects caused by loss of Rtf1 activity (Fig. 2 Supplement 1).

      With respect to the transcriptional pausing defects in the Rtf1 deficient embryos, it is not clear from the data how this eUect relates to the expression of the cardiac markers. This could have been directly analyzed with some additional sequencing, such as PRO-seq, which would provide a direct analysis of transcriptional elongation. 

      We showed that Rtf1 deficiency results in a nearly genome-wide decrease in promoterproximal pausing and downregulation of cardiac makers. Attenuating transcriptional pause release could restore cardiomyocyte formation in Rtf1 deficient embryos. In this revised manuscript, we provide additional RNAseq data showing that the expression levels of critical cardiac development genes such as nkx2.5, tbx5a, tbx20, mef2ca, mef2cb, ttn.2, and ryr2b are significantly rescued.  We agree with the reviewer that further analyses using the PRO-seq approach could provide additional insights, but it is beyond the scope of this manuscript. 

      Some additional minor issues include the rationale that sequence conservation suggests an important requirement of a gene (line 137), which there are many examples this isn't the case, referencing figures panels out of order in Figs. 4, 7, and 8) as described in the text, and using the morphants for some experiments, such as the rescue, that could have been done in a blinded manner with the mutants. 

      We have clarified the rationale in this revised manuscript and made the eRort to reference figures in order. 

      The reviewer commented that rescue experiments “could have been done in a blinded manner with the mutants”. This was indeed how the flavopiridol rescue and cdk9 knockdown experiments were carried out. Embryos from crosses of Rtf1 heterozygotes were collected, fixed after treatment and subjected to in situ hybridization. Embryos were then scored for cardiac phenotype and genotyped (Fig.8 d-g). Morpholino knockdown was used in genomic experiments because our characterization of rtf1 morphants showed that they faithfully recapitulate the rtf1 mutant phenotype during the timeframe of interest (Fig. 2).

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors): 

      This reviewer has a few suggestions below, aimed at improving the clarity and impact of the current study. Once these items are addressed, the manuscript should be of interest to the Elife reader. 

      Item 1. Strengthening the interaction between Rfh1 and CDK9 on Pol2 pausing. 

      The authors have convincingly shown that the chemical inhibition of CDK9 by flavopiridol can partially rescue the expression of cardiac genes in the zebrafish model. Although flavopiridol is FDA approved and has been a classical inhibitor for the dissection of CDK9 function, it also inhibits related CDKs (such as Flavopiridol (Alvocidib) competes with ATP to inhibit CDKs including CDK1, CDK2, CDK4, CDK6, and CDK9 with IC50 values in the 20-100 nM range) Therefore, this study could be more impactful if the authors can provide evidence on which of these CDKs may be most relevant during Rtf1-dependent cardiogenesis. To determine whether the observed cardiac defect indicates a preferential role for CDK9, or that other CDKs may also be able to provide partial rescue may be clarified using additional, more selective small molecules (e.g., BAY1251152, LDC000067 are commercially available). 

      The reviewer raised a reasonable concern about the specificity of flavopiridol. We thank the reviewer for the insightful suggestion and share the concern about specificity. To address this question, we have used an orthogonal testing through morpholino inhibition where we directly targeted CDK9 and observed the same level of rescue, supporting a critical role of transcription pausing in cardiogenesis.

      Item 2. Differences between CRISPR lines and morphants 

      Much of the work presented used Rtf1 morphants while the authors have already generated 2 CRISPR lines. What is the diUerence between morphants and mutants? The authors should comment on the similarities and/or differences between using morphants or mutants in their study and whether the same Rtf1- CDK9 connection also occurs in the CRISPR lines. 

      The morphology of our mutants (rtf1<sup>LA2678</sup> and rtf1<sup>LA2679</sup>) resembles the morphants and the previously reported ENU-induced rtf1<sup>KT641</sup> allele. Extensive in situ hybridization analysis showed that the morphants faithfully recapitulate the mutant phenotypes (Fig.2). We have performed rescue experiments (flavopiridol and CDK9 morpholino) using Rtf1 mutant embryos and found that inhibiting Cdk9 restores cardiomyocyte formation (Fig.8). 

      Item 3. Discuss the therapeutic relevance of study 

      The authors have already generated a mouse model of Rtf1 Mesp1-Cre knockout where cardiac muscle development is severely derailed (Fig 3B). Thus, a demonstration of a conserved role for CDK9 inhibitor in rescuing cardiogenesis using mouse cells or the mouse model will provide important information on a conserved pathway function relevant to mammalian heart development. In the Discussion, how this underlying mechanistic role may be useful in the treatment of congenital heart disease should be provided.  

      Thank you for the insight. We have incorporated your comments in the discussion. 

      Item 4. Insights into the role of CDK9-Rtf1 in response to stress versus in cardiogenesis. 

      In the Discussion, the authors commented on the role of additional stress-related stimuli such as heat shock and inflammation that have been linked to CDK9 activity. However, the current ms provides the first, endogenous role of Pol2 pausing in a critical developmental step during normal cardiogenesis. The authors should emphasize the novelty and significance of their work by providing a paragraph on the state of knowledge on the molecular mechanisms governing cardiogenesis, then placing their discovery within this framework. This minor addition will also clarify the significance of this work to the broad readership of eLife. 

      Thank you for the suggestion. We have incorporated your comments and elaborate on the novelty and significance of our work in the discussion. 

      Reviewer #2 (Recommendations For The Authors): 

      (1) It is diUicult to assess what the overt defects are in the embryos at any stages. Images of live images were not included in the supplement. Do these have a small, malformed heart tube later or are the embryos just deteriorating due to broad defects? 

      The Rtf1 deficient embryos do not produce nkx2.5+ cardiac progenitors. Consequently, we never observed a heart tube or detected cells expressing cardiomyocyte marker genes such as myl7. This finding is consistent with previous reports using rtf1 morphants and rtf<sup>1KT64</sup>, an ENU-induced point mutation allele (Langenbacher et al., 2011 and Akanuma, 2007). In this revised manuscript, we provide a live image of 2-day-old wild type and rtf1<sup>LA2679/LA2679</sup> embryos (Fig. 2 Supplement 1). After two days, rtf1 mutant embryos undergo broad cell death. 

      (2) Fig. 2, although the in situs are convincing, there is not a quantitative assessment of expression changes for these genes. This could have been done for the bulk or single cell RNA-seq experiments, but was not and these genes weren't not included in the heat maps. A quantitative assessment of these genes would benefit the study. 

      The top 40 most significantly differentially expressed genes are displayed in the heatmap presented in Fig.5d. The complete differential gene expression analysis results for our hand2 FACS-based comparison of rtf1 morphants and controls is presented in Supplementary Data File 1.  In this revised manuscript, we provide a new supplemental figure with violin plots showing the expression levels of genes of interest in our single cell sequencing dataset (Fig.6 Supplement 5).

      (3) It doesn't not appear that any statistical tests were used for the comparisons in Fig. 2.

      We now provide the statistical data in the legend and Fig.2 b, d, f, h and i.

      (4) It's not clear the magnifications and orientations of the embryos in Fig. 3b are the same. 

      Embryos shown in Fig.3b are at the same magnification. However, because Rtf1 mutant embryos display severe morphological defects, the orientation of mutant embryos was adjusted to examine the cardiac tissue.

      (5) The n's for analysis of MLC2v in WT Rtf1 CKO embryos in Fig. 3b are only 1. At least a few more embryos should be analyzed to confirm that the phenotype is consistent. 

      We have revised the figure and present the number of embryos analyzed and statistics in Fig.3c. 

      (6) A number of figure panels are referred to out of order in the text. Fig. 4E-G are before Fig. 4C, D, Fig. 7C  before 7B, Fig. 8D-I before 8A ,B. In general, it is easier for the reader if the figures panels are presented in the order they are referred to in the text. 

      Revised as suggested.

      (7) While additional genes can be included, it is not clear why the same sets of genes are not examined in the bulk or single-cell RNA-seq as with the in situs or expression was analyzed in embryos. I suggest including the genes like nkx2.5, tbx20, myl7, in all the sequencing analysis. 

      We used the same set of genes in all analyses when possible. However, the low expression of genes such as nkx2.5 and myl7 in our sc-seq dataset preclude them from the clustering/trajectory analysis. In this revised manuscript, we present violin plots showing their expression in wild type and rtf1 morphants (Fig. 6 Supplement 5).

      (8) If a multiomic approach was used, why wasn't its analysis incorporated more into the manuscript? In general, a clearer presentation and deeper analysis of the single cell data would benefit the study. The integration of the RNA and ATAC would benefit the analysis.

      As addressed in our response to the reviewer’s public review, both datasets were used in clustering. Examining changes in chromatin accessibility is certainly interesting, but beyond the scope of this study. 

      (9) Many of the markers analyzed are not cardiac specific or it is not clear they are expressed in cardiac progenitors at the stage of the analysis. Hand2 has broader expression. Additional confirmation of some of the genes through in situ would help the interpretations. 

      Markers used for the in situ hybridization analysis (myl7, mef2ca, nkx2.5, tbx5a, and tbx20) are known for their critical role in heart development. For sc-seq trajectory analyses, most displayed genes (sema3e, bmp6, ttn.2, mef2cb, tnnt2a, ryr2b, and myh7bb) were identified based on their differential expression along the LPM-cardiac progenitor pseudotime trajectory. Rather than selecting genes based on their cardiac specificity, our goal was to examine the progressive gene expression changes associated with cardiac progenitor formation and compare gene expression of wild type and rtf1 deficient embryos.

      (10) Additional labels of the cell clusters are needed for Supplemental Figs. 2 and 3. 

      The cluster IDs were presented on Supplementary Figures 2 and 3. In this revised version, we added predicted cell types to the UMAP (revised Fig.6 Supplement 1) and provided an excel file with this information (revised Supplementary Table 2). 

      (11) On lines 101-102, the interpretation from the previous data is that diUerentiation of the LPM requires Rtf1. However, later from the single cell data the interpretation based on the markers is that Rtf1 loss aUects maturation. However, it is not clear this interpretation is correct or what changed from the single cell data. If that were the case, one would expect to see maintenance of more early marks and subsequent loss of maturation markers, which does not appear to the be the case from the presented data.

      Our data suggests that cardiac progenitor formation is not accomplished by simultaneously switching on all cardiac marker genes. Our pseudotime trajectory analysis highlights tnnt2a, ryr2b, and myh7bb as genes that increase in expression in a lagged manner compared to mef2cb (Fig. 6). Thus, the abnormal activation of mef2cb without subsequent upregulation of tnnt2a, ryr2b, and myh7bb in rtf1 morphants suggests a requirement for rtf1 in the progressive gene expression changes required for proper cardiac progenitor differentiation. Our single cell experiment focuses on the process of cardiac progenitor differentiation and does not provide insights into cardiomyocyte maturation. We have edited the text to clarify these interpretations. 

      (12) The interpretation that there is not "transfating" is not supported by the shown data. Analysis of markers in other tissues, again with in situ, to show spatially would benefit the study. 

      As stated in our response to the reviewer’s public review, we observed a dramatic increase of ALPM cells, but a decrease of ALPM derivatives including the cardiac lineage. We did not observe the expansion of one ALPM-derived subpopulation at the expense of the others. These observations suggest a defect in ALPM differentiation and argue against the notion that the region of the ALPM that would normally give rise to cardiac progenitors is instead differentiating into another cell type.

      (13) The rationale that sequence conservation means a gene is important (lines 137-139) is not really true. There are examples a lot of highly conserved genes whose mutants don't have defects. 

      We have revised the text to avoid confusion. 

      (14) The data showing that the 8 bp mutations do not aUect the RNA transcript is not shown or at least indicated in Fig. 7. It would seem that this experiment could have been done in the mutant embryos, in which case the experiment would have been semi-blinded as the genotyping would occur after imaging. 

      The modified Rtf1 wt RNA (Rtf1 wt* in revised Fig. 7) robustly rescued nkx2.5 expression in rtf1 deficient embryos, demonstrating that the 8 bp modifications do not negatively impact the activity of the injected RNA. As stated previously, morpholino knockdown was used in some experiments because our characterization of rtf1 morphants showed that they faithfully recapitulate the rtf1 mutant phenotype during the timeframe of interest.

      (15) Using a technique like PRO-seq at the same stage as the ChIP-seq would complement the ChIP-seq and allow a more detailed analysis of the transcriptional pausing on specific genes observed in WT and mutant embryos. 

      As stated in our response to the reviewer’s public review, we appreciate the suggestion but PRO-seq is beyond the scope of this study.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife assessment 

      This useful study reports that the exogenous expression of the microRNA miR-195 can partially compensate in early B cell development for the loss of EBF1, one of the key transcription factors in B cells. While this finding will be of interest to those studying lymphocyte development, the evidence, particularly with regard to the molecular mechanisms that underpin the effect of miR-195, is currently incomplete. 

      Public Reviews: 

      Reviewer #1 (Public review):

      Summary: 

      Here, the authors are proposing a role for miR-196, a microRNA that has been shown to bind and enhance the degradation of mRNA targets in the regulation of cell processes, and has a novel role in allowing the emergence of CD19+ cells in cells in which Ebf1, a critical B-cell transcription factor, has been genetically removed. 

      Strengths: 

      That over-expression of mR-195 can allow the emergence of CD19+ cells missing Ebf1 is somewhat novel. 

      Their data does perhaps support to a degree the emergence of a transcriptional network that may bypass the absence of Ebf1, including the FOXO1 transcription factor, but this data is not strong or definitive. 

      Weaknesses: 

      It is unclear whether this observation is in fact physiological. When the authors analyse a knockout model of miR-195, there is not much of a change in the B-cell phenotype. Their findings may therefore be an artefact of an overexpression system. 

      The authors have provided insufficient data to allow a thorough appraisal of the stepwise molecular changes that could account for their observed phenotype. 

      Reviewer #2 (Public review): 

      Summary: 

      The authors investigate miRNA miR-195 in the context of B-cell development. They demonstrate that ectopic expression of miR-195 in hematopoietic progenitor cells can, to a considerable extent, override the consequences of deletion of Ebf1, a central Blineage defining transcription factor, in vitro and upon short-term transplantation into immunodeficient mice in vivo. In addition, the authors demonstrate that the reverse experiment, genetic deletion of miR-195, has virtually no effect on B-cell development. Mechanistically, the authors identify Foxo1 phosphorylation as one pathway partially contributing to the rescue effect of miR-195. An additional analysis of epigenetics by ATACseq adds potential additional factors that might also contribute to the effect of ectopic expression of miR-195. 

      Strengths: 

      The authors employ a robust assay system, Ebf1-KO HPC, to test for B-lineage promoting factors. The manuscript overall takes on an interesting perspective rarely employed for the analysis of miRNA by overexpressing the miRNA of interest. Ideally, this approach may reveal, if not the physiological function of this miRNA, the role of distinct pathways in developmental processes. 

      Weaknesses: 

      At the same time, this approach constitutes a major weakness: It does not reveal information on the physiological role of miR-195. In fact, the authors themselves demonstrate in their KO approach, that miR-195 has virtually no role in B-cell development, as has been demonstrated already in 2020 by Hutter and colleagues. While the authors cite this paper, unfortunately, they do so in a different context, hence omitting that their findings are not original. 

      Conceptually, the authors stress that a predominant function of miRNA (in contrast to transcription factors, as the authors suggest) lies in fine-tuning. However, there appears to be a misconception. Misregulation of fine-tuning of gene expression may result in substantial biological effects, especially in developmental processes. The authors want to highlight that miR-195 is somewhat of an exception in that regard, but this is clearly not the case. In addition to miR-150, as referenced by the authors, also the miR-17-92 or miR-221/222 families play a significant role in B-cell development, their absence resulting in stage-specific developmental blocks, and other miRNAs, such as miR-155, miR-142, miR-181, and miR-223 are critical regulators of leukocyte development and function. Thus, while in many instances a single miRNA moderately affects gene expression at the level of an individual target, quite frequently targets converge in common pathways, hence controlling critical biological processes. 

      The paper has some methodological weaknesses as well: For the most part, it lacks thorough statistical analysis, and only representative FACS plots are provided. Many bar graphs are based on heavy normalization making the T-tests employed inapplicable. No details are provided regarding the statistical analysis of microarrays. Generation of the miR-195-KO mice is insufficiently described and no validation of deletion is provided. Important controls are missing as well, the most important one being a direct rescue of Ebf1-KO cells by re-expression of Ebf1. This control is critical to quantify the extent of override of Ebf1-deficiency elicited by miR-195 and should essentially be included in all experiments. A quantitative comparison is essential to support the authors' main conclusion highlighted in the title of the manuscript. As the manuscript currently stands, only negative controls are provided, which, given the profound role of Ebf1, are insufficient, because many experiments, such as assessment of V(D)J recombination, IgM surface expression, or class-switch recombination, are completely negative in controls. In addition, the authors should also perform long-term reconstitution experiments. While it is somewhat surprising that the authors obtained splenic IgM+ B cells after just 10 days, these experiments would be certainly much more informative after longer periods of time. Using "classical" mixed bone marrow chimeras using a combination of B-cell defective (such as mb1/mb1) bone marrow and reconstituted Ebf1-KO progenitors would permit much more refined analyses. 

      With regard to mechanism, the authors show that the Foxo1 phosphorylation pathway accounts for the rescue of CD19 expression, but not for other factors, as mentioned in the discussion. The authors then resort to epigenetics analysis, but their rationale remains somewhat vague. It remains unclear how miR-195 is linked to epigenetic changes. 

      Reviewer #3 (Public review): 

      Summary: 

      In this study, Miyatake et al. present the interesting finding that ectopic expression of miR-195 in EBF1-deficient hematopoietic progenitor cells can partially rescue their developmental block and allow B cells to progress to a B220+ CD19+ cells stage. Notably, this is accompanied by an upregulation of B-cell-specific genes and, correspondingly, a downregulation of T, myeloid, and NK lineage-related genes, suggesting that miR-195 expression is at least in part equivalent to EBF1 activity in orchestrating the complex gene regulatory network underlying B cell development. Strengthening this point, ATAC sequencing of miR-195-expressing EBF1-deficient B220+CD19+ cells and a comparison of these data to public datasets of EBF1-deficient and -proficient cells suggest that miR-195 indirectly regulates gene expression and chromatin accessibility of some, but not all regions regulated by EBF1. 

      Mechanistically, the authors identify a subset of potential target genes of miR-195 involved in MAPK and PI3K signaling. Dampening of these pathways has previously been demonstrated to activate FOXO1, a key transcription factor for early B cells downstream of EBF1. Accordingly, the authors hypothesize that miR-195 exerts its function through FOXO1. Supporting this claim, also exogenous FOXO1 expression is able to promote the development of EBF1-deficient cells to the B220+CD19+ stage and thus recapitulates the miR-195 phenotype. 

      Strengths: 

      The strength of the presented study is the detailed assessment of the altered chromatin accessibility in response to ectopic miR-195 expression. This provides insight into how miR-195 impacts the gene regulatory network that governs B-cell development and allows the formation of mechanistic hypotheses. 

      Weaknesses: 

      The key weakness of this study is that its findings are based on the artificial and ectopic expression of a miRNA out of its normal context, which in my opinion strongly limits the biological relevance of the presented work. 

      While the authors performed qPCRs for miR-195 on different B cell populations and show that its relative expression peaks in early B cells, it remains unclear whether the absolute miR-195 expression is sufficiently high to have any meaningful biological activity. In fact, other miRNA expression data from immune cells (e.g. DOI

      10.1182/blood-2010-10-316034 and DOI 10.1016/j.immuni.2010.05.009) suggest that miR-195 is only weakly, if at all, expressed in the hematopoietic system. 

      The authors support their finding by a CRISPR-derived miR-195 knockout mouse model which displays mild, but significant differences in the hematopoietic stem cell compartment and in B cell development. However, they fail to acknowledge and discuss a lymphocyte-specific miR-195 knockout mouse that does not show any B cell defects in the bone marrow or spleen and thus contradicts the authors' findings (DOI

      10.1111/febs.15493). Of note, B-1 B cells in particular have been shown to be elevated upon loss of miR-15-16-1 and/or miR-15b-16-2, which contradicts the data presented here for loss of the family member miR-195. 

      A second weakness is that some claims by the authors appear overstated or at least not fully backed up by the presented data. In particular, the findings that miR-195expressing cells can undergo VDJ recombination, express the pre-BCR/BCR and class switch needs to be strengthened. It would be beneficial to include additional controls to these experiments, e.g. a RAG-deficient mouse as a reference/negative control for the ddPCR and the surface IgM staining, and cells deficient in class switching for the IgG1 flow cytometric staining. 

      Moreover, the manuscript would be strengthened by a more thorough investigation of the hypothesis that miR-195 promotes the stabilization and activity of FOXO1, e.g. by comparing the authors' ATACseq data to the FOXO1 signature. 

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors): 

      Miyatake et al., present a manuscript that explores the role of miR-195 in B cell development. 

      Their data suggests a role for this microRNA: 

      Using an Ebf1 fetal liver knockout of B-cell differentiation that a small population of CD19 expressing with some evidence of V(D)J recombination capable of class switch can be derived by transduction of miR-195. 

      In the emergent CD19+ Ebf1-/- cells, the authors provide some evidence that Mapk and Akt3 may be miR-195 targets that are downregulated allowing FOXO1 transcription factor pathway may be involved in the emergent CD19+ cells arising from miR-195 transduction. 

      Perhaps less compelling data is provided with regards to a role for miR-195 in normal Bcell development through analysis of a miR-195 knockout model. 

      While there are some interesting preliminary data presented for a role for miR-195 in the context of Ebf1-/- cells, there are some questions I think the authors could consider. 

      Comments: 

      (1-1) It is difficult to ascertain the potential role of miR-195 transduction in allowing the emergence of CD19+ cells from the data provided. miR-195 has been generally shown to destabilize mRNA transcripts by 3' UTR binding that targets mRNA transcripts for degradation. The effect of transduction of miR-195 would therefore be expected to be related to the degradation of factors opposing aspects of B-lineage specification or maintenance. I would be particularly interested in transcriptional or epigenetic regulators that may be modified in this way, at an mRNA as well as protein level.

      We appreciate the reviewerʼs thoughtful comments and agree that miRNAs often exert their effects through the degradation or translational repression of mRNAs encoding regulatory factors. In our study, we attempted to address this point by combining predictive analysis (using TargetScan and starBase) with luciferase reporter assays and qPCR to validate several potential targets of miR-195, including Mapk3 and Akt3. We acknowledge that this is not a comprehensive mechanistic analysis. We agree that a broader and systematic identification of direct targets of miR-195, particularly those involved in transcriptional and epigenetic regulation, would further clarify the mechanisms involved. However, due to limitations in resources and time, we are currently unable to perform global proteomic or ChIP-based validations. Nevertheless, our ATAC-seq and microarray data indicate that miR-195 overexpression leads to increased accessibility and expression of several key B-lineage transcription factors (Pax5, Runx1, Irf8), suggesting that miR-195 indirectly activates transcriptional programs relevant to B cell commitment. We have now clarified this limitation in the revised Discussion section (lines 505‒524), and we emphasize that our current findings represent the potential of miR-195 rather than its physiological role. We hope that this clarification addresses the concern.

      (1-2) While I acknowledge the authors have undertaken TargetScan and starBase analysis to try and predict miR-195 interactions, they do not provide a comprehensive list of putative targets that can be referenced against their cDNA data. Though they postulate Mapk3 and Akt3 as putative miR-195 targets and assay these in luciferase reporter systems (Figure 4), these were not clearly differentially regulated in the microarray data they provided (Figure 1E) as being downregulated on miR-195 transduction in Ebf1-/- cells.

      We thank the reviewer for pointing out the need for a more comprehensive list of predicted miR-195 targets. In response, we have now included a supplementary table 4 (human) and 5 (mouse) listing all putative miR-195 targets predicted by TargetScan and starBase. As noted, Mapk3 expression was indeed downregulated upon miR-195 transduction, consistent with our luciferase reporter and qPCR results. For Akt3, we observed variability in the microarray data depending on the probe used, resulting in inconsistent expression levels. We acknowledge this and have added a clarification in the revised manuscript (lines 335‒339), noting that the regulation of Akt3 by miR-195 is potentially probe-dependent and may require further validation. We hope this clarification resolves the concern.

      (1-3) The authors should provide a more comprehensive analysis of transcriptional changes induced by miR-195 Ebf1-/- specifically in the preproB cell stage of development in Ebf1-/- and miR-195 Ebf1-/- cells. The differentially expressed gene list should be provided as a supplemental file. The gene expression data should be provided for the different B-cell differentiation stages, eg. Ebf1-/- preproB cells, and Ebf1-/- miR-195 preproB cells, CD19+ cells and more differentiated subsets induced by miR-195 transduction.

      We appreciate the reviewerʼs suggestion to provide a more comprehensive transcriptomic analysis at different B-cell differentiation stages. Unfortunately, due to the limited availability of cells and technical constraints, we were unable to perform RNA-seq on miR-195 transduced Ebf1<sup>−/−</sup> pre-pro-B or CD19+ cells. However, to address this point, we referenced publicly available RNA-seq data (GEO accession: GSE92434), which includes transcriptomic profiles of Ebf1<sup>−/−</sup> pro-B cells and wild-type controls. By comparing our microarray data from miR-195 transduced Ebf1<sup>−/−</sup> cells with this dataset, we found partial restoration of expression for several key B-lineage genes, such as Pax5, Runx1, and Irf8, which are normally downregulated in the absence of EBF1. This comparison supports the notion that miR-195 partially reactivates the transcriptional network essential for B cell development. We have added this interpretation to the Discussion section (lines 528‒533).

      (1-4) More replicates (at least 3 of each genotype) are required for their Western Blots for FOXO1 and pFOXO1 (Fig 4C, D). Western blots should also be provided for other known B-lineage transcriptional regulators such as PAX5 and ERG.

      We thank the reviewer for these valuable suggestions. In response, we have now quantified and added the relative band intensities of FOXO1 and pFOXO1 from three independent experiments in the revised Figure 4C, and we include statistical analysis to support the reproducibility of these results. Additionally, as requested, we performed western blotting for PAX5 and ERG using the same samples. The results showed no significant change in these protein levels between miR-195-transduced and control Ebf1<sup>−/−</sup> cells, consistent with the modest upregulation observed in our microarray data. We have included the PAX5 and ERG western blot images in Supplementary Figure S3 and have revised the text in the Results section (lines 351‒35)

      (1-5) The authors have not shown a transcriptional binding by ChIPseq or other methods such as cut and tag/ cut and run for FOXO1 binding to B-lineage genes in their Ebf1-/- miR-195 CD19+ cells to be able to definitively show this TF is critical for the emergence of the C19+ cell phenotype by demonstrating direct binding to "upregulated" genes cis-regulatory regions in the Ebf1-/- miR-195 CD19+ cells

      We appreciate the reviewerʼs suggestion regarding the use of ChIP-seq or related methods to demonstrate direct FOXO1 binding to cis-regulatory regions of B-lineage genes in Ebf1<sup>−/−</sup> miR-195 CD19⁺ cells. We agree that such data would provide definitive evidence of FOXO1's direct involvement in promoting the B cell-like transcriptional program. However, due to current technical limitations, including the scarcity of CD19⁺ cells derived from Ebf1<sup>−/−</sup> miR-195 transduction and the requirement for large cell numbers in ChIP-seq or CUT&RUN protocols, we were unable to perform these assays in this study. Nevertheless, our current data provide multiple lines of indirect evidence supporting the involvement of FOXO1:

      miR-195 transduction leads to reduced phosphorylation and increased accumulation of FOXO1 protein (Fig. 4C).

      Overexpression of FOXO1 in Ebf1<sup>−/−</sup> HPCs partially recapitulates the miR-195 phenotype (Fig. 4D).

      ATAC-seq data show increased chromatin accessibility at known FOXO1 target gene loci (e.g., Pax5, Runx1, Irf8) in miR-195-induced CD19⁺ cells, many of which overlap with FOXO1 motifs(Fig.5)

      These observations collectively suggest that FOXO1 activity is functionally important for the emergence of CD19⁺ cells, even though direct binding has not been confirmed. We have added this limitation to the Discussion (lines 531‒537), and we note that future studies using FOXO1 CUT&RUN in this system would be valuable to further define the underlying mechanism.

      (1-6) The authors have not shown significant upregulation of expression of other critical B-cell regulatory transcription factors in their Ebf1-/- miR-195 CD19+ cells that could account for the emergence of these cells such as Pax5 or Erg. The legend in Figure 1E suggests for example the change in expression of Pax5 is modest if anything at best as no LogFC or western blot data is presented. 

      We thank the reviewer for raising this point. In our microarray analysis (Figure 1D, original Figure 1E), we observed that both Pax5 and Erg mRNA levels were upregulated in Ebf1<sup>−/−</sup> cells upon miR-195 transduction. Specifically, Pax5 showed an increase of approximately log₂FC 1.2, and Erg was also consistently elevated across biological replicates. These changes, although modest, were statistically significant and consistent with the upregulation of other B-lineage-associated transcription factors, such as Runx1 and Irf8. We agree that the magnitude of Pax5 upregulation is not as high as typically seen during full B cell commitment, and therefore may not have been immediately apparent in Figure 1D (original Figure 1E). To clarify this point, we have now revised the text in the Results section (lines 170‒174) to highlight the observed changes in Pax5 and Erg expression. We believe that the upregulation of these transcription factors, together with increased FOXO1 activity and changes in chromatin accessibility (Figure 5), contributes to the partial reactivation of the B cell gene regulatory network in the absence of EBF1.

      (1-7) Which V(D)J transcripts have been produced? A more detailed analysis other than ddPCR is required to help understand the emergence of this population that can presumably proceed through the preBCR and BCR checkpoints.

      We appreciate the reviewerʼs interest in understanding the nature of the V(D)J rearrangements in Ebf1<sup>−/−</sup> miR-195 CD19⁺ cells. As noted, our current data rely on droplet digital PCR (ddPCR), which was used to detect rearranged VH-JH segments in the bone marrow of engrafted mice. While this approach does not allow for detailed mapping of specific V, D, or J gene usage, it provides a sensitive and quantitative measure of V(D)J recombination activity. The detection of rearranged VH-JH fragments in miR-195-transduced Ebf1<sup>−/−</sup> cells suggests that at least partial recombination of the immunoglobulin heavy chain locus is occurring̶an essential checkpoint for progression past the pro-B cell stage. Given the lack of such rearrangements in control-transduced Ebf1<sup>−/−</sup> cells, we interpret this as evidence that miR-195 enables cells to initiate the recombination process. We acknowledge the limitations of ddPCR and agree that a more detailed analysis using VDJ-seq or singlecell RNA-seq would be valuable in determining the diversity and completeness of the V(D)J transcripts produced. This is a direction we intend to pursue in future work. We have added this limitation to the Discussion section (lines 538‒543).

      (1-8) The authors reveal that the Foxo1 transduced Ebf1-/- cells (Fig. 4D) do not persist in vitro or be detected via transplant assay (line 256) and therefore does not represent a truly "rescued" B cell, suggesting that CD19+ cells Ebf1-/- miR-195 transduced cells have more B-cell potential. Further characterisation is therefore warranted of this cell population. For instance, can these cells be induced to undergo myeloid differentiation in myeloid cytokine conditions? What other B-lineage transcriptional regulators are expressed in this cell population that could account for VDJ recombination and expression of a B-lineage transcriptional program (see comments 1, 3, and 5) that allow transition through preBCR and BCR checkpoints as well as undergo class switching?

      We thank the reviewer for this insightful comment. We agree that the persistence and lineage potential of the CD19⁺ cells emerging from Ebf1<sup>−/−</sup> miR-195-transduced progenitors deserve further characterization. Although we were unable to perform additional lineage re-direction assays, our current data provide several lines of evidence suggesting that these cells are stably committed toward the B-lineage:

      Gene expression profiling revealed upregulation of multiple B cell transcriptional regulators, including Pax5, Runx1, and Irf8.

      ATAC-seq analysis showed increased chromatin accessibility at B cell‒specific loci and enrichment of motifs bound by key B-lineage factors such as FOXO1 and E2A.

      The cells express surface IgM and undergo class switch recombination to IgG1 upon stimulation, indicating successful transition through the pre-BCR and BCR checkpoints and acquisition of mature B cell functions.

      Importantly, no upregulation of myeloid- or T-lineage genes was detected in the microarray analysis, arguing against multipotency at this stage.We acknowledge that functional tests for lineage plasticity under altered cytokine conditions would provide important insights and plan to address this question in future studies. This limitation has now been noted in the revised Discussion (lines 544‒550).

      (1-9) In the original Ebf1-/- miR-195 CD19+ experiments, a wild-type control should be provided for each experiment. 

      We appreciate the reviewerʼs suggestion to include wild-type controls in all experiments. While we did not include wild-type samples side-by-side in every assay, we carefully designed our experiments to include biologically appropriate and informative comparisons. For example, in the bone marrow transplantation experiments (Figure 2), Ebf1<sup>−/−</sup> cells transduced with empty vector served as negative controls, clearly lacking CD19 expression, V(D)J recombination, IgM surface expression, and class switch capability. This allowed us to specifically assess the gain-of-function effects of miR-195 in the EBF1-deficient background. In several analyses̶such as the ATAC-seq and microarray comparisons̶we did incorporate or refer to existing wild-type datasets (e.g., GSE92434), providing context for the extent of recovery toward a WT-like profile. We agree, however, that including parallel WT controls across all experimental platforms would enhance interpretability.

      (1-10) For ATACseq data, a comparison between Ebf1-/- preproB cells and Ebf1-/- miR-195 CD19+ cells should be undertaken.

      We thank the reviewer for this important point. As suggested, we have performed a direct comparison of chromatin accessibility between Ebf1<sub>−/−</sub> pre-pro-B‒like cells (CD19<sub>-</sub>, control transduction) and Ebf1<sub>−/−</sub> miR-195‒transduced CD19⁺ cells. This comparison is shown in green in Figure 5B and represents the ATAC-seq peaks differentially accessible between these two populations.  

      (1-11) I cannot agree with the authors with some of their statements such as Line 242 - "therefore miR-195 considered to have similar function with EBF1 to some extent" - how can this be the case when miR-195 is a miRNA and EBF1 is a transcription factor with pioneering transcriptional activity? Surely the effects of miR-195 must be secondary.

      We thank the reviewer for pointing out the inappropriateness of comparing miR-195 to EBF1 in terms of functional similarity. We agree that miR-195, as a microRNA, operates through post-transcriptional regulation and does not possess the pioneering transcriptional activity characteristic of EBF1. To avoid confusion or overstatement, we have removed the sentence in line 242 ("therefore miR-195 is considered to have similar function with EBF1 to some extent").

      (1-12) It is unclear whether this observation is in fact physiological. When the authors analyse a knockout model of miR-195, there is not much of a change in the B-cell phenotype. Their findings may therefore be an artefact of an overexpression system. The authors should comment on this observation in their discussion.  

      We thank the reviewer for this important observation. We agree that the mild phenotype observed in our miR-195 knockout mice suggests that miR-195 is not essential for B cell development under steady-state physiological conditions. Accordingly, we do not claim a physiological requirement for miR-195. Rather, our study demonstrates that miR-195 possesses the potential to activate a B-lineage program in the absence of EBF1 when ectopically expressed. This functional potential̶rather than its endogenous necessity̶ is the main focus of our work. We have now clarified this distinction in the revised Discussion section (lines 551‒560), and we emphasize that our findings highlight an alternative regulatory pathway that can be artificially engaged under specific conditions.

      (1-13) I recommend the authors check spelling and grammar throughout their manuscript.

      We thank the reviewer for the suggestion. In response, we have carefully reviewed the manuscript for spelling, grammar, and clarity. Minor corrections have been made throughout the text to improve readability and ensure consistency. We hope that the revised version addresses any language-related concerns. In addition, the manuscript has been reviewed by professional editing service to improve the language quality.

      (1-14) In general, I recommend more comprehensive primary data be presented in the manuscript or supplementary files to add value to their submission.

      We thank the reviewer for this helpful suggestion. In response, we have revised the manuscript and supplementary materials to include additional primary data wherever possible. The bar graphs have been updated to include individual data points to show variability and replicate information. Uncropped western blot images are now provided in Supplementary Figure S2. We hope these additions provide greater transparency and value to the manuscript. 

      Reviewer #2 (Recommendations for the authors): 

      I have a number of suggestions with regard to inclusion of details and controls: 

      (2-1) The authors need to provide more details on in vitro differentiation, especially culture times. 

      Thank you for your comment. The culture conditions for in vitro differentiation of Ebf1<sup>−/−</sup> hematopoietic progenitor cells are described in the Methods section (lines 648‒ 649) under “Culture of lineage-negative (Lin‒) cells from the fetal liver.” As stated, cells were cultured more than 7 days under the specified conditions.

      (2-2) In Figure 1E, the authors need to provide information on statistics (FDR or similar). 

      I thank the reviewer for the suggestion. In Figure 1D (Original Figure 1E) (the microarray analysis), only two biological replicates were available for each condition (n = 2 per group). Due to this limited sample size, we did not perform statistical testing, as the power would be insufficient to produce reliable p-values or adjusted FDRs. Instead, we focused on genes with consistent and biologically meaningful changes in expression, and presented representative examples based on fold change values.

      (2-3) For in vivo experiments (Figure 2) the authors should comment on their use of two different recipient mouse strains despite very low n numbers. As described above, classical mixed BM chimeras would be much more informative. In these experiments, the authors should also show the formation of other lymphoid lineages. This would answer the question of whether miR-195 redirects cells to the B lineage. Most importantly, absolute numbers need to be provided, especially in conjunction with Ebf1 rescue as described above. 

      We thank the reviewer for the thoughtful and detailed suggestions regarding our in vivo experiments. Regarding the use of different recipient mouse strains, our initial intention was to perform the transplantations in BRG mice; however, due to facility restrictions and animal husbandry considerations, we had to switch to NOG mice. All in vivo experiments were performed with n = 3 per group, in accordance with ethical guidelines and efforts to minimize animal use while still ensuring reproducibility. With respect to the suggestion of mixed bone marrow chimeras, we agree that this approach can provide valuable information on lineage competitiveness. However, in our system, miR-195 confers only a very limited B cell developmental potential in Ebf1<sup>−/−</sup> progenitors. In such a setting, the inclusion of wild-type competitor cells would overwhelmingly dominate the B cell compartment, likely masking any measurable effect of miR-195. Therefore, we opted to assess the gain-of-function potential of miR-195 in a noncompetitive setting. Regarding the assessment of other lymphoid lineages, we focused our analysis on the emergence of B-lineage cells, as the frequency of CD19⁺ cells induced by miR-195 is quite low. Given this low efficiency, we consider it unlikely that miR-195 significantly alters the development of non-B lineages, and thus did not observe substantial lineage diversion effects. Our aim was not to demonstrate lineage redirection, but rather to show that miR-195 can confer partial B cell potential in the absence of EBF1.

      Finally, we acknowledge the importance of presenting absolute cell numbers. However, the cell number collected from the mice were so few that we did not get the reliable results, we described it in the manuscript. (lines 498-501)

      (2-4) The statistics in Figure 3 are inadequate. No S.D. is provided for WT. How then was normalization performed? Student's T-test cannot be applied to ratios. 

      We thank the reviewer for highlighting the need for more appropriate statistical analysis. Due to considerable inter-batch variability in absolute measurements, we normalized the KO values to their paired WT counterparts from the same experimental batch. Specifically, for each replicate, we calculated the KO/WT ratio to control for batch-specific variation. We then applied a one-sample t-test (against a null hypothesis of ratio = 1) to determine statistical significance. We have now revised the figure to show individual ratio values for each replicate and updated the legend and Methods to clearly explain the statistical approach. We hope this addresses the concern and improves the clarity and rigor of the analysis.

      (2-5) In Figure 4A, the authors should comment on the strong repression of the Akt3UTR. 

      We appreciate the reviewerʼs observation regarding the strong repression observed with the Akt3 3'UTR construct. Indeed, we also noted that luciferase activity was markedly reduced in the presence of the Akt3 3'UTR, even in cells transduced with a control vector. We hypothesize that the Akt3 3'UTR contains strong post-transcriptional regulatory elements̶such as AU-rich elements or binding sites for endogenous miRNAs or RNA-binding proteins̶which may suppress mRNA stability or translation independent of miR-195. Alternatively, the secondary structure or length of the UTR may inherently reduce luciferase expression. We have added this limitation to the Discussion section (lines 561‒569).

      (2-6) The Western blot in Figure 4C is of insufficient quality. The authors need to provide unspliced versions of the bands including markers. 

      We thank the reviewer for this important comment. In response, we have included the unprocessed, full-length Western blot images corresponding to Figure 4C as Fig. S2. This provides a transparent view of the original data and addresses the concern about image cropping.

      (2-7) The ATACseq experiment in Figure 5 is difficult to comprehend. A simpler design including Ebf1 rescue controls would clearly improve this part. 

      We thank the reviewer for this valuable feedback. We agree that the original presentation of the ATAC-seq data may have been difficult to interpret. To address this, we have included a clear interpretation of the overlapping regions in the revised figure legend (lines 1018-1022). We hope this improves the clarity of the data and facilitates understanding of the chromatin changes mediated by EBF1 and miR-195.

      (2-8) The miR-195 KO mouse lacks validation (RT-PCR, genomic PCR) as well as a clear description of the deleted region and whether miR-497 is affected. In addition, the genetic background and number of backcrosses for the removal of potential off-target effects need to be mentioned. 

      We thank the reviewer for this important comment. The miR-195 knockout mouse was generated via CRISPR/Cas9, and Sanger sequencing confirmed a 628 bp deletion on chromosome 11 (GRCm38/mm10 chr11:70,234,425‒70,235,103). This deletion includes the entire miR-497 locus and part of the miR-195 precursor sequence. Although we do not show PCR gel images, the deletion was validated by sequencing, and the results are now clearly described in the revised Methods section (lines 607619). All transgenic mice in this study were backcrossed to the C57BL/6 background for at least eight generations.

      (2-9) The manuscript requires extensive editing for language. 

      We appreciate the reviewerʼs comment. The manuscript has now been revised and professionally edited for language by a native English-speaking editor. We believe clarity and readability have been significantly improved.

      Reviewer #3 (Recommendations for the authors): 

      (3-1) What is the expression level of miR-195 after viral overexpression? In Figure 4B, the authors show a 2.5-fold increase, but this appears very low for the experimental system (expression through the MDH1 retroviral construct) and the observed repressive effects (e.g. Figure 4A and B). 

      We thank the reviewer for this insightful comment. We agree that the apparent ~2.5fold increase in miR-195 levels (Figure 4B) may seem modest in the context of retroviral overexpression and the associated functional effects. However, due to the high sequence similarity within the miR-15/16/195/497 family, it is technically challenging to measure mature miR-195 levels with complete specificity. The baseline signal observed in control samples likely reflects cross-reactivity with endogenous miRNAs such as miR-497 or miR-16, which share similar seed sequences. Therefore, the reported fold-change may underestimate the true level of ectopic miR-195 expression. Despite this, we observed robust repression of validated targets (e.g., Mapk3, Akt3) in both qPCR and luciferase assays, indicating that functionally effective levels of miR-195 were achieved. We have now clarified this limitation and interpretation in the revised Results sections (lines 332‒335).

      (3-2) In alignment with the transparency of the data, I would encourage the authors to display the individual data points for all bar graphs. 

      We thank the reviewer for this helpful suggestion. In the revised manuscript, we have updated bar graphs to include individual data points to increase transparency and allow better visualization of data variability. In the ddPCR experiments, we provided the raw data in Fig. S1 for full transparency. In Fig. 1A, we have confirmed miR-195 expression profiles using the deposit data which the reviewer suggested, but miR-195 expression was very lower than we expected. We also performed scRNA-seq using hematopoietic lineage cells in 8-week-old C57BL/6 mice, but we could not get the reproducibility of miR-195 expression profiles. Therefore, we determined that this is an artifact caused by the miR-195 probe used for qPCR, and deleted Fig. 1A.

      (3-3) The references appear to be compromised. For example, the authors state that "The Ebf1−/+ mouse was originally generated by R. Grosschedl (39)" (line 297), but this is not the respective paper. Likewise, the knockout mouse was generated "based on the CRISPR/Cas9 system established by C. Gurumurthy (40)" (line 299), but he/she is not involved in the referenced study. 

      We thank the reviewer for pointing out the discrepancies in the reference citations. Upon revising the Methods section to integrate it with the main text, the reference numbering became misaligned. We have corrected the reference in the revised manuscript, and we thank the reviewer for bringing this to our attention.

      (3-4) Given that the miRNA Taqman assays the authors used here have difficulties to discriminate closely related miRNAs such as e.g. miR-16 (highly expressed in the hematopoietic system) and miR-195, I would suggest that the authors test their qPCR in an appropriate setup, e.g. in their knockout mouse model. In this context, did the authors use another small RNA as a reference for the qPCR analysis? In the methods, only GAPDH is mentioned, but in my opinion, another RNA that uses the same stemloop-based cDNA synthesis protocol would be better suited.

      We thank the reviewer for this valuable and technically insightful comment.

      As correctly pointed out, TaqMan-based qPCR assays for miRNAs such as miR-195 can show cross-reactivity with closely related family members, particularly miR-16, which is abundantly expressed in hematopoietic cells. Indeed, due to this limitation, we do not treat the qPCR results shown in the original Figures 1A and 4B as definitive quantification of miR-195 expression. Rather, these data are used to provide a suggestion and a rough estimate of overexpression efficiency, while our core functional analyses rely on phenotypic and molecular outcomes such as target gene repression and lineage emergence. With this in mind, although we acknowledge that a small RNA reference based on the same stem-loop cDNA synthesis would offer a more compatible normalization in principle, the inherent variability and lack of absolute specificity in such assays also limits their interpretive value. Therefore, we used GAPDH as a normalization control for consistency with other qPCR analyses in the manuscript. We have now clarified this rationale and limitation in the revised Methods sections (lines 712‒716), and we thank the reviewer again for highlighting this important technical consideration.

      (3-5) The Western blot data used to support the hypothesis that FOXO1 phosphorylation is reduced upon overexpression of miR-195 are not convincing. The authors should not crop everything but the band. 

      We thank the reviewer for the helpful comment. In response, we have now provided the full-length, uncropped Western blot images corresponding to Figure 4C, including both total FOXO1 and phospho-FOXO1 blots. These images are included in Fig. S2.

    1. Author response:

      The following is the authors’ response to the original reviews

      Comment from the editors at eLife:

      You could consider further strengthening the manuscript with the incorporation of new relevant public datasets for network modeling, but that is entirely your choice.

      We thank the editors and reviewers for their thoughtful and positive feedback on our article. We are particularly appreciative of the eLife assessment describing our work as valuable with a convincing methodology.

      As suggested, we have expanded our neuron class analysis by incorporating transcriptomic data from young adult animals (Kaletsky et al., 2016 Nature; Ghaddar et al., 2023 Science Advances; St Ange et al., 2024 Cell Genomics) to complement our existing analysis of larval stage 4 (L4) animals.

      In addition, we have updated Table S1 to include the outcross status of all strains used in this study, providing clearer information on the genotypes tested. We have also corrected the typographical errors noted by the reviewers. Please note that page and line numbers below refer to the MS Word Document with tracked changes set to ‘simple markup’.

      We greatly appreciate the reviewers’ input and hope these revisions further enhance the value and clarity of our study.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Rahmani et al. utilize the TurboID method to characterize global proteome changes in the worm's nervous system induced by a salt-based associative learning paradigm. Altogether, they uncover 706 proteins tagged by the TurboID method in worms that underwent the memory-inducing protocol. Next, the authors conduct a gene enrichment analysis that implicates specific molecular pathways in salt-associative learning, such as MAP kinase and cAMP-mediated pathways, as well as specific neuronal classes including pharyngeal neurons, and specific sensory neurons, interneurons, and motor neurons. The authors then screen a representative group of hits from the proteome analysis. They find that mutants of candidate genes from the MAP kinase pathway, namely dlk-1 and uev-3, do not affect performance in the learning paradigm. Instead, multiple acetylcholine signaling mutants, as well as a protein-kinase-A mutant, significantly affected performance in the associative memory assay (e.g., acc-1, acc-3, lgc-46, and kin-2). Finally, the authors demonstrate that protein-kinase-A mutants, as well as acetylcholine signaling mutants, do not exhibit a phenotype in a related but distinct conditioning paradigm-aversive salt conditioning-suggesting their effect is specific to appetitive salt conditioning.

      Overall, the authors addressed the concerns raised in the previous review round, including the statistics of the chemotaxis experiments and the systems-level analysis of the neuron class expression patterns of their hits. I also appreciate the further attempt to equalize the sample size of the chemotaxis experiments and the transparent reporting of the sample size and statistics in the figure captions and Table S9. The new results from the panneuronal overexpression of the kin-2 gain-of-function allele also contribute to the manuscript. Together, these make the paper more compelling. The additional tested hits provide a comprehensive analysis of the main molecular pathways that could have affected learning. However, the revised manuscript includes more information and analysis, raising additional concerns.

      Major comments:

      As reviewer 4 noted, and as also shown to be relevant for C30G12.6 presented in Figure 6, the backcrossing of the mutants is important, as background mutations may lead to the observed effects. Could the authors add to Table 1, sheet 1, the outcrossing status of the tested mutants?

      We appreciate this important point. A column has now been added to Table S1 to indicate the outcross status of all strains used in this study. Additionally, we have updated the table legend on page 77 to clarify how to interpret the information provided in this column.

      It is important to validate that the results of the positive hits (where learning was affected), such as acc-1, acc-3, and lgc-46, do not stem from background mutations.

      While we agree that confirming the absence of background mutations is important, we have taken alternative steps to address this concern:

      - The outcross status of each strain is now clearly indicated in Table S1.

      - Observed phenotypes were consistent across multiple biological replicates over extended periods (months, sometimes years), reducing the likelihood that results stem from background mutations.

      We believe these measures provide confidence in the validity of our findings.

      The fold change in the number of hits for different neurons in the CENGEN-based rank analysis requires a statistical test (discussed on pages 17-19 and summarized in Table S7). Similar to the other gene enrichment analyses presented in the manuscript, the new rank analysis also requires a statistical test. Since the authors extensively elaborate on the results from this analysis, I think a statistical analysis is especially important for its interpretation. For example, if considering the IL1 neurons, which ranked highest, and assuming random groups of genes-each having the same size as those of the ranked neurons (209 genes in total for IL1 in Table S7)-how common would it be to get the calculated fold change of 1.38 or higher? Such bootstrapping analysis is common for enrichment analysis. Perhaps the authors could consult with an institutional expert (Dr. Pawel Skuza, Flinders University) for the statistical aspects of this analysis.

      We appreciate the suggestion and agree that statistical testing can be valuable for enrichment analyses. However, implementing additional tests such as bootstrapping is beyond the scope of this study. Our aim was to provide a descriptive overview rather than inferential statistics. To ensure transparency and interpretability, we have:

      - Clearly reported fold changes and rankings in Table S7.

      - Discussed the limitations of this approach in the manuscript text (page 18, lines 17–20).

      - Clearly outlined the methods used to perform this analysis (pages 53–54).

      We believe this descriptive analysis provides sufficient context for interpreting these results.

      The learning phenotypes from Figure S8, concerning acc-1, acc-3, and lgc-46 mutants, are summarized in a scheme in Figure 4; however, the chemotaxis results are found in the supplemental Figure S8. Perhaps I missed the reasoning, but for transparency, I think the relevant Figure S8 results should be shown together with their summary scheme in Figure 4.

      Thank you for this suggestion to improve clarity. We have now moved the panels corresponding to cholinergic signalling components from Figure S8 into Figure 4 on page 21, so that the summary scheme and underlying data are presented together. The figure legends and main text have been updated accordingly to reflect the correct figure numbers.

      Reviewer #2 (Public review):

      Summary:

      In this study by Rahmani in colleagues, the authors sought to define the "learning proteome" for a gustatory associative learning paradigm in C. elegans. Using a cytoplasmic TurboID expressed under the control of a pan-neuronal promoter, the authors labeled proteins during the training portion of the paradigm, followed by proteomics analysis. This approach revealed hundreds of proteins potentially involved in learning, which the authors describe using gene ontology and pathway analysis. The authors performed functional characterization of over two dozen of these genes for their requirement in learning using the same paradigm. They also compared the requirement for these genes across various learning paradigms and found that most hits they characterized appear to be specifically required for the training paradigm used for generating the "learning proteome".

      Strengths:

      The authors have thoughtfully and transparently designed and reported the results of their study. Controls are carefully thought-out, and hits are ranked as strong and weak. By combining their proteomics with behavioral analysis, the authors also highlight the biological significance of their proteomics findings, and support that even weak hits are meaningful.

      The authors display a high degree of statistical rigor, incorporating normality tests into their behavioral data which is beyond the field standard.

      The authors include pathway analysis that generates interesting hypotheses about processes involved learning and memory

      The authors generally provide thoughtful interpretations for all of their results, both positive and negative, as well as any unexpected outcomes.

      Weaknesses:

      - The authors use the Cengen single cell-transcriptomic atlas to predict where the proteins in the "learning proteome" are likely to be expressed and use this data to identify neurons that are likely significant to learning, and building hypothetical circuit. This is an excellent idea; however, the Cengen dataset only contains transcriptomic data from juvenile L4 animals, while the authors performed their proteome experiments in Day 1 Adult animals. It is well documented that the C. elegans nervous system transcriptome is significant different between these two stages (Kaletsky et al., 2016, St. Ange et al., 2024), so the authors might be missing important expression data, resulting in inaccurate or incomplete networks. The adult neuronal single-cell atlas data (https://cestaan.princeton.edu/) would be better suited to incorporate into neuronal expression analysis.

      Thank you for highlighting this important point. We have now incorporated transcriptomic data from young adult animals to complement the L4-based CeNGEN dataset. Specifically, we integrated data from CeSTAAN (https://cestaan.princeton.edu/, including St. Ange et al., 2024) and WormSeq (https://wormseq.org/, including Ghaddar et al., 2023), as outlined below. Importantly, CeSTAAN and WormSeq provide data for 79 and 104 neuron classes, respectively (compared to 128 from CeNGEN); for this reason, the main analysis focuses on CeNGEN due to its broader coverage, with additional datasets noted in brackets for completeness. This is stated on page 18, lines 15–17 to ensure transparency regarding our rationale.

      The main text has been updated to describe these datasets and their integration into our analysis (pages 18–20), and further details on how these resources were used have been added to the Experimental Procedures (pages 53–54).

      We also incorporated data from Kaletsky et al. (2016) and St. Ange et al. (2024) into our neuron identity checks for all assigned and unassigned hits (page 16, lines 8–19). This analysis shows that the nervous system is highly represented in our proteome data: 75–87% of assigned hits and 75–83% of all hits correspond to neuron-enriched genes identified by St. Ange et al. and Kaletsky et al.

      In addition, we used several transcriptomic databases to confirm that learning regulators identified in this study through TurboID and validation experiments are expressed in the same neuron classes as suggested by CenGEN (page 36).

      - The authors offer many interpretations for why mutants in "learning proteome" hits have no detectable phenotype, which is commendable. They are however overlooking another important interpretation, it is possible that these changes to the proteome are important for memory, which is dependent upon translation and protein level changes, and is molecularly distinct from learning. It is well established in the field mutating or knocking down memory regulators in other paradigms will often have no detectable effect on learning. Incorporating this interpretation into the discussion and highlighting it as an area for future exploration would strengthen the manuscript.

      Thank you for this suggestion. We have incorporated this interpretation into the Results section (page 31, lines 17–23), specifying the potential role of these proteomic changes in memory encoding and retention, which are molecularly distinct from learning.

      - A minor weakness - In the discussion, the authors state that the Lakhina, et al 2015 used RNA-seq to assess memory transcriptome changes. This study used microarray analysis.

      This has been corrected on page 38, line 5.

      Significance:

      The approach used in this study is interesting and has the potential to further our knowledge about the molecular mechanisms of associative behaviors. There have been multiple transcriptomic studies in the worm looking at gene expression changes in the context of behavioral training. This study compliments and extends those studies, by examining how the proteome changes in a different training paradigm. This approach here could be employed for multiple different training paradigms, presenting a new technical advance for the field. This paper would be of interest to the broader field of behavioral and molecular neuroscience. Though it uses an invertebrate system, many findings in the worm regarding learning and memory translate to higher organisms, making this paper of interest and significant to the broader field of behavioral neuroscience.

      Reviewer #4 (Public review):

      Summary:

      In this manuscript, authors used a learning paradigm in C. elegans; when worms were fed in a saltless plate, its chemotaxis to salt is greatly reduced. To identify learning-related proteins, authors employed nervous system-specific transcriptome analysis to compare whole proteins in neurons between high-salt-fed animals and saltless-fed animals. Authors identified "learning-specific proteins" which are observed only after saltless feeding. They categorized these proteins by GO analyses, pathway analyses and expression site analyses, and further stepped forward to test mutants in selected genes identified by the proteome analysis. They find several mutants that are defective or hyper-proficient for learning, including acc-1/3 and lgc-46 acetylcholine receptors, F46H5.3 putative arginine kinase, and kin-2, a cAMP pathway gene. These mutants were not previously reported to have abnormality in the learning paradigm.

      Concerns:

      Upon revision, authors addressed all concerns of this reviewer, and the results are now presented in a way that facilitates objective evaluation. Authors' conclusions are supported by the results presented, and the strength of the proteomics approach is persuasively demonstrated.

      Thank you, we appreciate this positive feedback.

      Significance:

      (1) Total neural proteome analysis has not been conducted before for learning-induced changes, though transcriptome analysis has been performed for odor learning (Lakhina et al., http://dx.doi.org/10.1016/j.neuron.2014.12.029). This warrants the novelty of this manuscript, because for some genes, protein levels may change even though mRNA levels remain the same. Although in a few reports TurboID has been used in C. elegans, this is the first report of a systematic analysis of tissue-specific differential proteomics.

      (2) Authors found five mutants that have abnormality in the salt learning. These genes have not been described to have the abnormality, providing novel knowledge to the readers, especially those who work on C. elegans behavioural plasticity. Especially, involvement of acetylcholine neurotransmission has not been addressed before. Although transgenic rescue experiments have not been performed except kin-2, and the site of action (neurons involved) has not been tested in this manuscript, it will open the venue to further determine the way in which acetylcholine receptors, cAMP pathway etc. influences the learning process.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The authors stated in their response to reviewers that "referring to a phenotype as both a trend and non-significant may confuse readers, which was originally stated in the manuscript in two locations," and that such sentences were removed. Unfortunately, in the new text (page 28, lines 18-19), the authors write: "uev-3 mutants showed a lower average CI after training compared with wild-type, but this did not reach statistical significance." As stated before, I find such sentences confusing and not interpretable. If the changes are not significant, then the lower average CI is not informative.

      Thank you for pointing this out. This has been corrected to improve clarity – we say instead that “trained phenotypes between wild-type and uev-3 mutants were not statistically significant” (page 29, lines 21–22).

      In response to reviewers' comments, the authors added more information about the biotinylation efficiency of the experiment, which is also described in the text:

      Page 8, line 27: "we found that biotin exposure increased the signal 1.3-fold for non-Tg and 1.7-fold for TurboID C. elegans."

      Page 10, line 4: "Quantification of the signal within entire lanes showed a 1.1-fold increase in the 'TurboID, control' lane compared with the 'non-Tg, control' lane, and a 1.9-fold increase in the 'TurboID, trained' lane compared with the 'non-Tg, trained' lane."

      Is it common in this field not to show the actual raw quantified numbers? I was expecting either a bar graph or instead that the measured values would appear in the text alongside the fold-change information.

      Table S2 (and its table legend on page 77) have been edited to include raw area values.

      Figure 5: Typo? - "pan neuronal expression of ..." The allele number is written as 139, but I believe it should be 179, as in the rest of the paper.

      The typo has been corrected on page 25.

      The results describing the absence of a learning phenotype in backcrossed C30G12.6 are presented in the main figure. If the authors believe this is an important result, I understand keeping it in the main figure; however, I find this uncommon.

      Thank you for your comment. We consider the absence of a learning phenotype in backcrossed C30G12.6 to be an important control for interpreting the original findings, which is why we have retained it in the main figure.

      Reviewer #4 (Recommendations for the authors):

      I noted a few typos.

      (1) In Fig 5B, the transgene is depicted kin-2(ce139) but it is probably kin-2(ce179).

      The typo has been corrected on page 25.

      (2) In text, R97C and ce179 are used interchangeably, but in fact there is no description that they are identical.

      We now state the following in the manuscript: “We tested worms with the ce179 mutant allele in kin-2, in which a conserved residue in the inhibitory domain (which normally functions to keep PKA turned off in the absence of cAMP) is mutated to cause an R92C amino acid change – this results in increased PKA activity (Schade et al., 2005).” (page 25, lines 1–3),

      (3) p31 line 7, Figure S7 -> Fig S9 C-E

      We apologise for this typographical error. This figure number is meant to correspond to salt associative learning assay data (Fig. S8), not salt aversive learning (Fig. S9). Since the data from Fig. S8 was moved to Fig. 4, the figure citation has been changed from Fig. S7 (which was incorrect) to Fig. 4 (page 32, line 17).

      (4) p45 line 11, Fig S9 -> Fig S6

      The typo has been corrected (page 47, line 12).

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Bisht et al. investigate the role of PPE2, a Mycobacterium tuberculosis (Mtb) secreted virulence factor, in adipose tissue physiology during tuberculosis (TB) infection. Previous work by this group established the significance of PPE proteins in Mtb virulence and their role in modulating the innate immune response. Here, the authors present compelling evidence that PPE2 regulates host cell adipogenesis and lipolysis, thereby establishing a link to the development of insulin resistance during TB infection. These fundamental findings demonstrate, for the first time, that a bacterial virulence factor is directly involved in the profound body fat loss, or "wasting," which is a long-established clinical symptom of active TB.

      Key Strengths:

      The confidence in the major findings of this study is significantly strengthened by the authors' comprehensive approach. They judiciously employ multiple experimental systems, including:

      (1) Purified PPE2 protein.

      (2) A non-pathogenic Mycobacterium strain engineered to express PPE2.

      (3) A pathogenic clinical Mtb strain (CDC1551) utilizing a targeted PPE2 deletion mutant.

      (4) While the presence of Mtb in adipose tissues in human and animal models is well-documented, this study is groundbreaking in demonstrating that an Mtb virulence-associated factor actively modulates host fatty acid metabolism within the adipose tissue.

      We thank the reviewer for his appreciation that in this work we demonstrated for the first time that an Mtb virulent factor is directly linked to TB-associated wasting.

      Weakness:

      Although the manuscript provides solid evidence associating the presence of PPE2 with transcriptional changes in host fatty acid machinery within the adipose tissue, the underlying mechanistic details remain elusive. A focused, deep mechanistic follow-up study will be essential to fully appreciate the complex biological implications of the findings reported here.

      We agree with the reviewer that a deep-focused, mechanistic follow-up study is necessary to further elucidate the complex biological implications of PPE2 actions. However, we believe that we have uncovered at least one of the possible mechanisms by which PPE2 increases lipolysis and circulating free fatty acids during infection by targeting cAMP-PKA-HSL pathway (Figure 7). In future studies we will aim to dissect out the mechanisms by which PPE2 triggers hyperglycaemia and insulin resistance.

      Reviewer #2 (Public review):

      Summary:

      In the manuscript entitled "The PPE2 protein of Mycobacterium tuberculosis is respon,sible for the development of hyperglycemia and insulin resistance during tuberculosis" the authors identify PPE2, a secretory protein of Mycobacterium tuberculosis, as a modulator of adipose function. They show that PPE2 treatment in mice causes fat loss, immune cell infiltration into adipose, reduced gene expression of PPAR-γ, C/EBP-α, and adiponectin, and glucose intolerance. Overall, the authors link PPE2 with adipose tissue perturbation and insulin resistance following infection with M. tuberculosis. PPE2, a secretory protein of Mycobacterium tuberculosis, is a modulator of adipose function. They show that PPE2 treatment in mice causes fat loss, immune cell infiltration into adipose, reduced gene expression of PPAR-γ, C/EBP-α, and adiponectin, and glucose intolerance. Overall, the authors link PPE2 with adipose tissue perturbation and insulin resistance following infection with M. tuberculosis.

      Strengths:

      While it is known that M. tuberculosis persists in adipose, the mycobacterial factors contributing to adipose dysfunction are unknown. The study uses multiple mechanisms, including recombinant purified protein, non-pathogenic mycobacterium expressing PPE2, and a clinical strain of M. tuberculosis depleted of PPE2, to show that PPE2 may play an important role in causing fat loss, lipolysis, and insulin resistance following infection. The authors show that PPE2, through unknown mechanisms, decreases gene expression of proteins involved in adipogenesis. Although the mechanisms are unclear, this study advances the field as it is the first to identify a secreted factor (PPE2) from M. tuberculosis to play a role in disrupting adipose tissue.

      We thank the reviewer for his appreciation of our findings presented in the manuscript.

      Weaknesses:

      (1) There is a lack of completeness amongst the figures that greatly diminishes the claims and impact of the manuscript. For example, in Figures 2 and 5, the authors measure adipocyte area in H&E-stained adipose tissue to show adipose hypertrophy. However, this was not completed in Figures 3 and 4 despite the authors claiming that treatment with rPPE2 induces adipose hypertrophy. It is unclear why the adipocyte area was not measured in these figures, and having this included would support the author's claim and strengthen the manuscript. The same is true for immune cell infiltration, where the authors say there is increased immune cell infiltration following PPE2 treatment. This is based on H&E staining, but the data supporting this is limited. Although the authors measure CD3+ T cell infiltration in adipose tissue from mice infected with the clinical strain where PPE was depleted, staining was performed in only this experiment. Completing these experiments by showing data to support that PPE2 induces immune cell infiltration would greatly strengthen the manuscript.

      As per the suggestion of the esteemed reviewer, in the revised manuscript we will attempt to analyse adipocyte area in both Figures 3 and 4. In the original manuscript, immune cell infiltration analyses (H&E staining and CD3+ staining) was restricted to only M. tuberculosis-mouse infection model, which best reflects the human tuberculosis pathology.  In other experiments involving infection with M. smegmatis expressing PPE2, immune cell infiltration studies will be carried out.

      (2) The authors state that a Student's t-test was performed to calculate the significance between two samples. However, there is no discussion of what statistical method was used when there were more than 2 groups, which occurs throughout the manuscript, such as in Figure 5, where 4 groups are analyzed. Having the appropriate statistical analysis is important for the impact of the manuscript.

      We agree with the reviewer that we missed to include ANOVA in the statistical analyses. We will include one-way ANOVA analysis where more than two groups are present and mention the statistical methods in the figure legends as well in the text of the revised manuscript.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript titled "The PPE protein of Mycobacterium tuberculosis is responsible for the development of hyperglycemia and insulin resistance during tuberculosis", Bisht et al describe that PPE2 protein from Mtb is a key modulator of adipose tissue physiology that contributes to the development of insulin resistance. The authors have used 3T3-L1 preadipocyte cell lines, M. smegmatis overexpression strain, mice model, and genetically modified Mtb deletion strains to demonstrate that PPE promotes persistence in adipose tissue and regulates glucose homeostasis. Using qPCR and RNA-seq experiments, the authors demonstrate that PPE2 regulates the expression of key genes involved in adipogenesis.

      Strengths:

      Using purified protein, the authors show that PPE2 regulates adipose tissue physiology, and this effect was neutralised in the presence of anti-PPE2. The expression of several adipogenic markers was also reduced in 3TL-1 adipocytes treated with rPPE2 and in mice infected with M. smegmatis strains overexpressing PPE2. Using a mouse model of infection, the authors show that PPE2 contributes to enhanced mycobacterial survival within fat tissues. The authors also show infiltration of immune cells in the fat tissues of mice infected with wild-type and ppe2-complemented strains compared to the ppe2 KO strain. In order to gain a better mechanistic understanding of how PPE2 regulates adipogenesis, the authors employed an RNA-seq approach and identified 191 genes that were significantly differentially expressed in the fat tissues of mice infected with wild-type and ppe2 KO Mtb strains. The differentially expressed genes included transcripts encoding for proteins involved in chemokine/cytokine signalling, ER stress response. The expression of a few of these markers was also validated by qPCR and western blot analysis. Finally, the authors also show that PPE2 promotes lipolysis by reducing phosphodiesterase levels and activating PKA-HSL signalling. The experimental design is overall reasonable, and the methods used are reliable. Overall, the current study did provide some new information on the contribution of PPE2 in regulating adipose tissue physiology.

      We thank the reviewer for encouraging comments about the manuscript.

      Weaknesses:

      (1) The authors have used several methodologies to show that PPE2 regulates adipose tissue physiology and glucose homeostasis. But the exact mechanism is still not clear.

      We have clearly demonstrated that PPE2 inhibit PPAR-γ and C/EBP-α expression to block adipogenic differentiation. Further, we demonstrated a possible mechanism by which PPE2 trigger lipolysis via activation of the ER stress and cAMP/PKA/HSL pathway which is responsible for increasing free fatty acids in circulation (Figure 7) as confirmed by our observation that PPE2KO (ppe2 knock-out) Mtb infected mice had lower NEFA as compared to the those infected with wild-type Mtb (Figure 7F). Crucially, we showed that this mechanism is clinically relevant since NEFA levels in the sera of TB patients were higher as compared to the healthy controls (Figure 7G) confirming presence of dyslipidemia in TB patients which is an established risk factor for insulin resistance (Karpe et al., 2011; Bhattacharya et al., 2007), As increased free fatty acids have been shown to be linked to development of insulin resistance in several studies, this mechanism links PPE2 with the regulation of glucose homeostasis.

      (2) Mtb encodes several PE/PPE proteins? The authors have used PPE2 for their study. Will secretory PPE2 homologs also regulate similar cellular processes?

      It is known that Mtb encodes several PE/PPE family proteins and some of these have been implicated to play a role in host–pathogen interactions (Mukhopadhyay and Balaji, 2011; Dahiya et al., 2025). However, so far only PPE2 is shown to be present in the circulation (Bisht et al., 2023) which is the main reason we chose it for this study. Presence of PPE2 homologues in the circulation is not known so far.

      (3) How do the authors rule out that the differences observed in the fat tissues of mice infected with wild-type and mutant strains are not associated with reduced bacterial burdens? Is it possible to include another Mtb attenuated strain as a control in mice experiments for few critical experiments?

      We agree with the reviewer that the differences in bacterial burden can influence host tissue responses.  Precisely for this reason, we did not rely on just one infection model alone. We used a multi-pronged approach to de-couple the effects of PPE2 from the effects of bacterial load, like;

      (1) In vitro Model using recombinantly purified PPE2 protein (rPPE2) (Figure 1): In cultured 3T3-L1 adipocytes, purified rPPE2 protein directly inhibited adipogenesis by downregulating important factors like PPAR-g,C/EBP-α and Fatty acid synthase (which play a critical role in triglyceride metabolism) demonstrating a direct effect of PPE2 in the complete absence of infection.

      (2) Recombinant Protein Injection (Figure 3): By injecting recombinantly purified PPE2 protein (rPPE2) into mice, we observed similar metabolic perturbations (fat loss, impaired glucose tolerance) in the complete absence of any bacteria, demonstrating that PPE2 can drive these phenotypes independent of bacterial burden. Further study of rescuing of PPE2 action in rPPE2-immunized mice strongly confirm the specific role of PPE2 in establishing hyperglycaemia and insulin resistance (Figure 4).

      While the Mtb aerosol model can be questioned for bacterial load effects, it provides crucial in vivo validation that PPE2 function is relevant in the context of mycobacterial infection.

      References

      Bhattacharya S, Dey D, Roy SS. Molecular mechanism of insulin resistance. J Biosci. 2007 Mar;32(2):405-13. doi: 10.1007/s12038-007-0038-8. PMID: 17435330.

      Bisht MK, Pal R, Dahiya P, Naz S, Sanyal P, Nandicoori VK, Ghosh S, Mukhopadhyay S. The PPE2 protein of Mycobacterium tuberculosis is secreted during infection and facilitates mycobacterial survival inside the host. Tuberculosis (Edinb). 2023 Dec;143:102421. doi: 10.1016/j.tube.2023.102421. Epub 2023 Oct 12. PMID: 37879126.

      Dahiya P, Bisht MK, Mukhopadhyay S. Role of PE family of proteins in mycobacterial virulence: Potential on anti-TB vaccine and drug design. Int Rev Immunol. 2025; 44(4):213-228. doi: 10.1080/08830185.2025.2455161. Epub 2025 Jan 31. PMID: 39889764.

      Karpe F, Dickmann JR, Frayn KN. Fatty acids, obesity, and insulin resistance: time for a reevaluation. Diabetes. 2011 Oct;60(10):2441-9. doi: 10.2337/db11-0425. PMID: 21948998; PMCID: PMC3178283.

      Mukhopadhyay S, Balaji KN. The PE and PPE proteins of Mycobacterium tuberculosis. Tuberculosis (Edinb). 2011 Sep;91(5):441-7. doi: 10.1016/j.tube.2011.04.004. Epub 2011 May 6. PMID: 21527209.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Syed et al. investigate the circuit underpinnings for leg grooming in the fruit fly. They identify two populations of local interneurons in the right front leg neuromere of ventral nerve cord, i.e. 62 13A neurons and 64 13B neurons. Hierarchical clustering analysis identifies each 10 morphological classes for both populations. Connectome analysis reveals their circuit interactions: these GABAergic interneurons provide synaptic inhibition either between the two subpopulations, i.e. 13B onto 13A, or among each other, i.e. 13As onto other 13As, and/or onto leg motoneurons, i.e. 13As and 13Bs onto leg motoneurons. Interestingly, 13A interneurons fall into two categories with one providing inhibition onto a broad group of motoneurons, being called "generalists", while others project to few motoneurons only, being called "specialists". Optogenetic activation and silencing of both subsets strongly effects leg grooming. As well activating or silencing subpopulations, i.e. 3 to 6 elements of the 13A and 13B groups has marked effects on leg grooming, including frequency and joint positions and even interrupting leg grooming. The authors present a computational model with the four circuit motifs found, i.e. feed-forward inhibition, disinhibition, reciprocal inhibition and redundant inhibition. This model can reproduce relevant aspects of the grooming behavior.

      Strengths:

      The authors succeeded in providing evidence for neural circuits interacting by means of synaptic inhibition to play an important role in the generation of a fast rhythmic insect motor behavior, i.e. grooming. Two populations of local interneurons in the fruit fly VNC comprise four inhibitory circuit motifs of neural action and interaction: feed-forward inhibition, disinhibition, reciprocal inhibition and redundant inhibition. Connectome analysis identifies the similarities and differences between individual members of the two interneuron populations. Modulating the activity of small subsets of these interneuron populations markedly affects generation of the motor behavior thereby exemplifying their important role for generating grooming. The authors carefully discuss strengths and limitations of their approaches and place their findings into the broader context of motor control.

      We thank the reviewer for their thoughtful and constructive evaluation of our work.

      Weaknesses:

      Effects of modulating activity in the interneuron populations by means of optogenetics were conducted in the so-called closed-loop condition. This does not allow to differentiate between direct and secondary effects of the experimental modification in neural activity, as feedforward and feedback effects cannot be disentangled. To do so open loop experiments, e.g. in deafferented conditions, would be important. Given that many members of the two populations of interneurons do not show one, but two or more circuit motifs, it remains to be disentangled which role the individual circuit motif plays in the generation of the motor behavior in intact animals.

      Our optogenetic experiments show a role for 13A/B neurons in grooming leg movements – in an intact sensorimotor system - but we cannot yet differentiate between central and reafferent contributions. Activation of 13As or 13Bs disinhibits motor neurons and that is sufficient to induce walking/grooming. Therefore, we can show a role for the disinhibition motif.

      Proprioceptive feedback from leg movements could certainly affect the function of these reciprocal inhibition circuits. Given the synapses we observe between leg proprioceptors and 13A neurons, we think this is likely.

      Our previous work (Ravbar et al 2021) showed that grooming rhythms in dusted flies persist when sensory feedback is reduced, indicating that central control is possible. In those experiments, we used dust to stimulate grooming and optogenetic manipulation to broadly silence sensory feedback. We cannot do the same here because we do not yet have reagents to separately activate sparse subsets of inhibitory neurons while silencing specific proprioceptive neurons. More importantly, globally silencing proprioceptors would produce pleiotropic effects and severely impair baseline coordination, making it difficult to distinguish whether observed changes reflect disrupted rhythm generation or secondary consequences of impaired sensory input. Therefore, the reviewer is correct – we do not know whether the effects we observe are feedforward (central), feedback sensory, or both. We have included this in the revised results and discussion section to describe these possibilities and the limits of our current findings.

      Additionally, we have used a computational model to test the role of each motif separately and we show that in the results.  

      Comments on revisions:

      The careful revision of the manuscript improved the clarity of presentation substantially.

      Reviewer #2 (Public review):

      Summary:

      This manuscript by Syed et al. presents a detailed investigation of inhibitory interneurons, specifically from the 13A and 13B hemilineages, which contribute to the generation of rhythmic leg movements underlying grooming behavior in Drosophila. After performing a detailed connectomic analysis, which offers novel insights into the organization of premotor inhibitory circuits, the authors build on this anatomical framework by performing optogenetic perturbation experiments to functionally test predictions derived from the connectome. Finally, they integrate these findings into a computational model that links anatomical connectivity with behavior, offering a systems-level view of how inhibitory circuits may contribute to grooming pattern generation.

      Strengths:

      (1) Performing an extensive and detailed connectomic analysis, which offers novel insights into the organization of premotor inhibitory circuits.

      (2) Making sense of the largely uncharacterized 13A/13B nerve cord circuitry by combining connectomics and optogenetics is very impressive and will lay the foundation for future experiments in this field.

      (3) Testing the predictions from experiments using a simplified and elegant model.

      Thank you for the positive assessment of our work.

      Weaknesses:

      (1) In Figure 4-figure supplement 1, the inclusion of walking assays in dusted flies is problematic, as these flies are already strongly biased toward grooming behavior and rarely walk. To assess how 13A neuron activation influences walking, such experiments should be conducted in undusted flies under baseline locomotor conditions.

      We agree that there are better ways to assay potential contributions of 13A/13B neurons to walking. We intended to focus on how normal activity in these inhibitory neurons affects coordination during grooming, and we included walking because we observed it in our optogenetic experiments and because it also involves rhythmic leg movements. The walking data is reported in a supplementary figure because we think this merits further study with assays designed to quantify walking specifically. We will make these goals clearer in the revised manuscript and we are happy to share our reagents with other research groups more equipped to analyze walking differences.

      (2) Regarding Fig 5: The 70ms on/off stimulation with a slow opsin seems problematic. CsChrimson off kinetics are slow and unlikely to cause actual activity changes in the desired neurons with the temporal precision the authors are suggesting they get. Regardless, it is amazing the authors get the behavior! It would still be important for authors to mention the optogentics caveat, and potentially supplement the data with stimulation at different frequencies, or using faster opsins like ChrimsonR.

      We were also intrigued by the behavioral consequences of activating these inhibitory neurons with CsChrimson. We appreciate the reviewer’s point that CsChrimson’s slow off-kinetics limit precise temporal control. To address this, we repeated our frequency analysis using a range of pulse durations (10/10, 50/50, 70/70, 110/110, and 120/120 ms on/off) and compared the mean frequency of proximal joint extension/flexion cycles across conditions. We found no significant difference in frequency (LLMS, p > 0.05), suggesting that the observed grooming rhythm is not dictated by pulse period but instead reflects an intrinsic property of the premotor circuit once activated. We now include these results in ‘Figure 5—figure supplement 1’ and clarify in the text that we interpret pulsed activation as triggering, rather than precisely pacing, the endogenous grooming rhythm. We continue to note in the manuscript that CsChrimson’s slow off-kinetics may limit temporal precision. We will try ChrimsonR in future experiments.

      Overall, I think the strengths outweigh the weaknesses, and I consider this a timely and comprehensive addition to the field.

      Reviewer #3 (Public review):

      Summary:

      The authors set out to determine how GABAergic inhibitory premotor circuits contribute to the rhythmic alternation of leg flexion and extension during Drosophila grooming. To do this, they first mapped the ~120 13A and 13B hemilineage inhibitory neurons in the prothoracic segment of the VNC and clustered them by morphology and synaptic partners. They then tested the contribution of these cells to flexion and extension using optogenetic activation and inhibition and kinematic analyses of limb joints. Finally, they produced a computational model representing an abstract version of the circuit to determine how the connectivity identified in EM might relate to functional output. The study makes important contributions to the literature.

      The authors have identified an interesting question and use a strong set of complementary tools to address it:

      They analysed serial‐section TEM data to obtain reconstructions of every 13A and 13B neuron in the prothoracic segment. They manually proofread over 60 13A neurons and 64 13B neurons, then used automated synapse detection to build detailed connectivity maps and cluster neurons into functional motifs.

      They used optogenetic tools with a range of genetic driver lines in freely behaving flies to test the contribution of subsets of 13A and 13B neurons.

      They used a connectome-constrained computational model to determine how the mapped connectivity relates to the rhythmic output of the behavior.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I still have the following specific suggestions and questions, which need the attention of the authors:

      P5, 2nd para, li 1: shouldn't "(Figures 1E and 1E')" be (Figures 1G and 1H)?

      P7, last para, li 3: shouldn't "(Figures 2C and 2D)" be (Figures 2A and 2B)?

      P19, para 2, last 2li: "...we observe that optogenetic activation......triggers grooming movements." I could not find the place in the text or a figure, where this was reported or shown. Please specify

      P19, last para: "... shows that 13A neurons can generate rhyhtmic movements....." Given that the experiments were conducted in closed-loop, i.e. including the loop through the leg and its movements, the following formulation appears more justified: "....shows that 13A neurons significantly contribute to the generation of rhythmic movements,....."

      P28, para 1, li 3 from bottom: "...themselves, rather than solely between antagonistsic motor neurons." While the authors are correct that in the stick insect and locust alternating inhibitory synaptic drive to flexor and extensor motoneurons has been shown to underly alternating activity of these two antagonistic motoneuron pools the previous studies have not shown or claimed that these synaptic inputs arise from direct interactions between these motoneuron pools. Based on this this text should be moved to the part "feed-forward inhibition" on page 27.

      P28: "redundant inhibition": this motif has been shown to be instrumental in the locust flight CPG, e.g. Robertson & Pearson, 1985, Fig. 16.

      P28: "reciprocal inhibition" The reviewer agrees with the authors that this motif has been shown for the mouse spinal cord, but also for other CPGs in vertebrates and invertebrates, e.g. clione, leech, xenopus - see the initial comment "(3) Intro and Discussion"

      Thank you, we have incorporated the suggested corrections and clarifications into the revised manuscript.

      Reviewer #2 (Recommendations for the authors):

      I'm satisfied with the revised version

      Reviewer #3 (Recommendations for the authors):

      The authors have made a substantial effort to address my original points. They corrected the title, expanded Discussion and Methods sections, reran statistical tests using mixed models, added modelling clarifications and constraints, and fixed or removed confusing figure panels. Those changes have improved clarity and reduced some of the claims that I thought were exaggerated.

      That said, some of my concerns remain only partially addressed, which could be fixed with relatively small tweaks. The authors should:

      (1) Explicitly separate empirical findings from modelling inferences throughout the manuscript, including the Abstract, Results and Discussion (i.e., label claims of "intrinsic rhythmogenesis" as model-based inferences, not direct experimental demonstrations)

      (2) Provide supplemental information on modelling to quantify the role of the black-box input (e.g., quantitative coordination/phase/frequency metrics for full model vs constant-input vs no black box), show pre- vs post-fine-tuning weight changes and the exact tuning constraints/optimization details (I could not find these details)

      (3) To ensure results are reproducible, provide a supplemental table mapping each split line to EM-identified neuron(s) with NBLAST/morphological scores for each match;

      (4) Fully document the statistical models (exact LMM/GLMM formulas, software/packages, etc);

      (5) Deposit model code, trained weights and analysis scripts in a public repository.

      We have updated the GitHub repository with the full statistical analysis documentation and model code, including trained weights and scripts.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      (1) As such amount of work has been put into developing this community tool, it would be worth thinking about how it could serve other multiplex-immunofluorescence methods (such as immunoSABER, 4i, etc). Adding an extra tab where the particular method that uses those reagents is mentioned. This would also help as IBEX itself and related methods evolve in the future.

      We agree and currently support six other methods beyond the original ”IBEX2D Manual”, with the most generic being ”Multiplexed 2D Imaging”: standard, single cycle (non-iterative) imaging method applied to thin, 2D (5-30 micron) tissue sections. Descriptions of supported methods are given in the reagent glossary. We plan to evolve to include multiplex IF methods such as Immuno-SABER, 4i, Cell DIVE, etc. The current structure of the reagent resources table can support other immunofluorescence methods without modifications. The table contains information for IBEX and related methods. The particular method for which a reagent validation was evaluated is specified in the column titled ”Method”. Descriptions of supported methods are given in the reagent glossary.

      (2) It has a rather minimal description of the software. In particular, there is software that has not been developed for IBEX specifically but that could be used for IBEX datasets (ASHLAR, WSIReg, VALIS, WARPY, and QuPath, etc). It would be nice if there was mention of those.

      ASHLAR, WSIReg, VALIS, and Warpy have been added to the Knowledge-Base. These software components are specifically relevant for iterative imaging protocols which require image alignment. With respect to QuPath, Fiji, Napari and other general microscopy image analysis frameworks, these are not listed. Such frameworks provide a wide range of operations relevant for many microscopy image analysis tasks and are likely already familiar to researchers who are interested in the information contained in the Knowledge-Base.

      (3) There is a concern about how the negative data information will be added, as no publication or peer-review process can back it up. Perhaps the particular conditions of the experiment should be very well described to allow future users to assess the validity.

      We agree with this observation and have added the following language to the contribute page:

      ”When reporting information that has not appeared in a peer-reviewed publication, both negative and positive results, include more details with respect to experimental conditions and provide sample images as part of the supporting material files. In all cases, peer reviewed or not, we encourage providing additional details in the supporting material that you deem important and are not part of the csv file structure. These include, but are not limited to, lot numbers, versioned protocols used in the work, and any other information which will facilitate validation reproducibility.”

      (4) The proposed scheme where a reagent can be validated or recommended against by up to 4 different labs should be good. It may be good to make sure that researchers who validate belong to different labs and are not only different ORCID that belong to the same group. Similar to making a case of recommendations against a reagent.

      We generally support this recommendation. Based on our experience, even members within the same laboratory encounter challenges when attempting to validate reagents contributed by current or former colleagues. Additionally, research labs often experience significant personnel turnover, with minimal overlap over a five year span.

      To address these concerns, we have updated the instructions on the contribute page as follows: ”We only accept up to 5 ORCID additions in the Agree or Disagree columns. This means that the original contributor’s work was replicated by up to 4 individuals or refuted by up to 5 people. Priority is given to contributions from individuals in laboratories distinct from the original source.”

      (5) It is very interesting to keep track of the protocol versions used. Perhaps users should be able to validate independent versions and it will be important to know how information is kept.

      Thank you for your suggestion. We encourage members of the community to cite the latest version of the Knowledge-Base in the “Citing the Knowledge-Base” section.

      (6) The final point I would make is that the need to form a GitHub repository may deter some people from submitting data. For sporadic contributions, authors could think that users could either reach out to main developers and/or provide a submission form that can help less experienced users of command-line and GitHub programming, but still promote the contribution from the community.

      We have given this significant thought and now support a secondary path for contributing that does not require familiarity with git or GitHub. This path involves downloading a zip file, modifying the contents of the csv files and providing supporting material text files and images. Once the work is completed, the contributor contacts the Knowledge-Base maintainers and we complete the submission together, with the maintainers dealing with the usage of git and GitHub. This information has been added to the notes which are listed at the top of the Contribute page. We have recently completed the first contribution that followed this new workflow.

      We still encourage researchers to familiarize themselves with git and the GitHub repository hosting service. These tools have been shown to be useful for collaborative and reproducible laboratory research.

      Reviewer #2:

      (1) The potential impact of IBEX KB is very clear. However, the paper would benefit by also discussing more on KB maintenance and outreach, and how higher participation could be incentivized.

      We have added the following details to the discussion:

      The KB is actively maintained by its chairs, who meet bi-weekly to ensure its continued development and maintenance. In addition to these regular meetings, we engage with both current and prospective community members to gather feedback, encourage contributions, and expand the collective knowledge supporting the KB. To broaden outreach and foster sustained engagement, the IBEX community will collaborate with synergistic initiatives such as the HuBMAP Affinity Reagents Working Group, the European Society for Spatial Biology (ESSB), and the Global Alliance for Spatial Technologies (GESTALT).

      As a further incentive for participation, we intend to launch an annual “Reagent Validation Week”, a community driven event inspired by software hackathons. During this dedicated week, researchers would focus on validating or reproducing validation for selected reagents and contribute their findings to the KB. We have also discussed hosting an “Around the World” symposium, featuring presentations from both junior and senior scientists across the community, to showcase diverse perspectives and foster global collaboration.

      (2) Use of resources like GitHub may limit engagement from non-coding members of the scientific community. Will there be alternative options like a user-friendly web interface to contribute more easily?

      We agree with this observation and have addressed it. Please see detailed response to point 6 from Reviewer 1.

      Reviewer #3:

      (1) IBEX is a specific immunofluorescence method. However, the utility of the Knowledge base is not limited to the specific IBEX method. Therefore, I suggest removing the unnecessary branding of the term IBEX from the KB and citing potentially other similar cyclic immunofluorescence methods in the manuscript (e.g. CycIF Lin et al 2018). This would also emphasize the wider impact and applicability of the KB to the wider imaging community.

      For now, we have decided to keep the original reference to the IBEX method in the resource name and re-brand it in the next development phase. In that phase we intend to solicit reagent validations for methods unrelated to IBEX. We have added the reference to the CycIF publication. The manuscript text now reads: “We are optimistic that future versions will include extension of the IBEX method to other tissues and species and we intend to solicit contributions of reagent validations for other multiplexed imaging techniques such as CycIF Lin et al. (2015). At that point in time we expect to re-brand the KB as the IBEX++ Knowledge-Base...”

      (2) I believe reporting negative results with reagents is highly valuable. However, the way to report antibodies must include more details. To ensure data quality, every report should be linked to a specific protocol + images (or doc with the standard document variations, and sample information. This should be a mandatory requirement.

      We agree that this information is desirable, but we do not agree that it should be mandatory. In the contribution instructions we now explicitly list lot numbers and versioned protocols as examples of details that we encourage contributors to include in their supporting material files. We believe that requiring this information for a contribution sets the bar too high and will deter many from contributing information that can benefit others.

      (3) While cross-validation among researchers is beneficial, even if five individuals fail to reproduce results with a given antibody, their findings may be influenced by techniquespecific factors. It is also important to consider whether these researchers come from the same group, institution, or geographical region, as this could impact reproducibility. Additionally, entries that have not been reproduced at least five times using the same protocol should still be considered valuable information. To address this, an ”insufficient validation data” flag could be implemented, ensuring that incomplete but useful findings remain accessible.

      The contribution instructions now state that ”Priority is given to contributions from individuals in laboratories distinct from the original source”.

      While our goal is to support reproducing reagent validations, we do not expect these type of contributions be the rule as the only incentive we can provide to encourage this behavior is co-authorship on the authoritative dataset. As a result, it is likely that many of the validations will have a single endorser, the original contributor. These results are valuable information and we do not think they should be singled out (insufficient validation label). We leave it up to the users of the KB to decide whether they trust recommendations with multiple endorsers or if endorsement by a single highly trusted contributor is sufficient for them. In all cases, issues with contributions can be rasied and discussed on the KB discussion forum.

      The rationale for limiting the number of reproduction studies to five was that this is a minimal, yet sufficiently large, number that provides confidence in the results. Placing an upper limit ensures that researchers do not provide reproduction results for widely used and well established reagents just because these results are readily available to them.

      (4) This system could flag reagents with inconsistent reports, highlight potential techniquespecific issues, and suggest alternative reagents with stronger validation records. Furthermore, a validation confidence ranking could be introduced, taking into account the number of independent confirmations, protocol consistency, and reproducibility data. These measures would help refine the reporting process while maintaining transparency and scientific rigor.

      We agree that the functionality described here is desirable, but this is not part of the KB. At its core the KB is a dataset and we do not envision developing dedicated tools to perform these tasks. Instead, we foresee using the KB as context for interacting with AI agents. Providing the KB as context to an AI, one can currently use it to answer domain specific questions and perform related tasks such as designing imaging panels (under subject matter expert supervision). This was added to the sample usecases in the manuscript with a transcript from interaction with an AI model using the website as context provided as supplemental material.

      (5) Regarding image formats for results reporting, while JPG files are convenient due to their small size, TIFF files offer significant advantages, such as preserving metadata and maintaining the integrity of real data values. Proper signal adjustments may not always be applied by researchers, making TIFF crucial for accurate data analysis. I suggest in this regard making available the possibility of including a link to the original TIFF data

      The goal of the supporting material image is similar to that of an image used in a manuscript and it should not be used for data analysis purposes. This is the reason we chose the JPG format. Sharing these images is not intended to be a substitute for publicly sharing the original images and their associated metadata. This is now noted in the contributing instructions.

      (6) Homepage:

      Include a brief summary of the knowledge base’s purpose and tabs to provide clarity for new users. The current homepage is a bit misleading for newcomers.

      The homepage has been modified to include information about the Knowledge-Base, contents and how to use it including as context for interaction with AI agents.

      (7) Reagent Resources Section: Enable users to search for a target name directly, rather than filtering through dropdown options.

      The dropdown menu explicitly shows all available targets and also allows for direct search of target name. To use it for direct search, once the dropdown is selected start typing the name of the target and the focus will jump to it. Thus, if looking for ”Zrf1” there is no need to scroll through all targets in the dropdown. This also facilitates easy clearing of a filter, select the dropdown and start typing the word ”clear”, then press enter when it is highlighted. This information has been added to the page.

      Provide an option to download the dataset as a CSV file. This feature will be highly valued by non-computational researchers.

      Links to download the reagent resources csv file and the whole Knowledge-Base have been added.

      Add the same column documentation here as in the contributor instructions. For example, you need to make clear the distinctions between ”Recommend,” ”Agree,” and ”Disagree” ratings, as they may be misleading to those who have not visited the rules to contribute.

      A link to the column documentation in the contributor instructions has been added here. Information on the website is displayed in one location and linked as needed. Duplicated display of information creates uncertainty for users and results in more complex instructions when referring to the information.

      Include additional details in the dataset, such as lot numbers, or the date of the contribution, that could be relevant in different settings.

      Please see response to point 2.

      (8) Data & Software Section:

      Add filtering options in the table based on organism and tissue availability

      This data is not encoded in the available information in an independent manner so we do not directly enable filtering. It is usually included in the ”Details” free form text. This text is duplicated from the original dataset descriptions. One can still search this page using the browsers search functionality to achieve behavior similar to filtering. While the ”Details” text may not be visible due to the usage of the accordion user interface, it is still searchable and will automatically expand when the search text is found under the collapsed accordion button.

      (9) Contributor Section:

      Incorporate figures from the manuscript to make it more visual and improve understanding of rules and standards.

      Figure 4 from the manuscript was added to this page.

      I believe reporting negative results with reagents is highly valuable. However, to ensure data quality, every report should be linked to a specific protocol and sample information. This should be a mandatory requirement. To streamline the process, warnings for certain reagents could be implemented, but a reagent should not be outright labeled as ineffective without proper validation.

      Please see response to point 2.

      Cross-validation among researchers is beneficial, but even if five individuals fail to reproduce results with a given antibody, it may still be due to technique-specific factorsparticularly for non-routine antibodies.

      We agree with this observation and have modified the contribution instructions accordingly:

      When overturning previously reported results, the number of ORCIDs in the Disagree column becomes greater than those in the Agree column, we will open the contribution for public discussion on the Knowledge-Base forum before accepting it.

      The intent is to increase the community’s confidence in the results, particularly when dealing with non-routine antibodies. This allows the original contributor and other members of the community to engage with the researchers who were unable to replicate a specific validation, possibly helping them to replicate the original results by adding missing details to the KB, or explicitly identifying and documenting issues with the original work.

      Regarding image formats, JPG files are convenient due to their small size, but TIFF offers significant advantages, such as preserving metadata and maintaining the integrity of real data values. Proper signal adjustments may not always be applied by researchers, making TIFF crucial for accurate data analysis.

      Please see response to point 5.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      The authors assess the impact of E-cigarette smoke exposure on mouse lungs using single cell RNA sequencing. Air was used as control and several flavors (fruit, menthol, tobacco) were tested. Differentially expressed genes (DEGs) were identified for each group and compared against the air control. Changes in gene expression in either myeloid or lymphoid cells were identified for each flavor and the results varied by sex. The scRNAseq dataset will be of interest to the lung immunity and e-cig research communities and some of the observed effects could be important. Unfortunately, the revision did not address the reviewers' main concerns about low replicate numbers and lack of validations. The study remains preliminary, and no solid conclusions could be drawn about the effects of E-cig exposure as a whole or any flavor-specific phenotypes.

      Strengths:

      The study is the first to use scRNAseq to systematically analyze the impact of e-cigarettes on the lung. The dataset will be of broad interest.

      Weaknesses:

      scRNAseq studies may have low replicate numbers due to the high cost of studies but at least 2 or 3 biological replicates for each experimental group is required to ensure rigor of the interpretation. This study had only N=1 per sex per group and some sex-dependent effects were observed. This could have been remedied by validating key observations from the study using traditional methods such as flow cytometry and qPCR, but the limited number of validation experiments did not support the conclusions of the scRNA seq analysis. An important control group (PG:VG) had extremely low cell numbers and was basically not useful. Statistical analysis is lacking in almost all figures. Overall, this is a preliminary study with some potentially interesting observations, but no solid conclusions can be made from the data presented.

      The only new validation experiment is the immunofluorescent staining of neutrophils in Figure 4. The images are very low resolution and low quality and it is not clear which cells are neutrophils. S100A8 (calprotectin) is highly abundant in neutrophils but not strictly neutrophil-specific. It's hard to distinguish positive cells from autofluorescence in both Ly6g and S100a8 channels. No statistical analysis in the quantification.

      We thank the reviewer for identifying the strengths of this study and pointing out the gaps in knowledge. Overall, our purpose to present this data is to provide the scRNA seq results as a resource to a wider community. We have used techniques like flow cytometry, multianalyte cytokine array and immunofluorescence to validate some of the results. We agree with the reviewer that we were unable to rightly point out the significance of our findings with the immunofluorescent stain in the previous edit. We have revised the manuscript and included the quantification for both Ly6G+ and S100A8+ cells in e-cig aerosol exposed and control lung tissues. Briefly, we identified a marked decrease in the staining for S100A8 (marker for neutrophil activation) in tobacco-flavored e-cig exposed mouse lungs as compared to controls. Upon considering the corroborating evidence from scRNA seq and flow cytometry with regards to increased neutrophil percentages in experimental group and lowered staining for active neutrophils using immunofluorescence, we speculate that exposure to e-cig (tobacco) aerosols may alter the neutrophil dynamics within the lungs. Also, co-immunofluorescence identified a more prominent co-localization of the two markers in control samples as compared to the treatment group which points towards some changes in the innate immune milieu within the lungs upon exposures. Future work is required to validate these speculations.

      We have now discussed all the above-mentioned points in the Discussion section of the revised manuscript and toned down our conclusions regarding sex-dependent changes from scRNA seq data.

      It is unclear what the meaning of Fig. 3A and B is, since these numbers only reflect the number of cells captured in the scRNAseq experiment and are not biologically meaningful. Flow cytometry quantification is presented as cell counts, but the percentage of cells from the CD45+ gate should be shown. No statistical analysis is shown, and flow cytometry results do not support the conclusions of scRNAseq data.

      We thank the reviewer for this question. However, we would like to highlight that scRNA seq and flow cytometry may show similar trends but cannot be identical as one relies on cell surface markers (protein) for identification of cell types, while other is dependent on the transcriptomic signatures to identify the cell types. In our data, for the myeloid cells (alveolar macrophages and neutrophils), the scRNA and flow cytometry data match in trend. However, the trends do not match with respect to the lymphoid cells being studied (CD4 and CD8 T cells). The possible explanation for such a finding could be possible high gene dropout rates in scRNA seq, different analytical resolution for the two techniques and pooling of samples in our single cell workflow. We realize these shortcomings in our analyses and mention it clearly in the discussion as limitation of our work. It is important to note also that cell frequencies identified in scRNA seq just provide wide and indistinct indications which need to be further validated, which we tried to accomplish in our work to some degree. Our flow-based results clearly highlight the sex-specific variations in the immune cell percentages (something we could not have anticipated earlier). In future studies, we will include more replicates to tease out sex-based variations upon acute and chronic exposure to e-cig aerosols.

      We have now replotted the graphs in Fig 3A and B and plotted the flow quantification as the percentage of total CD45+ cells. The gating strategy for the flow plots is also included as Figure S6 in the revised manuscript.

      Reviewer #2 (Public review):

      This study provides some interesting observations on how different flavour e-cigarettes can affect lung immunology; however, there are numerous flaws, including a low replicate number and a lack of effective validation methods, meaning findings may not be repeated. This is a revised article but several weaknesses remain related to the analysis and interpretation of the data.

      Strengths:

      The strength of the study is the successful scRNA-seq experiment which gives some preliminary data that can be used to create new hypotheses in this area.

      Weaknesses:

      Although some text weaknesses have been addressed since resubmission, other specific weaknesses remain: The major weakness is the n-number and analysis methods. Two biological n per group is not acceptable to base any solid conclusions. Any validatory data was too little (only cell % data) and not always supporting the findings (e.g. figure 3D does not match 3B/4A). Other examples include:

      There aren't enough cells to justify analysis - only 300-1500 myeloid cells per group with not many of these being neutrophils or the apparent 'Ly6G- neutrophils'.

      We thank the reviewer for the comment, but we disagree with the reviewer in terms of the justification of analyses. All the flavored e-cig aerosol groups were compared with air controls to deduce the outcomes in the current study. We already acknowledge low sample quality for PGVG group and have only included the comparisons with PGVG upon reviewer’s request which is open to interpretation by the reader.

      By that measure, each treatment group (except PGVG group) has over 1000 cells with 24777 genes being analyzed for each cell type, which by the standards of single cell is sufficient. We understand that this strategy should not be used for detection of rare cell populations, which was neither the purpose of this manuscript nor was attempted. We conduct comparisons of broader cell types and mention more samples need to be added in the Discussion section of the revised manuscript.

      As for the Ly6G neutrophil category, we don’t only base our results on scRNA analyses but also perform co-immunofluorescence and multi-analyte analyses and use evidence from previous literature to back our outcome. To avoid over-stating our results we have revamped the whole manuscript and ensured to tone down our results with relation to the presence of Ly6G- neutrophils. We do understand that more work is required in the future, but our work clearly shows the shift in neutrophil dynamics upon exposure which should be reported, in our opinion.

      The dynamic range of RNA measurement using scRNAseq is known to be limited - how do we know whether genes are not expressed or just didn't hit detection? This links into the Ly6G negative neutrophil comments, but in general the lack of gene expression in this kind of data should be viewed with caution, especially with a low n number and few cells. The data in the entire paper is not strong enough to base any solid conclusion - it is not just the RNA-sequencing data.

      We acknowledge this to be a valid point and have revamped the manuscript and toned down our conclusions. However, such limitations exist with any scRNA seq dataset and so must be interpreted accordingly by the readers. We do understand that due to the low cell counts and the limitations with scRNA seq we should not perform DESeq2 analyses for Ly6G+ versus Ly6G- neutrophil categories, which was never attempted at the first place. However, our results with co-immunofluorescence, multianalyte assay and scRNA expression analyses in myeloid cluster do point towards a shift in neutrophil activation which needs to be further investigated. Furthermore, Ly6G deficiency has been linked to immature neutrophils in many previous studies and is not an unlikely outcome that needs to be treated with immense skepticism.

      We wish to make this dataset available as a resource to influence future research. We are aware of its limitations and have been transparent with regards to our experimental design, capture strategy, the quality of obtained results, and possible caveats to make it is open for discussion by the readers.

      There is no data supporting the presence of Ly6G negative neutrophils. In the flow cytometry only Ly6G+ cells are shown with no evidence of Ly6G negative neutrophils (assuming equal CD11b expression). There is no new data to support this claim since resubmission and the New figures 4C and D actually show there are no Ly6G negative cells - the cells that the authors deem Ly6G negative are actually positive - but the red overlay of S100A8 is so strong it blocks out the green signal - looking to the Ly6G single stains (green only) you can see that the reported S100A8+Ly6G- cells all have Ly6G (with different staining intensities).

      We thank the reviewer for this query and do understand the skepticism. We have now quantified the data to provide more clarity for interpretation. As we were using paraffin embedded tissues, some autofluorescence is expected which could explain some of reviewer’s concerns. However we expect that the inclusion of better quality images and quantification must address some of the concerns raised by the reviewer.

      Eosinophils are heavily involved in lung macrophage biology, but are missing from the analysis - it is highly likely the RNA-sequence picked out eosinophils as Ly6G- neutrophils rather than 'digestion issues' the authors claim

      We thank the reviewer for raising a valid concern. However, the Ly6G- cluster cannot be eosinophils in our case. Literature suggests SiglecF as an important biomarker of eosinophils which was absent in the Ly6G- cluster our in scRNA seq analyses as shown in File S18 and Figure 6B of the revised manuscript. We have now provided a detailed explanation (Lines 476-488; 503-506) of the observed results pertaining to eosinophil population in the revised manuscript to further address some of the concerns raised by this reviewer.

      After author comments, it appears the schematic in Figure 1A is misleading and there are not n=2/group/sex but actually only n=1/group/sex (as shown in Figure 6A). Meaning the n number is even lower than the previous assumption.

      We concur with reviewers’ valid concern and so are willing to provide this data as a resource for a wider audience to assist future work. Pooling of samples have been practiced by many groups previously to save resources and expense. We did it for the very same reason. It may not be the preferred approach, but it still has its merit considering the vast amount of cell-specific data generated using this strategy. To avoid overstating our results we have ensured to maintain transparency in our reporting and acknowledge all the limitations of this study.

      We do not believe that the strength of scRNA seq lies in drawing conclusive results, but to tease our possible targets and direction that need to be validated with more work. In that respect, our study does identify the target cell types and biological processes which could be of importance for future studies.

      Reviewer #3 (Public review):

      This work aims to establish cell-type specific changes in gene expression upon exposure to different flavors of commercial e-cigarette aerosols compared to control or vehicle. Kaur et al. conclude that immune cells are most affected, with the greatest dysregulation found in myeloid cells exposed to tobacco-flavored e-cigs and lymphoid cells exposed to fruit-flavored e-cigs. The up- and down-regulated genes are heavily associated with innate immune response. The authors suggest that a Ly6G-deficient subset of neutrophils is found to be increased in abundance for the treatment groups, while gene expression remains consistent, which could indicate impaired function. Increased expression of CD4+ and CD8+ T cells along with their associated markers for proliferation and cytotoxicity is thought to be a result of activation following this decline in neutrophil-mediated immune response.

      Strengths:

      Single cell sequencing data can be very valuable in identifying potential health risks and clinical pathologies of lung conditions associated with e-cigarettes considering they are still relatively new.

      Not many studies have been performed on cell-type specific differential gene expression following exposure to e-cig aerosols.

      The assays performed address several factors of e-cig exposure such as metal concentration in the liquid and condensate, coil composition, cotinine/nicotine levels in serum and the product itself, cell types affected, which genes are up- or down-regulated and what pathways they control.

      Considerations were made to ensure clinical relevance such as selecting mice whose ages corresponded with human adolescents so that data collected was relevant.

      Weaknesses:

      The exposure period of 1 hour a day for 5 days is not representative of chronic use and this time point may be too short to see a full response in all cell types. The experimental design is not well-supported based on the literature available for similar mouse models. Clinical relevance of this short exposure remains unclear.

      We thank the reviewer for this query. However, we would like to emphasize that chronic exposure was never the intention of this study. We wished to design a study for acute nose-only exposure owing to which the study duration was left shorter. Shorter durations limit the stress and discomfort to the animal. The in vivo study using nose-only exposure regimen is still developing with multiple exposure regimen being used by different groups. To our knowledge there is no gold standard of e-cig aerosol exposure which is widely accepted other than the CORESTA recommendations, which we followed. Also, we show in our study how the daily exposure to leached metals vary in a flavor-dependent manner thus validating that exposure regime does need more attention in terms of equal dosing, particle distribution and composition- something we have started doing in our future studies. We have included all the explanations in the revised manuscript (Lines 82-85, 425-435, 648-654).

      Several claims lack supporting evidence or use data that is not statistically significant. In particular, there were no statistical analyses to compare results across sex, so conclusions stating there is a sex bias for things like Ly6G+ neutrophil percentage by condition are observational.

      We agree with reviewer’s comment and have taken this into consideration. We have now revamped the whole manuscript and toned down most of the sex-based conclusions stated in this work. Having said that, it is important to note that most of the work relying solely on scRNA seq, as is the case for this study, is observational in nature and needs to be assessed bearing this in mind.

      Overall, the paper and its discussion are relatively surface-level and do not delve into the significance of the findings or how they fit into the bigger picture of the field. It is not clear whether this paper is intended to be used as a resource for other researchers or as an original research article.

      We have now reworked on the Discussion and tried to incorporate more in-depth discussion and the results providing our insights regarding the observations, discrepancies and the possible explanations. We have also made it clear that this paper is intended to be used as a resource by other researchers (Lines 577-579)

      The manuscript has some validation of findings but not very comprehensive.

      We have now revamped the manuscript. We have Included quantification for immunofluorescence data with better representation of the GO analyses. We have worked on the Results and Discussion sections to make this a useful resource for the scientific community.

      This paper provides a strong foundation for follow-up experiments that take a closer look at the effects of e-cig exposure on innate immunity. There is still room to elaborate on the differential gene expression within and between various cell types.

      We thank the reviewer for pointing out the strength of this paper. The reason why we refrained from elaborating of the differential gene expressions within and between various cell types was due to low sample number and sequencing depth for this study. However the raw data will be provided with the final publication, which should be freely accessible to the public to re-analyze the data set as they deem fit.

      Comments on revisions:

      The reviewers have addressed major concerns with better validation of data and improved organization of the paper. However, we still have some concerns and suggestions pertaining to the statistical analyses and justifications for experimental design.

      We appreciate the nuance of this experimental design, and the reviewers have adequately commented on why they chose nose-only exposure over whole body exposure. However, the justification for the duration of the exposure, and the clinical relevance of a short exposure, have not been addressed in the revised manuscript.

      We thank the editor for this query. We have now addressed this query briefly in Lines 82-85, 425-435, 648-654 of the revised manuscript. We would like to add, however, that we intend to design a study for acute nose-only exposure for this project. Shorter durations limit the stress and discomfort to the animal, owing to which a duration of 1hour per day was chosen. The in vivo study using nose-only exposure regimen is still developing with multiple exposure regimen being used by different groups. Ours is one such study in that direction just intended to identify cell-specific changes upon exposure. Considering our results in Figure 1B showing variations in the level of metals leached in each flavor per day, the appropriate exposure regimen to design a controlled, reproducible experiment needs to be discussed. There could be room for improvement in our strategy, but this was the best regimen that we found to be appropriate per the literature and our prior knowledge in the field.

      The presentation of cell counts should be represented by a percentage/proportion rather than a raw number of cells. Without normalization to the total number of cells, comparisons cannot be made across groups/conditions. This comment applies to several figures.

      We thank the editor for this comment and have now made the requested change in the revised manuscript.

      We appreciate that the authors have taken the reviewers' advice to validate their findings. However, we have concerns regarding the immunofluorescent staining shown in Figure 4. If the red channel is showing a pan-neutrophil marker (S100A8) and the green channel is showing only a subset of neutrophils (LY6G+), then the green channel should have far less signal than the red channel. This expected pattern is not what is shown in the figure, with the Ly6G marker apparently showing more expression than S100A8. Additionally, the FACS data states that only 4-5% of cells are neutrophils, but the red channel co-localizes with far more than 4-5% of the DAPI stain, meaning this population is overrepresented, potentially due to background fluorescence (noise). In addition, some of the shapes in the staining pattern do not look like true neutrophils, although it is difficult to tell because there remains a lot of background staining. The authors need to verify that their S100A8 and Ly6G antibodies work and are specific to the populations they intend to target. It is possible that only the brightest spots are truly S100A8+ or Ly6G+.

      We thank the editor for this comment and acknowledge that we may have made broad generalizations in our interpretation of our data previously. We have now revisited the data and quantified the two fluorescence for better interpretation of our results. We have also reassessed our conclusions from this data and reworded the manuscript accordingly. Briefly we believe that Ly6G deficiency could be an indication of the presence of immature neutrophils in the lungs. This is a common process of neutrophil maturation. An active neutrophil population has Ly6G and should also express S100A8 indicating a normal neutrophilic response against stressors. However, our results, despite some autofluorescence which is common with lung tissues, shows a marked decline in the S100A8+ cells in the lung of tobacco-flavored e-cig aerosol exposed mice as compared to air controls. We also do not see prominent co-localization of the two markers in exposed group thus proving a shift in neutrophil dynamics which requires further investigation. We would also like to mention here that S100A8 is predominantly expressed in neutrophils, but is also expressed by monocytes and macrophages, so that could explain the over-representation of these cells in our immunofluorescence results. We have now included this in the Discussion section (Lines 489- 538) of the revised manuscript.

      Paraffin sections do not always yield the best immunostaining results and the images themselves are low magnification and low resolution.

      We agree with the editor that paraffin sections may not yield best results, we have worked on the final figure to improve the quality of the displayed results and zoomed-in some parts of the merged image to show the differences in the co-localization patterns for the two markers in our treated and control groups for easier interpretation.

      Please change the scale bars to white so they are more visible in each channel.

      The merged image in Figure 6C now has a white scale bar.

      We appreciate that this is a preliminary test used as a resource for the community, but there is interesting biology regarding immune cells that warrants DEG analysis by the authors. This computational analysis can be easily added with no additional experiments required.

      We thank the editor for this comment and agree that interesting biology regarding immune cells could be explored upon performing the DEG analyses on individual immune populations. However, due to the small sample size, low sequencing depth and pooling of same sex animals in each treatment group, we refrained from performing that analyses fearing over-representation of our results. We will be providing the link to the raw data with this publication which will be freely accessible to public on NIH GEO resource to allow further analyses on this dataset by the judgement of the investigator who utilizes it as a resource.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (Minor) The pathway analyses in Fig. 6-8 have different fonts than what's used in all other figures.

      We have now made the requested change in the revised manuscript.

    1. Author response:

      The following is the authors’ response to the current reviews.

      We would like to proceed with this paper as a Version of Record but we will correct the mistake that we made in the Key resources table. As the reviewer noted we had added the wrong guide RNA sequence here. We are super thankful to the reviewer and apologize for the mistake.


      The following is the authors’ response to the original reviews.

      eLife Assessment 

      This important study identifies a new key factor in orchestrating the process of glial wrapping of axons in Drosophila wandering larvae. The evidence supporting the claims of the authors is convincing and the EM studies are of outstanding quality.

      We are thankful for this kind and very positive judgment.

      However, the quantification of the wrapping index, the role of Htl/Uif/Notch signaling in differentiation vs growth/wrapping, and the mechanism of how Uif "stabilizes" a specific membrane domain capable of interacting with specific axons might require further clarification or discussion.

      This is now addressed

      Reviewer #1 (Public review):

      Summary:

      A central function of glial cells is the ensheathment of axons. Wrapping of larger-diameter axons involves myelin-forming glial classes (such as oligodendrocytes), whereas smaller axons are covered by non-myelin-forming glial processes (such as olfactory ensheathing glia). While we have some insights into the underlying molecular mechanisms orchestrating myelination, our understanding of the signaling pathways at work in non-myelinating glia remains limited. As non-myelinating glial ensheathment of axons is highly conserved in both vertebrates and invertebrates, the nervous system of Drosophila melanogaster, and in particular the larval peripheral nerves, have emerged as a powerful model to elucidate the regulation of axon ensheathment by a class of glia called wrapping glia. Using this model, this study seeks to specifically address the question, as to which molecular mechanisms contribute to the regulation of the extent of glial ensheathment focusing on the interaction of wrapping glia with axons. 

      Strengths and Weaknesses:

      For this purpose, the study combines state-of-the-art genetic approaches with high-resolution imaging, including classic electron microscopy. The genetic methods involve RNAi-mediated knockdown, acute Crispr-Cas9 knock-outs, and genetic epistasis approaches to manipulate gene function with the help of cell-type specific drivers. The successful use of acute Crispr-Cas9 mediated knockout tools (which required the generation of new genetic reagents for this study) will be of general interest to the Drosophila community. 

      The authors set out to identify new molecular determinants mediating the extent of axon wrapping in the peripheral nerves of third-instar wandering Drosophila larvae. They could show that over-expressing a constitutive-active version of the Fibroblast growth factor receptor Heartless (Htl) causes an increase in wrapping glial branching, leading to the formation of swellings in nerves close to the cell body (named bulges). To identify new determinants involved in axon wrapping acting downstream of Htl, the authors next conducted an impressive large-scale genetic interaction screen (which has become rare, but remains a very powerful approach), and identified Uninflatable (Uif) in this way. Uif is a large single-pass transmembrane protein that contains a whole series of extracellular domains, including Epidermal growth factor-like domains. Linking this protein to glial branch formation is novel, as it has so far been mostly studied in the context of tracheal maturation and growth. Intriguingly, a knock-down or knock-out of uif reduces branch complexity and also suppresses htl over-expression defects. Importantly, uif over-expression causes the formation of excessive membrane stacks. Together these observations are in in line with the notion that htl may act upstream of uif. 

      Further epistasis experiments using this model implicated also the Notch signaling pathway as a crucial regulator of glial wrapping: reduction in Notch signaling reduces wrapping, whereas over-activation of the pathway increases axonal wrapping (but does not cause the formation of bulges). Importantly, defects caused by the over-expression of uif can be suppressed by activated Notch signaling. Knock-down experiments in neurons suggest further that neither Delta nor Serrate act as neuronal ligands to activate Notch signaling in wrapping glia, whereas knock-down of Contactin, a GPI anchored Immunoglobulin domain-containing protein led to reduced axon wrapping by glia, and thus could act as an activating ligand in this context. 

      Based on these results the authors put forward a model proposing that Uif normally suppresses Notch signaling, and that activation of Notch by Contactin leads to suppression of Htl, to trigger the ensheathment of axons. While these are intriguing propositions, future experiments would need to conclusively address whether and how Uif could "stabilize" a specific membrane domain capable of interacting with specific axons.

      We absolutely agree with the reviewer that it would be fantastic to understand whether and how Uif could stabilize specific membrane domains that are capable of interacting with axons. To address this we need to be able to label such membrane domains and unfortunately we still cannot do so. We analyzed the distribution of PIP2/PIP3 but failed to detect any differences. Thus we still lack wrapping glial membrane markers that are able to label specific compartments.

      Moreover, to obtain evidence for Uif suppression by Notch to inhibit "precocious" axon wrapping and for a "gradual increase" of Notch signaling that silences uif and htl, (1) reporters for N and Htl signaling in larvae, (2) monitoring of different stages at a time point when branch extension begins, and (3) a reagent enabling to visualize Uif expression could be important next tools/approaches. Considering the qualitatively different phenotypes of reduced branching, compared to excessive membrane stacks close to cell bodies, it would perhaps be worthwhile to explore more deeply how membrane formation in wrapping glia is orchestrated at the subcellular level by Uif.

      In the revised version of the manuscript we have now included the use of Notch and RTK-signaling reporters.

      (1) reporters for N and Htl signaling in larvae,

      We had already employed the classic reporter generated by the Bray lab: Gbe-Su(H)-lacZ. This unfortunately failed to detect any activity in larval wrapping glia nuclei but was able to detect Notch activity in the adult wrapping glia (Figure S5C,F).

      We did, as requested, the analysis of a RTK signaling reporter.  The activity of sty-lacZ that we had previously characterized in the lab (Sieglitz et al., 2013) increases by 22% when Notch is silenced. Given the normal distribution of the data points, this shows a trend which, however, is not in the significance range. We have not included this in the paper, but would be happy to do so, if requested.

      Author response image 1.

       

      (2) monitoring of different stages at a time point when branch extension begins,

      The reviewer asks for an important question; however, this is extremely difficult to tackle experimentally. It would require a detailed electron microscopic analysis of early larval stages which cannot be done in a reasonable amount of time. We have however added additional information on wrapping glia growth summarizing recently published work from the lab (Kautzmann et al., 2025).

      (3) a reagent enabling to visualize Uif expression could be important next tools/approaches.

      The final comment of the reviewer also addresses an extremely relevant and important issue. We employed antibodies generated by the lab of R. Ward, but they did not allow detection of the protein in larval nerves. We also attempted to generate anti-Uif peptide antibodies but these antibodies unfortunately do not work in tissue. We are still trying to generate suitable reagents but for the current revision cannot offer any solution.

      Lastly, we agree with the reviewer that it would be worthwhile to explore how Uif controls membrane formation at the subcellular level. This, however, is a completely new project and will require the identification of the binding partners of Uif in wrapping glia to start working on a link between Uif and membrane extension. The reduced branching phenotype might well be a direct consequence of excessive membrane formation as it likely blocks recourses needed for efficient growth of glial processes.

      Finally, in light of the importance of correct ensheathment of axons by glia for neuronal function, this study will be of general interest to the glial biology community. 

      We are very grateful for this very positive comment.

      Reviewer #2 (Public review): 

      The FGF receptor Heartless has previously been implicated in Drosophila peripheral glial growth and axonal wrapping. Here, the authors perform a large-scale screen of over 2600 RNAi lines to find factors that control the downstream signaling in this process. They identify a transmembrane protein Uninflatable to be necessary for the formation of plasma membrane domains. They further find that a Uif regulatory target, Notch, is necessary for glial wrapping. Interestingly, additional evidence suggests Notch itself regulates uif and htl, suggesting a feedback system. Together, they propose that Uif functions as a "switch" to regulate the balance between glial growl and wrapping of axons. 

      Little is known about how glial cell properties are coordinated with axons, and the identification of Uif is a promising link to shed light on this orchestration. The manuscript is well-written, and the experiments are generally well-controlled. The EM studies in particular are of outstanding quality and really help to mechanistically dissect the consequences of Uif and Notch signaling in the regulation of glial processes. Together, this valuable study provides convincing evidence of a new player coordinating the interactions controlling the glial wrapping of axons.

      Reviewer #1 (Recommendations for the authors): 

      (1) To be reproducible and understandable, it would be important to provide detailed information about crosses and genotypes, as reagents are currently listed individually and genotypes are provided in rather simplified versions. 

      We have added the requested information to the text.

      (2) Neurons are inherently resistant to RNAi-mediated knockdown and it thus may be necessary to introduce the over-expression of UAS-dcr2 when assessing neuronal requirements and to specifically exclude Delta or Serrate as ligands. 

      We agree with the reviewer and have repeated the knockdown experiments using UAS-dcr2 and obtained the same results. To use an RNAi independent approach we also employed sgRNA expression in the presence of Cas9. The neuron specific gene knockout also showed no glial wrapping phenotype. These results are now added to the manuscript.

      (3) Throughout the manuscript, the authors use the terms "growth" and "differentiation" referring to the extent of branch formation versus axon wrapping. However glial differentiation and growth could have different meanings (for instance, growth could implicate changes in cell size or numbers, while differentiation could refer to a change from an immature precursor-like state to a mature cell identity). It may thus be useful to replace these general terms with more specific ones. 

      This is a very good point. When we use the term “growth” we only infer on glial cell growth and thus, the increase in cell mass. Proliferation is excluded and this is now explicitly stated in the manuscript. The term “differentiation” is indeed difficult and therefore we changed it either directly addressing the morphology or to axon wrapping.

      (4) Page 4. "remake" fibers should be Remak fibers. 

      We have corrected this typo.

      (5) Page 5. "Heartless controls glial growth but does promote axonal wrapping", this sentence is not clear in its message because of the "but".

      We have corrected this sentence.

      (6) Generally, many gene names are used as abbreviations without introductions (e.g. Sos, Rl, Msk on page 7). These would require an introduction.

      All genetic elements are now introduced.

      (7) Page 8. When Cas9 is expressed ubiquitously ... It would be helpful to add how this is done (nsyb-Gal4, nrv2-Gal4, or another Gal4 driver are used to express UAS-Cas9, as the listed Gal4 drivers seem to be specific to neurons or glia?).

      This now added. We used the following genotype for ubiquitous knockout using the four different uif specific sgRNAs (UAS-uif<sup>sgRNA X</sup>): [w; UAS-Cas9/ Df(2L)ED438; da-Gal4 /UAS-uif<sup>sgRNA X</sup>]. We used the following genotype for a glial knockout in wrapping glia ([+/+; UAS-Cas9/+; nrv2-Gal4,UAS-CD8::mCherry/UAS-uif<sup>sgRNA X</sup>].

      We had previously shown that nrv2-Gal4 is a wrapping glia specific driver in the larval PNS (Kottmeier et al., 2020).

      Moreover, the authors mention that "This indicates that a putatively secreted version of Uif is not functional". This conclusion would need to be explained in detail.

      First, because it requires quite some detective work to understand the panels in Figure 1 on which this statement is based; second, since the acutely induced double-stranded breaks in the DNA and subsequent repair may cause variable defects, it may indeed be not certain what changes have been induced in each cell; and third considering that there is a putative cleavage site, would it be not be expected that the protein is not functional, when it is not cleaved, and there is no secreted extracellular part (unless the cleavage site is not required). The latter could probably only be addressed by rescue experiments with UAS transgenes with identified changes.

      We agree with the reviewer. The rescue experiments are unfortunately difficult, since even expression of a full length uif construct does not fully rescue the uif mutant phenotype (Loubéry et al., 2014). We therefore explained the conclusion taken from the different sgRNA knockout experiments better and also removed the statement that secreted Uif forms are non-functional.

      In the Star Method reagent table, it is not clear, why all 8 oligonucleotides are for "uif cleavage just before transmembrane domain" despite targeting different locations. 

      We are very sorry for this mistake and corrected it now. Thank you very much for spotting this.

      (8) Page 13. However, we expressed activated Notch,... the word "when" seems to be missing, and it would be helpful to specify how this was done (over-expression of N[ICD].

      We corrected it now accordingly.

      (9) To strengthen the point similarity of phenotypes caused by Htl pathway over-activation and Uif over-expression, it would be helpful to also show an EM electron micrograph of the former.

      We now added an extensive description of the phenotype caused by activated Heartless. This is shown as new Figure 2.

      (10) Figure 4C, the larval nerve seems to be younger, as many extracellular spaces between axons are detected.

      This perception is a misunderstanding and we are sorry for not explaining this better. The third instar larvae are all age matched. The particular specimen in Figure 4C shows some fixation artifacts that result in the loss of material. Importantly, however, membranes are not affected. Similar loss of material is also seen in Figure 6C. For further examples please see a study on nerve anatomy by (Kautzmann et al., 2025).

      (11) The model could be presented as a figure panel in the manuscript. To connect the recommendation section with the above public review, a step forward could be to adjust the model and the wording in the Result section and to move some of the less explored points and thoughts to the discussion.

      We are thankful for this advice and have moved an updated model figure to the end of the main text (now Figure 7).

      Reviewer #2 (Recommendations for the authors):

      (1) Screen and the interest in Uif: Out of the ~62 genes that came out of the RNAi screen, why did the authors prioritize and focus on Uif? What were the other genes that came out of the screen, and did any of those impinge on Notch signaling? 

      We have now more thoroughly described the results of the screen.  We selected Uif as it was the only transmembrane // adhesion protein identified and given the findings that Uif decorate apical membrane domains in epithelial cells, we hoped to identify a protein specific for a similar membrane domain in wrapping glia.

      Notch as well as its downstream transcription factors were not included in the initial screen, and were only analyzed, once we had seen the contribution of Notch. Interestingly, here is one single hit in our screen linked to Notch signaling: Gp150. Here however, we have tested additional dsRNA expressing lines and were not able to reproduce the phenotype. This information is added to the discussion.

      The authors performed a large-scale screen of 2600 RNAi lines, it seems more details about what came out of the screen and why the focus on Uif would benefit the manuscript. 

      See above comment.

      Relatedly, there would be a discussion of the limitations of the screen, and that it was really a screen looking to modify a gain-of-function phenotype from the activated Htl allele; it seems a screen of this design may lead to artifacts that may not reflect endogenous signaling.

      We have now added a short paragraph on suppressor screens, employing gain of function alleles to the introduction.

      “In Drosophila, such suppressor screens have been used successfully many times (Macagno et al., 2014; Rebay et al., 2000; Therrien et al., 2000). Possibly, such screens also uncover genes that are not directly linked to the signaling pathway under study but this can be tested in further experiments. Our screen led to the unexpected identification of the large transmembrane protein Uninflatable, which in epithelial cells localizes to the apical plasma membrane. Loss of uninflatable suppresses the phenotype caused by activated RTK signaling. In addition, we find that uif knockdown and uif knockout larvae show impaired glial growth while an excess of Uninflatable leads to the formation of ectopic wrapping membrane processes that, however, fail to interact with axons. uninflatable is also known to inhibit Notch.  “

      (2) In general this study relies on RNAi knockdown, and is generally well controlled in using multiple RNAi lines giving the same phenotype, and also controlled for by tissue-specific gene knockout. However, there is little in the way of antibody staining to directly confirm the target of interest is lost/reduced, which would obviously strengthen the study. 

      Lacking the tools or ability to assess RNAi efficiency (qPCR, antibody staining), some conclusions need to be tempered. For example, in the experiments in Figure S6 regarding canonical Notch signaling, the authors do not find a phenotype by Delta or Serrate knockdown, but there are no experiments that show Delta or Serrate are lost. Thus, if the authors cannot directly test for RNAi efficiency, these conclusions should be tempered throughout the manuscript. 

      We agree with the reviewer and now provide information on the use of Dicer in our RNAi experiments and conducted new sgRNA/Cas9 experiments. In addition we tempered our wording stating that Dl and or Ser are still possible ligands.

      (3) More description is needed regarding how the authors are measuring and calculating the "wrapping index". In principle, the approach seems sound. However, are there cases where axons are "partially" wrapped of various magnitudes, and how are these cases treated in the analysis? Are there additional controls of previously characterized mutants to illustrate the dynamic range of the wrapping index in various conditions?

      This is now explained.

      Further, can the authors quantify the phenotypes in the axonal "bulges" in Figures 1, 3, and 5?

      This is a difficult question. Although we can easily quantify the number of bulges we cannot quantify the severity of the phenotype as this will require EM analysis. Sectioning nerves at a specific distance of the ventral nerve cord already requires very careful adjustments. Sectioning at the level of a bulge is way more difficult and it is not possible to get the number of sections needed to quantify the bulge phenotype.

      The fact is that all wrapping glial cells develop swellings (bulges) at the position of the nucleus. As there are in general three wrapping glial cells per segmental nerve, the number of bulges is three.

      (4) It seems difficult to clearly untangle the functions of Htl/Uif/Notch in differentiation itself vs subsequent steps in growth/wrapping. For example, if the differentiation steps are not properly coordinated, couldn't this give rise to some observed differences in growth or wrapping at later stages? I'm not sure of any obvious experiments to pursue here, but at least a brief discussion of these issues in the manuscript would be of use.

      We have discussed this in our discussion now more carefully. To discriminate the function of the three genes in either differentiation or in a stepwise mode of growth and differentiation.

      When comparing the different loss of function phenotypes they al appear the same, which would argue all three genes act in a common process.

      However, when we look at gain of function phenotypes, Htl and Uif behave different compared to Notch. This would favor for two distinct processes.

      We have now added activity markers for RTK signaling to directly show that Notch silences RTK activity. Unfortunately we were not able to do a similar reciprocal experiment.

      Minor:

      (1) The Introduction is too long, and would benefit from revisions to make it shorter and more concise.

      We have shortened the introduction and hopefully made it more concise.

      (2) A schematic illustrating the model the authors propose about Htl, Uif, and Notch in glial differentiation, growth, and wrapping would benefit the clarity of this work. 

      We had previously added the graphical abstract below that we updated and included as a Figure in the main text.

      References

      Kautzmann, S., Rey, S., Krebs, A., and Klämbt, C. (2025). Cholinergic and glutamatergic axons differentially require glial support in the Drosophila PNS. Glia. 10.1002/glia.70011.

      Kottmeier, R., Bittern, J., Schoofs, A., Scheiwe, F., Matzat, T., Pankratz, M., and Klämbt, C. (2020). Wrapping glia regulates neuronal signaling speed and precision in the peripheral nervous system of Drosophila. Nature communications 11, 4491-4417. 10.1038/s41467-020-18291-1.

      Loubéry, S., Seum, C., Moraleda, A., Daeden, A., Fürthauer, M., and González-Gaitán, M. (2014). Uninflatable and Notch control the targeting of Sara endosomes during asymmetric division. Current biology : CB 24, 2142-2148. 10.1016/j.cub.2014.07.054.

      Macagno, J.P., Diaz Vera, J., Yu, Y., MacPherson, I., Sandilands, E., Palmer, R., Norman, J.C., Frame, M., and Vidal, M. (2014). FAK acts as a suppressor of RTK-MAP kinase signalling in Drosophila melanogaster epithelia and human cancer cells. PLoS Genet 10, e1004262. 10.1371/journal.pgen.1004262.

      Rebay, I., Chen, F., Hsiao, F., Kolodziej, P.A., Kuang, B.H., Laverty, T., Suh, C., Voas, M., Williams, A., and Rubin, G.M. (2000). A genetic screen for novel components of the Ras/Mitogen-activated protein kinase signaling pathway that interact with the yan gene of Drosophila identifies split ends, a new RNA recognition motif-containing protein. Genetics 154, 695-712. 10.1093/genetics/154.2.695.

      Sieglitz, F., Matzat, T., Yuva-Adyemir, Y., Neuert, H., Altenhein, B., and Klämbt, C. (2013). Antagonistic Feedback Loops Involving Rau and Sprouty in the Drosophila Eye Control Neuronal and Glial Differentiation. Science signaling 6, ra96. 10.1126/scisignal.2004651.

      Therrien, M., Morrison, D.K., Wong, A.M., and Rubin, G.M. (2000). A genetic screen for modifiers of a kinase suppressor of Ras-dependent rough eye phenotype in Drosophila. Genetics 156, 1231-1242.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews: 

      Reviewer #1 (Public review): 

      Summary 

      In this manuscript, Weir et al. investigate why the 13-lined ground squirrel (13LGS) retina is unusually rich in cone photoreceptors, the cells responsible for color and daylight vision. Most mammals, including humans, have rod-dominant retinas, making the 13LGS retina both an intriguing evolutionary divergence and a valuable model for uncovering novel mechanisms of cone generation. The developmental programs underlying this adaptation were previously unknown. 

      Using an integrated approach that combines single-cell RNA sequencing (scRNAseq), scATACseq, and histology, the authors generate a comprehensive atlas of retinal neurogenesis in 13LGS. Notably, comparative analyses with mouse datasets reveal that in 13LGS, cones can arise from late-stage neurogenic progenitors, a striking contrast to mouse and primate retinas, where late progenitors typically generate rods and other late-born cell types but not cones. They further identify a shift in the timing (heterochrony) of expression of several transcription factors.

      Further, the authors show that these factors act through species-specific regulatory elements. And overall, functional experiments support a role for several of these candidates in cone production. 

      Strengths 

      This study stands out for its rigorous and multi-layered methodology. The combination of transcriptomic, epigenomic, and histological data yields a detailed and coherent view of cone development in 13LGS. Cross-species comparisons are thoughtfully executed, lending strong evolutionary context to the findings. The conclusions are, in general, well supported by the evidence, and the datasets generated represent a substantial resource for the field. The work will be of high value to both evolutionary neurobiology and regenerative medicine, particularly in the design of strategies to replace lost cone photoreceptors in human disease. 

      Weaknesses 

      (1) Overall, the conclusions are strongly supported by the data, but the paper would benefit from additional clarifications. In particular, some of the conclusions could be toned down slightly to reflect that the observed changes in candidate gene function, such as those for Zic3 by itself, are modest and may represent part of a more complex regulatory network.  

      We have revised the text to qualify these conclusions as suggested.

      “Zic3 promotes cone-specific gene expression and is necessary for generating the full complement of cone photoreceptors”

      “Pou2f1 overexpression upregulated an overlapping but distinct, and larger, set of cone-specific genes relative to Zic3, while also downregulating many of the same rod-specific genes, often to a greater extent (Fig. 3C).”

      “This resulted in a statistically significant ~20% reduction in the density of cone photoreceptors in the mutant retina (Fig. 3E,F), while the relative numbers of rods and horizontal cells remained unaffected (Fig. S4A-D).”

      “Our analysis suggests that gene regulatory networks controlling cone specification are highly redundant, with transcription factors acting in complex, redundant, and potentially synergistic combinations. This is further supported by our findings on the synergistic effects of combined overexpression of Zic3 and Pou2f1 increasing both the number of differentially expressed genes and their level of change in expression relative to the modest changes seen with overexpression of either gene alone (Fig. 3) and the relatively mild or undetectable phenotypes observed following loss of function of Zic3 and Mef2c (Fig. 3, Fig. S6), as well as other cone-promoting factors such as Onecut1 and Pou2f1[18,19].“

      (2) Additional explanations about the cell composition of the 13LGS retina are needed. The ratios between cone and rod are clearly detailed, but do those lead to changes in other cell types? 

      The 13LGS retina, like most cone-dominant retinas, shows relatively lower numbers of rod and cone photoreceptors (~20%) than do nocturnal species such as mice (~80%). The difference is made up by increased numbers of inner retinal neurons and Muller glia. While rigorous histological quantification of the abundance of inner retinal cell types has not yet been performed for 13LGS, we can estimate these values using our snATAC-Seq data.  These numbers are provided in Table ST1, and are now discussed in the text.  

      (3) Could the lack of a clear trajectory for rod differentiation be just an effect of low cell numbers for this population? 

      This is indeed likely to be the case. This is now stated explicitly in the text.

      “However, no clear trajectory for rod differentiation was detected, likely due to the very low number of rod cells detected prior to P17 (Fig. 2A).”

      (4) The immunohistochemistry and RNA hybridization experiments shown in Figure S2 would benefit from supporting controls to strengthen their interpretability. While it has to be recognized that performing immunostainings on non-conventional species is not a simple task, negative controls are necessary to establish the baseline background levels, especially in cases where there seems to be labeling around the cells. The text indicates that these experiments are both immunostainings and ISH, but the figure legend only says "immunohistochemistry". Clarifying these points would improve readers' confidence in the data. 

      The figure legend has been corrected, and negative controls for P24 have been added. The figure legend has been modified as follows:

      “Fluorescent in situ hybridization showing co-expression of (A) Pou2f1 and Otx2 or (B) Zic3, Rxrg, and Otx2 in P1, P5, P10, and P24 retinas. Insets show higher power images of highlighted areas. (C) Zic3, Rxrg, and Otx2 fluorescent in situ hybridization from P24 with matched (C’) negative controls.  (D) Pou2f1 and Otx2 fluorescent in situ hybridization from P24 with matched (D’) negative controls. (E) Quantification of the fraction of Otx2-positive cells in the outer neuroblastic layer (P1, P5) and ONL (P10, P24) that also express Zic3. (F) Immunohistochemical analysis Mef2c and Otx2 expression in P1, P5, P10, and P24 retinas. (G) Mef2c and Otx2 immunohistochemistry from P24 with matched (G’) negative controls. Negative controls for fluorescent in situ hybridization omit the probe and for immunohistochemistry omit primary antibodies. Scale bars, 10 µm (S2A-F), 50 µm (S2G) and 5 µm (inset). Cell counts in E were analyzed using one-way ANOVA analysis with Sidak multiple comparisons test and 95% confidence interval. ** = p <0.01, **** = p <0.0001, and ns = non-significant. N=3 independent experiments.”

      (5) Figure S3: The text claims that overexpression of Zic3 alone is sufficient to induce the conelike photoreceptor precursor cells as well as horizontal cell-like precursors, but this is not clear in Figure S3A nor in any other figure. Similarly, the effects of Pou2f1 overexpression are different in Figure S3A and Figure S3B. In Figure S3B, the effects described (increased presence of cone-like and horizontal-like precursors) are very clear, whereas it is not in Figure S3A. How are these experiments different? 

      These UMAP data represent two independent experiments. Total numbers and relative fractions of each cell type are now included in Table ST5.

      In these experiments, cone-like precursors were identified by both cell type clustering and differential gene expression. Cells from all conditions were found in the cone-like precursor cluster. However, cells electroporated with a plasmid expressing GFP alone only showed GFP as a differentially expressed gene, identifying them most likely as GFP+ rods. In contrast, Zic3 overexpression resulted in increased expression of cone-specific genes and decreased expression of rod-specific genes in both cone-like precursors and rods relative to controls electroporated with GFP alone. Cell type proportions across independent overexpression singlecell experiments could be influenced by a number of factors, including electroporation efficiency and ex vivo growth conditions. 

      (6) The analyses of Zic3 conditional mutants (Figure S4) reveal an increase in many cone, rod, and pan-photoreceptor genes with only a reduction in some cone genes. Thus, the overall conclusion that Zic3 is essential for cones while repressing rod genes doesn't seem to match this particular dataset. 

      We observe that loss of function of Zic3 in developing retinal progenitors leads to a reduction in the total number of cones (Fig. 4E,F). In Fig. S4, we investigate how gene expression is altered in both the remaining cones and in other retinal cell types. We only observed significant changes in mutant cones and Muller glia relative to controls. We observe a mixed phenotype in cones, with a subset of cone-specific genes downregulated (notably including Thrb), a subset of others upregulated (including Opn1sw). We also find that genes expressed both in rods and cones, as well as rod-specific genes, are downregulated in cKO cones. Since rods are fragile cells that are located immediately adjacent to cones, some level of contamination of rod-specific genes is inevitable in single-cell analysis of dissociated cones (c.f. PMID: 31128945, 34788628), and this reduced level of rod contamination could result from altered adhesion between mutant rods and cones. In mutant Muller glia, in contrast, we see a broad decrease in expression of Muller glia-specific genes, which likely reflects the indirect effects of Zic3 loss of function in retinal progenitors, and an upregulation of both broadly photoreceptor-specific genes and a subset of rod-specific genes, which may also result from altered adhesion between Muller glia and rods. 

      This is consistent with the conclusions in the text, although we have both modified the text and included heatmaps showing downregulation of rod-specific genes in mutant cones, to clarify this finding.

      “In addition, we observe a broad decrease in expression of genes expressed at high levels in both cones and rods (Rpgrip1, Drd4) and rod-specific genes (Rho, Cnga1, Pde6b) in mutant cones (Fig. S4F). Since rods are fragile cells that are located immediately adjacent to cones, some level of contamination of rod-specific genes is inevitable in single-cell analysis of dissociated cones (c.f. PMID: 31128945, 34788628), and this reduced level of rod contamination could result from altered adhesion between mutant rods and cones. In contrast, increased expression of rod-specific genes (Rho, Nrl, Pde6g, Gngt1) and pan-photoreceptor genes (Crx, Stx3, Rcvrn) was observed in Müller glia (Fig. S4G), which may likewise result from altered adhesion between Muller glia and rods. Finally, several Müller glia-specific genes were downregulated, including Clu, Aqp4, and Notch pathway components such as Hes1 and Id3, with the exception of Hopx, which was upregulated (Fig. S4G). This likely reflects the indirect effects of Zic3 loss of function in retinal progenitors. These findings indicate that Zic3 is essential for the proper expression of photoreceptor genes in cones while also playing a role in regulating expression of Müller glia-specific genes.”

      (7) Throughout the text, the authors used the term "evolved". To substantiate this claim, it would be important to include sequence analyses or to rephrase to a more neutral term that does not imply evolutionary inference. 

      We have modified the text as requested to replace “evolved” and “evolutionarily conserved” where possible, with examples of revised text listed below:  

      “These results demonstrate that modifications to gene regulatory networks underlie the development of cone-dominant retina,...”

      “Our results demonstrate that heterochronic expansion of the expression of transcription factors that promote cone development is a key event in the development of the cone-dominant 13LGS retina.”

      “Conserved patterns of motif accessibility, identified using ChromVAR and theTRANSFAC2018 database, (Fig. S1F, Table ST1)...”

      “However, most of these elements  mapped to sequences that were not shared between 13LGS and mouse, with intergenic enhancers exhibiting particularly low levels of conservation (Fig. 5B).”

      “We conclude that the development of the cone-dominant retina in 13LGS is driven by novel cisregulatory elements…”

      “Based on our bioinformatic analysis, the cone-dominant 13LGS retina follows this paradigm, in which species-specific enhancer elements…”

      “Dot plots showing the enrichment of binding sites for Otx2 and Neurod1, TFs which are broadly expressed in both neurogenic RPC and photoreceptor precursors, which are enriched in both conserved cis-regulatory elements in both species. (D) Bar plots showing the number of conversed and species-specific enhancers per TSS in four cone-promoting genes between 13LGS and mouse.”

      Reviewer #2 (Public review): 

      Summary: 

      This paper aims to elucidate the gene regulatory network governing the development of cone photoreceptors, the light-sensing neurons responsible for high acuity and color vision in humans. The authors provide a comprehensive analysis through stage-matched comparisons of gene expression and chromatin accessibility using scRNA-seq and scATAC-seq from the conedominant 13-lined ground squirrel (13LGS) retina and the rod-dominant mouse retina. The abundance of cones in the 13LGS retina arises from a dominant trajectory from late retinal progenitor cells (RPCs) to photoreceptor precursors and then to cones, whereas only a small proportion of rods are generated from these precursors. 

      Strengths: 

      The paper presents intriguing insights into the gene regulatory network involved in 13LGS cone development. In particular, the authors highlight the expression of cone-promoting transcription factors such as Onecut2, Pou2f1, and Zic3 in late-stage neurogenic progenitors, which may be driven by 13LGS-specific cis-regulatory elements. The authors also characterize candidate cone-promoting genes Zic3 and Mef2C, which have been previously understudied. Overall, I found that the across-species analysis presented by this study is a useful resource for the field. 

      Weaknesses: 

      The functional analysis on Zic3 and Mef2C in mice does not convincingly establish that these factors are sufficient or necessary to promote cone photoreceptor specification. Several analyses lack clarity or consistency, and figure labeling and interpretation need improvement. 

      We have modified the text and figures to more clearly describe the observed roles of Zic3 and Mef2c in cone photoreceptor development as detailed in our responses to reviewer recommendations.

      Reviewer #3 (Public review): 

      Summary: 

      The authors perform deep transcriptomic and epigenetic comparisons between mouse and 13lined ground squirrel (13LGS) to identify mechanisms that drive rod vs cone-rich retina development. Through cross-species analysis, the authors find extended cone generation in 13LGS, gene expression within progenitor/photoreceptor precursor cells consistent with a lengthened cone window, and differential regulatory element usage. Two of the transcription factors, Mef2c and Zic3, were subsequently validated using OE and KO mouse lines to verify the role of these genes in regulating competence to generate cone photoreceptors. 

      Strengths: 

      Overall, this is an impactful manuscript with broad implications toward our understanding of retinal development, cell fate specification, and TF network dynamics across evolution and with the potential to influence our future ability to treat vision loss in human patients. The generation of this rich new dataset profiling the transcriptome and epigenome of the 13LGS is a tremendous addition to the field that assuredly will be useful for numerous other investigations and questions of a variety of interests. In this manuscript, the authors use this dataset and compare it to data they previously generated for mouse retinal development to identify 2 new regulators of cone generation and shed insights into their regulation and their integration into the network of regulatory elements within the 13LGS compared to mouse. 

      Weaknesses: 

      (1) The authors chose to omit several cell classes from analyses and visualizations that would have added to their interpretations. In particular, I worry that the omission of 13LGS rods, early RPCs, and early NG from Figures 2C, D, and F is notable and would have added to the understanding of gene expression dynamics. In other words, (a) are these genes of interest unique to late RPCs or maintained from early RPCs, and (b) are rod networks suppressed compared to the mouse? 

      We were unable to include 13LGS rods in our analysis due to the extremely low number of cells detected prior to P17. Relative expression levels of cone-promoting transcription factors in 13LGS in early RPCs and early NG cells is shown in Fig. 2H. Particularly when compared to mice, we also observe elevated expression of cone-promoting genes in early-stage RPC and/or early NG cells. These include Zic3, Onecut2, Mef2c, and Pou2f1, as well as transcription factors that promote the differentiation of post-mitotic cone precursors, such as Thrb and Rxrg. Contrast this with genes that promote specification and differentiation of both rods and cones, such as Otx2 and Crx, which show similar or even slightly higher expression in mice. Genes such as Casz1, which act in late NG cells to promote rod specification, are indeed downregulated in 13LGS late NG cells relative to mice. We have modified the text to clarify these points, as shown below:

      “To further characterize species-specific patterns of gene expression and regulation during postnatal photoreceptor development, we analyzed differential gene expression, chromatin accessibility, and motif enrichment across late-stage primary and neurogenic progenitors, immature photoreceptor precursors, rods, and cones. Due to their very low number before time point P17, we were unable to include 13LGS rods in the analysis.”

      “In contrast, two broad patterns of differential expression of cone-promoting transcription factors were observed between mouse and 13LGS.”

      “First, transcription factors identified in this network that are known to be required for committed cone precursor differentiation, including Thrb, Rxrg, and Sall3 [25,26,45], consistently showed stronger expression in late-stage RPCs and early-stage primary and/or neurogenic RPCs of 13LGS compared to mice.”

      “Second, transcription factors in the network known to promote cone specification in early-stage mouse RPCs, such as Onecut2 and Pou2f1, exhibited enriched expression in early and latestage primary and/or neurogenic RPCs of 13LGS, implying a heterochronic expansion of conepromoting factors into later developmental stages.”

      “In contrast, genes such as Casz1, which act in late neurogenic RPCs to promote rod specification, are downregulated in 13LGS late neurogenic RPCs relative to mice.”

      (2) The authors claim that the majority of cones are generated by late RPCs and that this is driven primarily by the enriched enhancer network around cone-promoting genes. With the temporal scRNA/ATACseq data at their disposal, the authors should compare early vs late born cones and RPCs to determine whether the same enhancers and genes are hyperactivated in early RPCs as well as in the 13LGS. This analysis will answer the important question of whether the enhancers activated/evolved to promote all cones, or are only and specifically activated within late RPCs to drive cone genesis at the expense of rods. 

      This is an excellent question.  We have addressed this question by analyzing both expression of the cone-promoting genes identified in C2 and C3 in Figure 2C and accessibility of their associated enhancer sequences, which are shown in Figure 6B, in early and late-stage RPCs and cone precursors.  The results are shown in Author response image 1 below. We observe that cone-promoting genes consistently show higher expression in both late-stage RPCs and cones.  We do not observe any clear differences in the accessibility of the associated enhancer regions, as determined by snATAC-Seq.  However, since we have not performed CUT&RUN analysis in embryonic retina for H3K27Ac or any other marker of active enhancer elements, we cannot determine whether the total number of active enhancers differs between early and late-stage RPCs. We suspect, however, this is likely to be the case, given the differences in the expression levels of these genes.

      Author response image 1.

      Relative expression levels of cone-promoting genes and accessibility of enhancer elements associated with these genes in early- and late-stage RPCs and cone precursors.

      (3) The authors repeatedly use the term 'evolved' to describe the increased number of local enhancer elements of genes that increase in expression in 13LGS late RPCs and cones. Evolution can act at multiple levels on the genome and its regulation. The authors should consider analysis of sequence level changes between mouse, 13LGS, and other species to test whether the enhancer sequences claimed to be novel in the 13LGS are, in fact, newly evolved sequence/binding sites or if the binding sites are present in mouse but only used in late RPCs of the 13LGS. 

      Novel enhancer sequences here are defined as having divergent sequences rather than simply divergent activity. This point has been clarified in the text, with the following changes made:

      “However, most of these elements mapped to sequences that were not shared between 13LGS and mouse, with intergenic enhancers exhibiting particularly low levels of conservation (Fig. 5B).”

      “...demonstrated far greater motif enrichment in active regulatory elements in 13LGS than in mice, though few of these elements mapped to sequences that were shared between 13LGS and mouse (Fig. 5C,D, Table ST10).”

      (4) The authors state that 'Enhancer elements in 13LGS are predicted to be directly targeted by a considerably greater number of transcription factors than in mice'. This statement can easily be misread to suggest that all enhancers display this, when in fact, this is only the conepromoting enhancers of late 13LGS RPCs. In a way, this is not surprising since these genes are largely less expressed in mouse vs 13LGS late RPCs, as shown in Figure 2. The manuscript is written to suggest this mechanism of enhancer number is specific to cone production in the 13LGS- it would help prove this point if the authors asked the opposite question and showed that mouse late RPCs do not have similar increased predicted binding of TFs near rodpromoting genes in C7-8. 

      The Reviewer’s point is well taken, and we agree that this mechanism is unlikely to be specific to cone photoreceptors, since we are simply looking at genes that show higher expression in late-stage neurogenic RPCs in 13LGS. We have changed the relevant text to now state:

      “Enhancer elements associated with cone-specific genes in 13LGS are predicted to be directly targeted by a considerably greater number of transcription factors in late-stage neurogenic RPCs than in mice, as might be expected, given the higher expression levels of these genes.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors): 

      (1) Minor: Clusters C1-C8 (Figure 2) are labeled as "C1-8" in the text but "G1-8" in the figure. 

      This has been done.

      (2) Minor: Showing other neurogenic factors (Olig2, Ascl1, Otx2) and late-stage specific factors (Lhx2, Sox8, Nfia/b) could be shown in Figure 2 to better support the text. 

      This has been done. These motifs are consistent in both species, but Figure 2F shows differential motifs. The reference to Figure 2F has been altered to include Table ST4, while Neurod1 motifs are shown in Fig. 2F.

      Reviewer #2 (Recommendations for the authors): 

      (1) Figure 2 

      2A-B: The exclusion of early-stage data from the species-integrated analysis is puzzling, as it could reveal significant differences between early-stage neurogenic progenitors in mice and late-stage progenitors in 13LGS that both give rise to cones. This analysis would also shed light on how cone-promoting transcription factors are suppressed in mouse early-stage progenitors, limiting the window for cone genesis.

      2C: The figure labels G1-8, while C1-8 are referenced in the text. 

      2F: Neurog2, Olig2, Ascl1, and Neurod1 are mentioned in the text but not labeled in the figure. 

      2A-B: There are indeed substantial differences between early-stage RPC in 13LGS and latestage RPC in mice that are broadly linked to control of temporal patterning, which are mentioned in the text. For instance, early-stage RPCs in both animals express higher levels of Nr2f1/2, Meis1/2, and Foxp1/4, while late-stage RPCs express higher levels of Nfia/b/x, indicating that core distinction between early- and late-stage RPCs is maintained.  What most clearly differs in 13-LGS is the sustained expression of a subset of cone-promoting transcription factors in late-stage RPCs that are normally restricted to early-stage RPCs in mice. However, as mentioned in response to Reviewer #3’s first point, we do observe some evidence for increased expression of cone-promoting transcription factors in early-stage RPCs and NG cells of 13LGS relative to mice, although this is much less dramatic than observed at later stages.  We have modified the text to directly mention this point. G1-8 has been corrected to C1-8 in the figure, a reference to Table ST4 has been added in discussion of neurogenic bHLH factors, and Fig. 2F has been modified to label Neurod1. 

      “First, transcription factors identified in this network that are known to be required for committed cone precursor differentiation, including Thrb, Rxrg, and Sall3 [25,26,45], consistently showed stronger expression in late-stage RPCs and early-stage primary and/or neurogenic RPCs of 13LGS compared to mice.”

      “Second, transcription factors in the network known to promote cone specification in early-stage mouse RPCs, such as Onecut2 and Pou2f1, exhibited enriched expression in early and latestage primary and/or neurogenic RPCs of 13LGS, implying a heterochronic expansion of conepromoting factors into later developmental stages.”

      (2) Figure 3 

      In 3F, the cone density in the WT retina is approximately 0.25 cones per micron, while in the Zic3 cKO retina, it is about 0.2 cones per micron. However, the WT control in Figure S6C also shows about 0.2 cones per micron, raising questions about whether there is a genuine decrease in cone number or if it results from quantification variability. Additionally, the proportion of cone cells in the Zic3 cKO scRNA-seq data shown in Figure S4E appears comparable to the WT control, which is inconsistent with the conclusion that Zic3 cKO leads to reduced cone production. Therefore, I found that the conclusion that Zic3 is necessary for cone development is not supported by the data.

      The cone density counts in the two mutant lines and accompanying littermate controls were collected by blinded counting by two different observers (R.A. for the Zic3 cKO and N.P. for the Mef2c cKO). We believe that the ~20% difference in the observed cone density in the two control samples likely represents investigator-dependent differences. These can exceed 20% between even highly skilled observers when quantifying dissociated cells (PMID: 35198419) and are likely to be even higher for immunohistochemistry samples.  Since both controls were done in parallel with littermate mutant samples, we therefore stand by our interpretation of these results.

      (3) Figures 4 and 5

      These figures are duplicates. In Figure 4, Mef2C overexpression in postnatal progenitors leads to increased numbers of neurogenic RPCs, suggesting it may promote cell proliferation rather than inhibit rod cell fate or promote cone cell fate. Electroporation of plasmids into P0 retina typically does not label cone cells, as cones are born prenatally in mice. Given the widespread GFP signal in Figure 4D, the authors should consider that the high background of GFP signal may have misled the quantification of the result.

      The figure duplication has been corrected. We respectfully disagree with the Reviewer’s statement that ex vivo electroporation performed at P0, as is the case here, does not label cones. We routinely observe small numbers of electroporated cones when performing this analysis. Cones at this age are located on the scleral face of the retina at this age and therefore in direct contact with the buffer solution containing the plasmid in question (c.f. PMID: 20729845, 31128945, 34788628, 40654906). Furthermore, since the level of GFP expression that is used to gate electroporated cells for isolation using FACS is typically considerably less than that used to identify a GFP-positive cell using standard immunohistochemical techniques, making it difficult to directly compare the efficiency of cone electroporation between these approaches. We agree, however, that Mef2c overexpression seems to broadly delay the differentiation of rod photoreceptors, and have modified the text to include discussion of this point.

      “Although a few GFP-positive electroporated cells co-expressing the cone-specific marker Gnat2 were detected in control (likely due to the electroporation of cone precursors, which we have previously observed in P0 retinal explants (Clark et al., 2019; Leavey et al., 2025; Lyu et al., 2021; Onishi et al., 2010)), there was a significant increase in double-positive cells in the test condition, matching the novel cone-like precursor population found in the scRNA-Seq (Fig. 4E).”

      “Indeed, overexpression of Mef2c increased the number of both neurogenic RPCs and immature photoreceptor precursors, suggesting that rod differentiation was broadly delayed.”

      (4) Figure S2 

      The figure legend lacks information about panels A and B. It is unclear which panels represent immunohistochemistry and which represent RNA hybridization chain reaction. Overall, the staining results are difficult to interpret, as it appears that all examined RNAs/proteins are positively stained across the sections with varying background levels. Specificity is hard to assess. For instance, in Figure S2B, the background intensity of Zic3 staining varies inconsistently from P1 to P24. The number of Zic3 mRNA dots seems to peak at P5 and decrease at P10, which contradicts the scRNA-seq results showing peak expression in mature cones.

      The figure legend has been corrected. Negative controls are now included for both in situ hybridization (Fig. S2C’) and immunostaining (Fig. S2G) at P24, along with paired experimental data.  We have quantified the total fraction of Otx2+ cells that also contain Zic3 foci, and find that coexpression peaks at P5 and P10.  This is now included as Fig. S2E.

      The number of Zic3 foci is in fact higher at P5 than P10, with XX foci/Otx2+ cell at P5 vs. YY foci/Otx2+ cell at P10.

      “Fluorescent in situ hybridization showing co-expression of (A) Pou2f1 and Otx2 or (B) Zic3, Rxrg, and Otx2 in P1, P5, P10, and P24 retinas. Insets show higher power images of highlighted areas. (C) Zic3, Rxrg, and Otx2 fluorescent in situ hybridization from P24 with matched (C’) negative controls. (D) Pou2f1 and Otx2 fluorescent in situ hybridization from P24 with matched (D’) negative controls. (E) Quantification of the fraction of Otx2-positive cells in the outer neuroblastic layer (P1, P5) and ONL (P10, P24) that also express Zic3. (F) Immunohistochemical analysis Mef2c and Otx2 expression in P1, P5, P10, and P24 retinas. (G) Mef2c and Otx2 immunohistochemistry from P24 with matched (G’) negative controls. Negative controls for fluorescent in situ hybridization omit the probe and for immunohistochemistry omit primary antibodies. Scale bars, 10 µm (S2A-F),  50 µm (S2G) and 5 µm (inset). Cell counts in E were analyzed using one-way ANOVA analysis with Sidak multiple comparisons test and 95% confidence interval. ** = p <0.01, **** = p <0.0001, and ns = non-significant. N=3 independent experiments.”

      (5) Figure S3

      In S3A and S3B, the UMAPs of the empty vector-treated groups are distinctly different. The same goes for Zic3+Pou2F1 UMAPS.

      In S3A, Zic3 overexpression alone does not appear to have any impact on cell fate. It is not evident that Zic3, even in combination with Pou2F1, has any significant impact on cone or other cell type production, as the proportions of the cones and cone precursors seem similar across different groups.

      In S3B, Zic3+Pou2F1 seems to increase HC-like precursors without increasing cone-like procursors or cones.

      Moreover, the cone-like precursors described do not seem to contribute to cone generation, as there is no increase in cones in the adult mouse retina; rather, these cells resemble rod-cone mosaic cells with expression of both rod- and cone-specific genes.

      As the Reviewer states, we observe some differences in the proportion of cell types in both control and experimental conditions between the two experiments. Notably, relatively more photoreceptors and correspondingly fewer progenitors, bipolar, and amacrine cells are observed in the samples shown in Fig. S3A relative to Fig. S3B.  However, these represent two independent experiments. Cell type proportions seen across independent ex vivo electroporation experiments such as these can be affected by a number of variables, including precise developmental age of the samples, electroporation efficiency, cell dissociation conditions, and ex vivo growth conditions.  Some differences are inevitable, which is why paired negative controls must always be done for results to be interpretable.

      In both experiments, we observe that overexpression of Zic3, Pou2f1, and most notably Zic3 and Pou2f1 lead to an increase in the relative fraction of cone-like precursors. In the experiment shown in Fig. S3B, we also observe that Zic3 alone, Onecut1 alone, and Zic3 and Pou2f1 in combination also promote generation of horizontal-like cells. All treatments likewise induce expression of different subsets of cone-enriched genes in the cone-like precursors, while also suppressing rod-specific genes in these same cells.

      Total numbers and relative fractions of each cell type are now included in Table ST5.

      (6) Figure S4

      The proportion of cone cells in the Zic3 cKO scRNA-seq data shown in Figure S4E appears comparable to the WT control, contradicting the conclusion that Zic3 cKO leads to reduced cone production. 

      Total numbers and relative fractions of each cell type are now included in Table ST6.

      (7) Figure S5

      In Figure S5A, Mef2C overexpression does not decrease expression of the rod gene Nrl. 

      This is correct, and is mentioned in the text.

      “No obvious reduction in the relative number of Nrl-positive cells was observed (Fig. S5A).”

      Reviewer #3 (Recommendations for the authors): 

      (1) The authors make several broad and definitive statements that have the potential to confuse readers. In the first sections of Results: 'retinal ganglion cells and amacrine cells were generated predominantly by early stage progenitors' but later say 'late-stage RPCs in 13LGS retina are competent to generate cone photoreceptors but not other early born cell types.' In the discussion, the authors themselves point out limitations of analyses without birthdating. These definitive statements should be qualified/amended. 

      Both single-cell RNA and ATAC-Seq analysis can be used to accurately profile cells that have recently exited mitosis and committed to a specific cell fate. When applied to data obtained from a developmental timecourse such as is the case here, this can in turn serve as a reasonable proxy for generating birthdating data. Nonetheless, we have modified the text to state that BrdU/EdU labeling is indeed the gold standard for drawing conclusions about cell birthdates, and should be used to confirm these findings in future studies.

      “The expected temporal patterns of neurogenesis were observed in both species: retinal ganglion cells and amacrine cells were generated predominantly in the early stage, whereas bipolar cells and Müller glia were produced in the late stage.”

      “Though BrdU/EdU labeling would be required to unambiguously demonstrate species-specific differences in birthdating, our findings strongly indicate that 13LGS exhibit a selective expansion of the temporal window of cone generation, extending into late stages of neurogenesis.”

      This sentence does not make a definitive statement about 13LGS RPC competence, and we have left it unaltered. 

      “These findings suggest that late-stage RPCs in 13LGS retina are competent to generate cone photoreceptors but not other early-born cell types…”

      (2) Figure 2C clusters are referred to as C1-8 in the text but G1-8 in the figure. This is confusing and should be fixed. 

      This has been corrected.

      (3) The authors refer to many genes that show differential expression in Figure 2F, but virtually none of these are labelled in the heatmap, making it hard to follow the narrative. 

      Figure 2F represents transcription factor binding motifs that are differentially active between mouse and 13LGS, not gene expression. We have modified the figure to include names of all differentially active motifs discussed in the text, and otherwise refer the reader to Table ST4, which includes a list of all differentially expressed genes.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      We appreciate the reviewer for the critical review of the manuscript and the valuable comments. We have carefully considered the reviewer’s comments and have revised our manuscript accordingly.

      The reviewer’s comments in this letter are in Bold and Italics.

      Summary:

      This study identified three independent components of glucose dynamics-"value," "variability," and "autocorrelation", and reported important findings indicating that they play an important role in predicting coronary plaque vulnerability. Although the generalizability of the results needs further investigation due to the limited sample size and validation cohort limitations, this study makes several notable contributions: validation of autocorrelation as a new clinical indicator, theoretical support through mathematical modeling, and development of a web application for practical implementation. These contributions are likely to attract broad interest from researchers in both diabetology and cardiology and may suggest the potential for a new approach to glucose monitoring that goes beyond conventional glycemic control indicators in clinical practice.

      Strengths:

      The most notable strength of this study is the identification of three independent elements in glycemic dynamics: value, variability, and autocorrelation. In particular, the metric of autocorrelation, which has not been captured by conventional glycemic control indices, may bring a new perspective for understanding glycemic dynamics. In terms of methodological aspects, the study uses an analytical approach combining various statistical methods such as factor analysis, LASSO, and PLS regression, and enhances the reliability of results through theoretical validation using mathematical models and validation in other cohorts. In addition, the practical aspect of the research results, such as the development of a Web application, is also an important contribution to clinical implementation.

      We appreciate reviewer #1 for the positive assessment and for the valuable and constructive comments on our manuscript.

      Weaknesses:

      The most significant weakness of this study is the relatively small sample size of 53 study subjects. This sample size limitation leads to a lack of statistical power, especially in subgroup analyses, and to limitations in the assessment of rare events. 

      We appreciate the reviewer’s concern regarding the sample size. We acknowledge that a larger sample size would increase statistical power, especially for subgroup analyses and the assessment of rare events.

      We would like to clarify several points regarding the statistical power and validation of our findings. Our sample size determination followed established methodological frameworks, including the guidelines outlined by Muyembe Asenahabi, Bostely, and Peters Anselemo Ikoha. “Scientific research sample size determination.” (2023). These guidelines balance the risks of inadequate sample size with the challenges of unnecessarily large samples. For our primary analysis examining the correlation between CGM-derived measures and %NC, power calculations (a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4) indicated that a minimum of 47 participants was required. Our sample size of 53 exceeded this threshold and allowed us to detect statistically significant correlations, as described in the Methods section. Moreover, to provide transparency about the precision of our estimates, we have included confidence intervals for all coefficients. 

      Furthermore, our sample size aligns with previous studies investigating the associations between glucose profiles and clinical parameters, including Torimoto, Keiichi, et al. “Relationship between fluctuations in glucose levels measured by continuous glucose monitoring and vascular endothelial dysfunction in type 2 diabetes mellitus.” Cardiovascular Diabetology 12 (2013): 1-7. (n=57), Hall, Heather, et al. “Glucotypes reveal new patterns of glucose dysregulation.” PLoS biology 16.7 (2018): e2005143. (n=57), and Metwally, Ahmed A., et al. “Prediction of metabolic subphenotypes of type 2 diabetes via continuous glucose monitoring and machine learning.” Nature Biomedical Engineering (2024): 1-18. (n=32).

      Furthermore, the primary objective of our study was not to assess rare events, but rather to demonstrate that glucose dynamics can be decomposed into three main factors - mean, variance and autocorrelation - whereas traditional measures have primarily captured mean and variance without adequately reflecting autocorrelation. We believe that our current sample size effectively addresses this objective. 

      Regarding the classification of glucose dynamics components, we have conducted additional validation across diverse populations including 64 Japanese, 53 American, and 100 Chinese individuals. These validation efforts have consistently supported our identification of three independent glucose dynamics components.

      However, we acknowledge the importance of further validation on a larger scale. To address this, we conducted a large follow-up study of over 8,000 individuals (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which confirmed our main finding that glucose dynamics consist of mean, variance, and autocorrelation. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper; however, it provides further support for the clinical relevance and generalizability of our findings.

      To address the sample size considerations, we have added the following sentences in the Discussion section (lines 409-414): 

      Although our analysis included four datasets with a total of 270 individuals, and our sample size of 53 met the required threshold based on power calculations with a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4, we acknowledge that the sample size may still be considered relatively small for a comprehensive assessment of these relationships. To further validate these findings, larger prospective studies with diverse populations are needed.

      We appreciate the reviewer’s feedback and believe that these clarifications improve the manuscript.

      In terms of validation, several challenges exist, including geographical and ethnic biases in the validation cohorts, lack of long-term follow-up data, and insufficient validation across different clinical settings. In terms of data representativeness, limiting factors include the inclusion of only subjects with well-controlled serum cholesterol and blood pressure and the use of only short-term measurement data.

      We appreciate the reviewer’s comment regarding the challenges associated with validation. In terms of geographic and ethnic diversity, our study includes validation datasets from diverse populations, including 64 Japanese, 53 American and 100 Chinese individuals. These datasets include a wide range of metabolic states, from healthy individuals to those with diabetes, ensuring validation across different clinical conditions. In addition, we recognize the limited availability of publicly available datasets with sufficient sample sizes for factor decomposition that include both healthy individuals and those with type 2 diabetes (Zhao, Qinpei, et al. “Chinese diabetes datasets for data-driven machine learning.” Scientific Data 10.1 (2023): 35.). The main publicly available datasets with relevant clinical characteristics have already been analyzed in this study using unbiased approaches.

      However, we fully agree with the reviewer that expanding the geographic and ethnic scope, including long-term follow-up data, and validation in different clinical settings would further strengthen the robustness and generalizability of our findings. To address this, we conducted a large follow-up study of over 8,000 individuals with two years of follow-up (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which confirmed our main finding that glucose dynamics consist of mean, variance, and autocorrelation. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper; however, it provides further support for the clinical relevance and generalizability of our findings.

      Regarding the validation considerations, we have added the following sentences to the Discussion section (lines 409-414, 354-361): 

      Although our analysis included four datasets with a total of 270 individuals, and our sample size of 53 met the required threshold based on power calculations with a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4, we acknowledge that the sample size may still be considered relatively small for a comprehensive assessment of these relationships. To further validate these findings, larger prospective studies with diverse populations are needed.

      Although our LASSO and factor analysis indicated that CGM-derived measures were strong predictors of %NC, this does not mean that other clinical parameters, such as lipids and blood pressure, are irrelevant in T2DM complications. Our study specifically focused on characterizing glucose dynamics, and we analyzed individuals with well-controlled serum cholesterol and blood pressure to reduce confounding effects. While we anticipate that inclusion of a more diverse population would not alter our primary findings regarding glucose dynamics, it is likely that a broader data set would reveal additional predictive contributions from lipid and blood pressure parameters.

      In terms of elucidation of physical mechanisms, the study is not sufficient to elucidate the mechanisms linking autocorrelation and clinical outcomes or to verify them at the cellular or molecular level.

      We appreciate the reviewer’s point regarding the need for further elucidation of the physical mechanisms linking glucose autocorrelation to clinical outcomes. We fully agree with the reviewer that the detailed molecular and cellular mechanisms underlying this relationship are not yet fully understood, as noted in our Discussion section.

      However, we would like to emphasize the theoretical basis that supports the clinical relevance of autocorrelation. Our results show that glucose profiles with identical mean and variability can exhibit different autocorrelation patterns, highlighting that conventional measures such as mean or variance alone may not fully capture inter-individual metabolic differences. Incorporating autocorrelation analysis provides a more comprehensive characterization of metabolic states. Consequently, incorporating autocorrelation measures alongside traditional diabetes diagnostic criteria - such as fasting glucose, HbA1c and PG120, which primarily reflect only the “mean” component - can improve predictive accuracy for various clinical outcomes. While further research at the cellular and molecular level is needed to fully validate these findings, it is important to note that the primary goal of this study was to analyze the characteristics of glucose dynamics and gain new insights into metabolism, rather than to perform molecular biology experiments.

      Furthermore, our previous research has shown that glucose autocorrelation reflects changes in insulin clearance (Sugimoto, Hikaru, et al. “Improved detection of decreased glucose handling capacities via continuous glucose monitoring-derived indices.” Communications Medicine 5.1 (2025): 103.). The relationship between insulin clearance and cardiovascular disease has been well documented (Randrianarisoa, Elko, et al. “Reduced insulin clearance is linked to subclinical atherosclerosis in individuals at risk for type 2 diabetes mellitus.” Scientific reports 10.1 (2020): 22453.), and the mechanisms described in this prior work may potentially explain the association between glucose autocorrelation and clinical outcomes observed in the present study.

      Rather than a limitation, we view these currently unexplored associations as an opportunity for further research. The identification of autocorrelation as a key glycemic feature introduces a new dimension to metabolic regulation that could serve as the basis for future investigations exploring the molecular mechanisms underlying these patterns.

      While we agree that further research at the cellular and molecular level is needed to fully validate these findings, we believe that our study provides a theoretical framework to support the clinical utility of autocorrelation analysis in glucose monitoring, and that this could serve as the basis for future investigations exploring the molecular mechanisms underlying these autocorrelation patterns, which adds to the broad interest of this study. Regarding the physical mechanisms linking autocorrelation and clinical outcomes, we have added the following sentences in the Discussion section (lines 331-339, 341-352): 

      This study also provided evidence that autocorrelation can vary independently from the mean and variance components using simulated data. In addition, simulated glucose dynamics indicated that even individuals with high AC_Var did not necessarily have high maximum and minimum blood glucose levels. This study also indicated that these three components qualitatively corresponded to the four distinct glucose patterns observed after glucose administration, which were identified in a previous study (Hulman et al., 2018). Thus, the inclusion of autocorrelation in addition to mean and variance may improve the characterization of inter-individual differences in glucose regulation and improve the predictive accuracy of various clinical outcomes.

      Despite increasing evidence linking glycemic variability to oxidative stress and endothelial dysfunction in T2DM complications (Ceriello et al., 2008; Monnier et al., 2008), the biological mechanisms underlying the independent predictive value of autocorrelation remain to be elucidated. Our previous work has shown that glucose autocorrelation is influenced by insulin clearance (Sugimoto et al., 2025), a process known to be associated with cardiovascular disease risk (Randrianarisoa et al., 2020). Therefore, the molecular pathways linking glucose autocorrelation to cardiovascular disease may share common mechanisms with those linking insulin clearance to cardiovascular disease. Although previous studies have primarily focused on investigating the molecular mechanisms associated with mean glucose levels and glycemic variability, our findings open new avenues for exploring the molecular basis of glucose autocorrelation, potentially revealing novel therapeutic targets for preventing diabetic complications.

      Reviewer #2 (Public review):

      We appreciate the reviewer for the critical review of the manuscript and the valuable comments. We have carefully considered the reviewer’s comments and have revised our manuscript accordingly. The reviewer’s comments in this letter are in Bold and Italics.

      Sugimoto et al. explore the relationship between glucose dynamics - specifically value, variability, and autocorrelation - and coronary plaque vulnerability in patients with varying glucose tolerance levels. The study identifies three independent predictive factors for %NC and emphasizes the use of continuous glucose monitoring (CGM)-derived indices for coronary artery disease (CAD) risk assessment. By employing robust statistical methods and validating findings across datasets from Japan, America, and China, the authors highlight the limitations of conventional markers while proposing CGM as a novel approach for risk prediction. The study has the potential to reshape CAD risk assessment by emphasizing CGM-derived indices, aligning well with personalized medicine trends.

      Strengths:

      (1) The introduction of autocorrelation as a predictive factor for plaque vulnerability adds a novel dimension to glucose dynamic analysis.

      (2) Inclusion of datasets from diverse regions enhances generalizability.

      (3) The use of a well-characterized cohort with controlled cholesterol and blood pressure levels strengthens the findings.

      (4) The focus on CGM-derived indices aligns with personalized medicine trends, showcasing the potential for CAD risk stratification.

      We appreciate reviewer #2 for the positive assessment and for the valuable and constructive comments on our manuscript.

      Weaknesses:

      (1) The link between autocorrelation and plaque vulnerability remains speculative without a proposed biological explanation. 

      We appreciate the reviewer’s point about the need for a clearer biological explanation linking glucose autocorrelation to plaque vulnerability. We fully agree with the reviewer that the detailed biological mechanisms underlying this relationship are not yet fully understood, as noted in our Discussion section.

      However, we would like to emphasize the theoretical basis that supports the clinical relevance of autocorrelation. Our results show that glucose profiles with identical mean and variability can exhibit different autocorrelation patterns, highlighting that conventional measures such as mean or variance alone may not fully capture inter-individual metabolic differences. Incorporating autocorrelation analysis provides a more comprehensive characterization of metabolic states. Consequently, incorporating autocorrelation measures alongside traditional diabetes diagnostic criteria - such as fasting glucose, HbA1c and PG120, which primarily reflect only the “mean” component - can improve predictive accuracy for various clinical outcomes.

      Furthermore, our previous research has shown that glucose autocorrelation reflects changes in insulin clearance (Sugimoto, Hikaru, et al. “Improved detection of decreased glucose handling capacities via continuous glucose monitoring-derived indices.” Communications Medicine 5.1 (2025): 103.). The relationship between insulin clearance and cardiovascular disease has been well documented (Randrianarisoa, Elko, et al. “Reduced insulin clearance is linked to subclinical atherosclerosis in individuals at risk for type 2 diabetes mellitus.” Scientific reports 10.1 (2020): 22453.), and the mechanisms described in this prior work may potentially explain the association between glucose autocorrelation and clinical outcomes observed in the present study. 

      Rather than a limitation, we view these currently unexplored associations as an opportunity for further research. The identification of autocorrelation as a key glycemic feature introduces a new dimension to metabolic regulation that could serve as the basis for future investigations exploring the molecular mechanisms underlying these patterns.

      While we agree that further research at the cellular and molecular level is needed to fully validate these findings, we believe that our study provides a theoretical framework to support the clinical utility of autocorrelation analysis in glucose monitoring, and that this could serve as the basis for future investigations exploring the molecular mechanisms underlying these autocorrelation patterns, which adds to the broad interest of this study. Regarding the physical mechanisms linking autocorrelation and clinical outcomes, we have added the following sentences in the Discussion section (lines 331-339, 341-352): 

      This study also provided evidence that autocorrelation can vary independently from the mean and variance components using simulated data. In addition, simulated glucose dynamics indicated that even individuals with high AC_Var did not necessarily have high maximum and minimum blood glucose levels. This study also indicated that these three components qualitatively corresponded to the four distinct glucose patterns observed after glucose administration, which were identified in a previous study (Hulman et al., 2018). Thus, the inclusion of autocorrelation in addition to mean and variance may improve the characterization of inter-individual differences in glucose regulation and improve the predictive accuracy of various clinical outcomes.

      Despite increasing evidence linking glycemic variability to oxidative stress and endothelial dysfunction in T2DM complications (Ceriello et al., 2008; Monnier et al., 2008), the biological mechanisms underlying the independent predictive value of autocorrelation remain to be elucidated. Our previous work has shown that glucose autocorrelation is influenced by insulin clearance (Sugimoto et al., 2025), a process known to be associated with cardiovascular disease risk (Randrianarisoa et al., 2020). Therefore, the molecular pathways linking glucose autocorrelation to cardiovascular disease may share common mechanisms with those linking insulin clearance to cardiovascular disease. Although previous studies have primarily focused on investigating the molecular mechanisms associated with mean glucose levels and glycemic variability, our findings open new avenues for exploring the molecular basis of glucose autocorrelation, potentially revealing novel therapeutic targets for preventing diabetic complications.

      (2) The relatively small sample size (n=270) limits statistical power, especially when stratified by glucose tolerance levels. 

      We appreciate the reviewer’s concern regarding sample size and its potential impact on statistical power, especially when stratified by glucose tolerance levels. We fully agree that a larger sample size would increase statistical power, especially for subgroup analyses.

      We would like to clarify several points regarding the statistical power and validation of our findings. Our sample size followed established methodological frameworks, including the guidelines outlined by Muyembe Asenahabi, Bostely, and Peters Anselemo Ikoha. “Scientific research sample size determination.” (2023). These guidelines balance the risks of inadequate sample size with the challenges of unnecessarily large samples. For our primary analysis examining the correlation between CGM-derived measures and %NC, power calculations (a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4) indicated that a minimum of 47 participants was required. Our sample size of 53 exceeded this threshold and allowed us to detect statistically significant correlations, as described in the Methods section. Moreover, to provide transparency about the precision of our estimates, we have included confidence intervals for all coefficients. 

      Furthermore, our sample size aligns with previous studies investigating the associations between glucose profiles and clinical parameters, including Torimoto, Keiichi, et al. “Relationship between fluctuations in glucose levels measured by continuous glucose monitoring and vascular endothelial dysfunction in type 2 diabetes mellitus.” Cardiovascular Diabetology 12 (2013): 1-7. (n=57), Hall, Heather, et al. “Glucotypes reveal new patterns of glucose dysregulation.” PLoS biology 16.7 (2018): e2005143. (n=57), and Metwally, Ahmed A., et al. “Prediction of metabolic subphenotypes of type 2 diabetes via continuous glucose monitoring and machine learning.” Nature Biomedical Engineering (2024): 1-18. (n=32).

      Regarding the classification of glucose dynamics components, we have conducted additional validation across diverse populations including 64 Japanese, 53 American, and 100 Chinese individuals. These validation efforts have consistently supported our identification of three independent glucose dynamics components.

      However, we acknowledge the importance of further validation on a larger scale. To address this, we conducted a large follow-up study of over 8,000 individuals with two years of followup (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which confirmed our main finding that glucose dynamics consist of mean, variance, and autocorrelation. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper; however, it provides further support for the clinical relevance and generalizability of our findings.

      To address the sample size considerations, we have added the following sentences in the Discussion section (lines 409-414): 

      Although our analysis included four datasets with a total of 270 individuals, and our sample size of 53 met the required threshold based on power calculations with a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4, we acknowledge that the sample size may still be considered relatively small for a comprehensive assessment of these relationships. To further validate these findings, larger prospective studies with diverse populations are needed.

      (3) Strict participant selection criteria may reduce applicability to broader populations. 

      We appreciate the reviewer’s comment regarding the potential impact of strict participant selection criteria on the broader applicability of our findings. We acknowledge that extending validation to more diverse populations would improve the generalizability of our findings.

      Our study includes validation cohorts from diverse populations, including 64 Japanese, 53 American and 100 Chinese individuals. These cohorts include a wide range of metabolic states, from healthy individuals to those with diabetes, ensuring validation across different clinical conditions. However, we acknowledge that further validation in additional populations and clinical settings would strengthen our conclusions. To address this, we conducted a large follow-up study of over 8,000 individuals (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which confirmed our main finding that glucose dynamics consist of mean, variance, and autocorrelation. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper; however, it provides further support for the clinical relevance and generalizability of our findings.

      We have added the following text to the Discussion section to address these considerations (lines 409-414, 354-361):

      Although our analysis included four datasets with a total of 270 individuals, and our sample size of 53 met the required threshold based on power calculations with a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4, we acknowledge that the sample size may still be considered relatively small for a comprehensive assessment of these relationships. To further validate these findings, larger prospective studies with diverse populations are needed.

      Although our LASSO and factor analysis indicated that CGM-derived measures were strong predictors of %NC, this does not mean that other clinical parameters, such as lipids and blood pressure, are irrelevant in T2DM complications. Our study specifically focused on characterizing glucose dynamics, and we analyzed individuals with well-controlled serum cholesterol and blood pressure to reduce confounding effects. While we anticipate that inclusion of a more diverse population would not alter our primary findings regarding glucose dynamics, it is likely that a broader data set would reveal additional predictive contributions from lipid and blood pressure parameters.

      (4) CGM-derived indices like AC_Var and ADRR may be too complex for routine clinical use without simplified models or guidelines. 

      We appreciate the reviewer’s concern about the complexity of CGM-derived indices such as AC_Var and ADRR for routine clinical use. We acknowledge that for these indices to be of practical use, they must be both interpretable and easily accessible to healthcare providers. 

      To address this concern, we have developed an easy-to-use web application that automatically calculates these measures, including AC_Var, mean glucose levels, and glucose variability (https://cgmregressionapp2.streamlit.app/). This tool eliminates the need for manual calculations, making these indices more practical for clinical implementation.

      Regarding interpretability, we acknowledge that establishing specific clinical guidelines would enhance the practical utility of these measures. For example, defining a cut-off value for AC_Var above which the risk of diabetes complications increases significantly would provide clearer clinical guidance. However, given our current sample size limitations and our predefined objective of investigating correlations among indices, we have taken a conservative approach by focusing on the correlation between AC_Var and %NC rather than establishing definitive cutoffs. This approach intentionally avoids problematic statistical practices like phacking. It is not realistic to expect a single study to accomplish everything from proposing a new concept to conducting large-scale clinical trials to establishing clinical guidelines. Establishing clinical guidelines typically requires the accumulation of multiple studies over many years. Recognizing this reality, we have been careful in our manuscript to make modest claims about the discovery of new “correlations” rather than exaggerated claims about immediate routine clinical use.

      To address this limitation, we conducted a large follow-up study of over 8,000 individuals in the next study (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which proposed clinically relevant cutoffs and reference ranges for AC_Var and other CGM-derived indices. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper; however, by integrating automated calculation tools with clear clinical thresholds, we expect to make these measures more accessible for clinical use.

      We have added the following text to the Discussion section to address these considerations (lines 415-419):

      While CGM-derived indices such as AC_Var and ADRR hold promise for CAD risk assessment, their complexity may present challenges for routine clinical implementation. To improve usability, we have developed a web-based calculator that automates these calculations. However, defining clinically relevant thresholds and reference ranges requires further validation in larger cohorts.

      (5) The study does not compare CGM-derived indices to existing advanced CAD risk models, limiting the ability to assess their true predictive superiority. 

      We appreciate the reviewer’s comment regarding the comparison of CGMderived indices with existing CAD risk models. Given that our study population consisted of individuals with well-controlled total cholesterol and blood pressure levels, a direct comparison with the Framingham Risk Score for Hard Coronary Heart Disease (Wilson, Peter WF, et al. “Prediction of coronary heart disease using risk factor categories.” Circulation 97.18 (1998): 1837-1847.) may introduce inherent bias, as these factors are key components of the score.

      Nevertheless, to further assess the predictive value of the CGM-derived indices, we performed additional analyses using linear regression to predict %NC. Using the Framingham Risk Score, we obtained an R² of 0.04 and an Akaike Information Criterion (AIC) of 330. In contrast, our proposed model incorporating the three glycemic parameters - CGM_Mean, CGM_Std, and AC_Var - achieved a significantly improved R² of 0.36 and a lower AIC of 321, indicating superior predictive accuracy. 

      We have added the following text to the Result section (lines 115-122):

      The regression model including CGM_Mean, CGM_Std and AC_Var to predict %NC achieved an R² of 0.36 and an Akaike Information Criterion (AIC) of 321. Each of these indices showed statistically significant independent positive correlations with %NC (Fig. 1A). In contrast, the model using conventional glycemic markers (FBG, HbA1c, and PG120) yielded an R² of only 0.05 and an AIC of 340 (Fig. 1B). Similarly, the model using the Framingham Risk Score for Hard Coronary Heart Disease (Wilson et al., 1998) showed limited predictive value, with an R² of 0.04 and an AIC of 330 (Fig. 1C).

      (6) Varying CGM sampling intervals (5-minute vs. 15-minute) were not thoroughly analyzed for impact on results. 

      We appreciate the reviewer’s comment regarding the potential impact of different CGM sampling intervals on our results. To assess the robustness of our findings across different sampling frequencies, we performed a down sampling analysis by converting our 5minute interval data to 15-minute intervals. The AC_Var value calculated from 15-minute intervals was significantly correlated with that calculated from 5-minute intervals (R = 0.99, 95% CI: 0.97-1.00). Furthermore, the regression model using CGM_Mean, CGM_Std, and AC_Var from 15-minute intervals to predict %NC achieved an R² of 0.36 and an AIC of 321, identical to the model using 5-minute intervals. These results indicate that our results are robust to variations in CGM sampling frequency. 

      We have added this analysis to the Result section (lines 122-125):

      The AC_Var computed from 15-minute CGM sampling was nearly identical to that computed from 5-minute sampling (R = 0.99, 95% CI: 0.97-1.00) (Fig. S1A), and the regression using the 15‑min features yielded almost the same performance (R² = 0.36; AIC = 321; Fig. S1B).

      Reviewer #3 (Public review):

      We appreciate the reviewer for the critical review of the manuscript and the valuable comments. We have carefully considered the reviewer’s comments and have revised our manuscript accordingly. The reviewer’s comments in this letter are in Bold and Italics.

      Summary:

      This is a retrospective analysis of 53 individuals over 26 features (12 clinical phenotypes, 12 CGM features, and 2 autocorrelation features) to examine which features were most informative in predicting percent necrotic core (%NC) as a parameter for coronary plaque vulnerability. Multiple regression analysis demonstrated a better ability to predict %NC from 3 selected CGM-derived features than 3 selected clinical phenotypes. LASSO regularization and partial least squares (PLS) with VIP scores were used to identify 4 CGM features that most contribute to the precision of %NC. Using factor analysis they identify 3 components that have CGM-related features: value (relating to the value of blood glucose), variability (relating to glucose variability), and autocorrelation (composed of the two autocorrelation features). These three groupings appeared in the 3 validation cohorts and when performing hierarchical clustering. To demonstrate how these three features change, a simulation was created to allow the user to examine these features under different conditions.

      We appreciate reviewer #3 for the valuable and constructive comments on our manuscript.

      The goal of this study was to identify CGM features that relate to %NC. Through multiple feature selection methods, they arrive at 3 components: value, variability, and autocorrelation. While the feature list is highly correlated, the authors take steps to ensure feature selection is robust. There is a lack of clarity of what each component (value, variability, and autocorrelation) includes as while similar CGM indices fall within each component, there appear to be some indices that appear as relevant to value in one dataset and to variability in the validation. 

      We appreciate the reviewer’s comment regarding the classification of CGMderived measures into the three components: value, variability, and autocorrelation. As the reviewer correctly points out, some measures may load differently between the value and variability components in different datasets. However, we believe that this variability reflects the inherent mathematical properties of these measures rather than a limitation of our study.

      For example, the HBGI clusters differently across datasets due to its dependence on the number of glucose readings above a threshold. In populations where mean glucose levels are predominantly below this threshold, the HBGI is more sensitive to glucose variability (Fig. S3A). Conversely, in populations with a wider range of mean glucose levels, HBGI correlates more strongly with mean glucose levels (Fig. 3A). This context-dependent behaviour is expected given the mathematical properties of these measures and does not indicate an inconsistency in our classification approach.

      Importantly, our main findings remain robust: CGM-derived measures systematically fall into three components-value, variability, and autocorrelation. Traditional CGM-derived measures primarily reflect either value or variability, and this categorization is consistently observed across datasets. While specific indices such as HBGI may shift classification depending on population characteristics, the overall structure of CGM data remains stable.

      To address these considerations, we have added the following text to the Discussion section (lines 388-396):

      Some indices, such as HBGI, showed variation in classification across datasets, with some populations showing higher factor loadings in the “mean” component and others in the “variance” component. This variation occurs because HBGI calculations depend on the number of glucose readings above a threshold. In populations where mean glucose levels are predominantly below this threshold, the HBGI is more sensitive to glucose variability (Fig. S5A). Conversely, in populations with a wider range of mean glucose levels, the HBGI correlates more strongly with mean glucose levels (Fig. 3A). Despite these differences, our validation analyses confirm that CGM-derived indices consistently cluster into three components: mean, variance, and autocorrelation.

      We are sceptical about statements of significance without documentation of p-values. 

      We appreciate the reviewer’s concern regarding statistical significance and the documentation of p values.

      First, given the multiple comparisons in our study, we used q values rather than p values, as shown in Figure 1D. Q values provide a more rigorous statistical framework for controlling the false discovery rate in multiple testing scenarios, thereby reducing the likelihood of false positives.

      Second, our statistical reporting follows established guidelines, including those of the New England Journal of Medicine (Harrington, David, et al. “New guidelines for statistical reporting in the journal.” New England Journal of Medicine 381.3 (2019): 285-286.), which recommend that “reporting of exploratory end points should be limited to point estimates of effects with 95% confidence intervals” and that “replace p values with estimates of effects or association and 95% confidence intervals”. According to these guidelines, p values should not be reported in this type of study. We determined significance based on whether these 95% confidence intervals excluded zero - a method for determining whether an association is significantly different from zero (Tan, Sze Huey, and Say Beng Tan. "The correct interpretation of confidence intervals." Proceedings of Singapore Healthcare 19.3 (2010): 276-278.). 

      For the sake of transparency, we provide p values for readers who may be interested, although we emphasize that they should not be the basis for interpretation, as discussed in the referenced guidelines. Specifically, in Figure 1A-B, the p values for CGM_Mean, CGM_Std, and AC_Var were 0.02, 0.02, and <0.01, respectively, while those for FBG, HbA1c, and PG120 were 0.83,

      0.91, and 0.25, respectively. In Figure 3C, the p values for factors 1–5 were 0.03, 0.03, 0.03, 0.24, and 0.87, respectively, and in Figure S8C, the p values for factors 1–3 were <0.01, <0.01, and 0.20, respectively.

      We appreciate the opportunity to clarify our statistical methodology and are happy to provide additional details if needed.

      While hesitations remain, the ability of these authors to find groupings of these many CGM metrics in relation to %NC is of interest. The believability of the associations is impeded by an obtuse presentation of the results with core data (i.e. correlation plots between CGM metrics and %NC) buried in the supplement while main figures contain plots of numerical estimates from models which would be more usefully presented in supplementary tables. 

      We appreciate the reviewer’s comment regarding the presentation of our results and recognize the importance of ensuring clarity and accessibility of the core data. 

      The central finding of our study is twofold: first, that the numerous CGM-derived measures can be systematically classified into three distinct components-mean, variance, and autocorrelation-and second, that each of these components is independently associated with %NC. This insight cannot be derived simply from examining scatter plots of individual correlations, which are provided in the Supplementary Figures. Instead, it emerges from our statistical analyses in the main figures, including multiple regression models that reveal the independent contributions of these components to %NC.

      We acknowledge the reviewer’s concern regarding the accessibility of key data. To improve clarity, we have moved several scatter plots from the Supplementary Figures to the main figures (Fig. 1D-J) to allow readers to more directly visualize the relationships between CGM-derived measures and %NC. We believe this revision improved the transparency and readability of our results while maintaining the rigor of our analytical approach.

      Given the small sample size in the primary analysis, there is a lot of modeling done with parameters estimated where simpler measures would serve and be more convincing as they require less data manipulation. A major example of this is that the pairwise correlation/covariance between CGM_mean, CGM_std, and AC_var is not shown and would be much more compelling in the claim that these are independent factors.

      We appreciate the reviewer’s feedback on our statistical analysis and data presentation. The correlations between CGM_Mean, CGM_Std, and AC_Var were documented in Figure S1B. However, to improve accessibility and clarity, we have moved these correlation analyses to the main figures (Fig. 1F). 

      Regarding our modeling approach, we chose LASSO and PLS methods because they are wellestablished techniques that are particularly suited to scenarios with many input variables and a relatively small sample size. These methods have been used in the literature as robust approaches for variable selection under such conditions (Tibshirani R. 1996. Regression shrinkage and selection via the lasso. J R Stat Soc 58:267–288. Wold S, Sjöström M, Eriksson L. 2001. PLS-regression: a basic tool of chemometrics. Chemometrics Intellig Lab Syst 58:109–130. Pei X, Qi D, Liu J, Si H, Huang S, Zou S, Lu D, Li Z. 2023. Screening marker genes of type 2 diabetes mellitus in mouse lacrimal gland by LASSO regression. Sci Rep 13:6862. Wang C, Kong H, Guan Y, Yang J, Gu J, Yang S, Xu G. 2005. Plasma phospholipid metabolic profiling and biomarkers of type 2 diabetes mellitus based on high-performance liquid chromatography/electrospray mass spectrometry and multivariate statistical analysis.

      Anal Chem 77:4108–4116.). 

      Lack of methodological detail is another challenge. For example, the time period of CGM metrics or CGM placement in the primary study in relation to the IVUS-derived measurements of coronary plaques is unclear. Are they temporally distant or proximal/ concurrent with the PCI? 

      We appreciate the reviewer’s important question regarding the temporal relationship between CGM measurements and IVUS-derived plaque assessments. As described in our previous work (Otowa‐Suematsu, Natsu, et al. “Comparison of the relationship between multiple parameters of glycemic variability and coronary plaque vulnerability assessed by virtual histology–intravascular ultrasound.” Journal of Diabetes Investigation 9.3 (2018): 610615.), all individuals underwent continuous glucose monitoring for at least three consecutive days within the seven-day period prior to the PCI procedure. To improve clarity for readers, we have added the following text to the Methods section (lines 440-441):

      All individuals underwent CGM for at least three consecutive days within the seven-day period prior to the PCI procedure.

      A patient undergoing PCI for coronary intervention would be expected to have physiological and iatrogenic glycemic disturbances that do not reflect their baseline state. This is not considered or discussed. 

      We appreciate the reviewer’s concern regarding potential glycemic disturbances associated with PCI. As described in our previous work (Otowa‐Suematsu, Natsu, et al. “Comparison of the relationship between multiple parameters of glycemic variability and coronary plaque vulnerability assessed by virtual histology–intravascular ultrasound.” Journal of Diabetes Investigation 9.3 (2018): 610-615.), all CGM measurements were performed before the PCI procedure. This temporal separation ensures that the glycemic patterns analyzed in our study reflect the baseline metabolic state of the patients, rather than any physiological or iatrogenic effects of PCI. To avoid any misunderstanding, we have clarified this temporal relationship in the revised manuscript (lines 440-441):

      All individuals underwent CGM for at least three consecutive days within the seven-day period prior to the PCI procedure.

      The attempts at validation in external cohorts, Japanese, American, and Chinese are very poorly detailed. We could only find even an attempt to examine cardiovascular parameters in the Chinese data set but the outcome variables are unspecified with regard to what macrovascular events are included, their temporal relation to the CGM metrics, etc. Notably macrovascular event diagnoses are very different from the coronary plaque necrosis quantification. This could be a source of strength in the findings if carefully investigated and detailed but due to the lack of detail seems like an apples-to-oranges comparison. 

      We appreciate the reviewer’s comment regarding the validation cohorts and the need for greater clarity, particularly in the Chinese dataset. We acknowledge that our initial description lacked sufficient methodological detail, and we have expanded the Methods section to provide a more comprehensive explanation.

      For the Chinese dataset, the data collection protocol was previously documented (Zhao, Qinpei, et al. “Chinese diabetes datasets for data-driven machine learning.” Scientific Data 10.1 (2023): 35.). Briefly, trained research staff used standardized questionnaires to collect demographic and clinical information, including diabetes diagnosis, treatment history, comorbidities, and medication use. Physical examinations included anthropometric measurements, and body mass index was calculated using standard protocols. CGM was performed using the FreeStyle Libre H device (Abbott Diabetes Care, UK), which records interstitial glucose levels at 15-minute intervals for up to 14 days. Laboratory measurements, including metabolic panels, lipid profiles, and renal function tests, were obtained within six months of CGM placement. While previous studies have linked necrotic core to macrovascular events (Xie, Yong, et al. “Clinical outcome of nonculprit plaque ruptures in patients with acute coronary syndrome in the PROSPECT study.” JACC: Cardiovascular Imaging 7.4 (2014): 397-405.), we acknowledge the limitations of the cardiovascular outcomes in the Chinese data set. These outcomes were extracted from medical records rather than standardized diagnostic procedures or imaging studies. To address these concerns, we have added the following text to the Methods section (lines 496-504):

      The data collection protocol for the Chinese dataset was previously documented (Zhao et al., 2023). Briefly, trained research staff used standardized questionnaires to collect demographic and clinical information, including diabetes diagnosis, treatment history, comorbidities, and medication use. CGM records interstitial glucose levels at 15-minute intervals for up to 14 days. Laboratory measurements, including metabolic panels, lipid profiles, and renal function tests, were obtained within six months of CGM placement. While previous studies have linked necrotic core to macrovascular events, we acknowledge the limitations of the cardiovascular outcomes in the Chinese data set. These outcomes were extracted from medical records rather than from standardized diagnostic procedures or imaging studies.

      Finally, the simulations at the end are not relevant to the main claims of the paper and we would recommend removing them for the coherence of this manuscript. 

      We appreciate the reviewer’s feedback regarding the relevance of the simulation component of our manuscript. The primary contribution of our study goes beyond demonstrating correlations between CGM-derived measures and %NC; it highlights three fundamental components of glycemic patterns-mean, variability, and autocorrelation-and their independent relationships with coronary plaque characteristics. The simulations are included to illustrate how glycemic patterns with identical means and variability can have different autocorrelation structures. Because temporal autocorrelation can be conceptually difficult to interpret, these visualizations were intended to provide intuitive examples for the readers. 

      However, we agree with the reviewer’s concern about the coherence of the manuscript. In response, we have streamlined the simulation section by removing simulations that do not directly support our primary conclusions (old version of the manuscript, lines 239-246, 502526), while retaining only those that enhance understanding of the three glycemic components. Regarding reviewer 2’s minor comment #4, we acknowledge that autocorrelation can be challenging to understand intuitively. To address this, we kept Fig. 4A with a brief description.

      Recommendations for the authors:

      Reviewer 2# (Recommendations for the authors):

      Summary:

      The study by Sugimoto et. al. investigates the association between components of glucose dynamics-value, variability, and autocorrelation-and coronary plaque vulnerability (%NC) in patients with varying glucose tolerance levels. The research identifies three key factors that independently predict %NC and highlights the potential of continuous glucose monitoring (CGM)-derived indices in risk assessment for coronary artery disease (CAD). Using robust statistical methods and validation across diverse populations, the study emphasizes the limitations of conventional diagnostic markers and suggests a novel, CGMbased approach for improved predictive performance While the study demonstrates significant novelty and potential impact, several issues must be addressed by the authors.

      Major Comments:

      (1) The study demonstrates originality by introducing autocorrelation as a novel predictive factor in glucose dynamics, a perspective rarely explored in prior research. While the innovation is commendable, the biological mechanisms linking autocorrelation to plaque vulnerability remain speculative. Providing a hypothesis or potential pathways would enhance the scientific impact and practical relevance of this finding.

      We appreciate the reviewer’s point about the need for a clearer biological explanation linking glucose autocorrelation to plaque vulnerability. Our previous research has shown that glucose autocorrelation reflects changes in insulin clearance (Sugimoto, Hikaru, et al. “Improved detection of decreased glucose handling capacities via continuous glucose monitoring-derived indices.” Communications Medicine 5.1 (2025): 103.). The relationship between insulin clearance and cardiovascular disease has been well documented (Randrianarisoa, Elko, et al. “Reduced insulin clearance is linked to subclinical atherosclerosis in individuals at risk for type 2 diabetes mellitus.” Scientific reports 10.1 (2020): 22453.), and the mechanisms described in this prior work may potentially explain the association between glucose autocorrelation and clinical outcomes observed in the present study. We have added the following sentences to the Discussion section (lines 341-352):

      Despite increasing evidence linking glycemic variability to oxidative stress and endothelial dysfunction in T2DM complications (Ceriello et al., 2008; Monnier et al., 2008), the biological mechanisms underlying the independent predictive value of autocorrelation remain to be elucidated. Our previous work has shown that glucose autocorrelation is influenced by insulin clearance (Sugimoto et al., 2025), a process known to be associated with cardiovascular disease risk (Randrianarisoa et al., 2020). Therefore, the molecular pathways linking glucose autocorrelation to cardiovascular disease may share common mechanisms with those linking insulin clearance to cardiovascular disease. Although previous studies have primarily focused on investigating the molecular mechanisms associated with mean glucose levels and glycemic variability, our findings open new avenues for exploring the molecular basis of glucose autocorrelation, potentially revealing novel therapeutic targets for preventing diabetic complications.

      (2) The inclusion of datasets from Japan, America, and China adds a valuable cross-cultural dimension to the study, showcasing its potential applicability across diverse populations. Despite the multi-regional validation, the sample size (n=270) is relatively small, especially when stratified by glucose tolerance categories. This limits the statistical power and applicability to diverse populations. A larger, multi-center cohort would strengthen conclusions.

      We appreciate the reviewer’s concern regarding sample size and its potential impact on statistical power, especially when stratified by glucose tolerance levels. We fully agree that a larger sample size would increase statistical power, especially for subgroup analyses.

      We would like to clarify several points regarding the statistical power and validation of our findings. Our study adheres to established methodological frameworks for sample size determination, including the guidelines outlined by Muyembe Asenahabi, Bostely, and Peters Anselemo Ikoha. “Scientific research sample size determination.” (2023). These guidelines balance the risks of inadequate sample size with the challenges of unnecessarily large samples. For our primary analysis examining the correlation between CGM-derived measures and %NC, power calculations with a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4 indicated that a minimum of 47 participants was required. Our sample size of 53 exceeded this threshold and allowed us to detect statistically significant correlations, as described in the Methods section.

      Furthermore, our sample size aligns with previous studies investigating the associations between glucose profiles and clinical parameters, including Torimoto, Keiichi, et al. “Relationship between fluctuations in glucose levels measured by continuous glucose monitoring and vascular endothelial dysfunction in type 2 diabetes mellitus.” Cardiovascular Diabetology 12 (2013): 1-7. (n=57), Hall, Heather, et al. “Glucotypes reveal new patterns of glucose dysregulation.” PLoS biology 16.7 (2018): e2005143. (n=57), and Metwally, Ahmed A., et al. “Prediction of metabolic subphenotypes of type 2 diabetes via continuous glucose monitoring and machine learning.” Nature Biomedical Engineering (2024): 1-18. (n=32). Moreover, to provide transparency about the precision of our estimates, we have included confidence intervals for all coefficients.

      Regarding the classification of glucose dynamics components, we have conducted additional validation across diverse populations including 64 Japanese, 53 American, and 100 Chinese individuals. These validation efforts have consistently supported our identification of three independent glucose dynamics components. Furthermore, the primary objective of our study was not to assess rare events, but rather to demonstrate that glucose dynamics can be decomposed into three main factors - mean, variance and autocorrelation - whereas traditional measures have primarily captured mean and variance without adequately reflecting autocorrelation. We believe that our current sample size effectively addresses this objective. 

      However, we acknowledge the importance of further validation on a larger scale. To address this, we conducted a large follow-up study of over 8,000 individuals with two years of followup (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which confirmed our main finding that glucose dynamics consist of mean, variance, and autocorrelation. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper; however, it provides further support for the clinical relevance and generalizability of our findings.

      To address the sample size considerations, we have added the following sentences to the Discussion section (lines 409-414):

      Although our analysis included four datasets with a total of 270 individuals, and our sample size of 53 met the required threshold based on power calculations with a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4, we acknowledge that the sample size may still be considered relatively small for a comprehensive assessment of these relationships. To further validate these findings, larger prospective studies with diverse populations are needed.

      (3) The study focuses on a well-characterized cohort with controlled cholesterol and blood pressure levels, reducing confounding variables. However, this stringent selection might exclude individuals with significant variability in these parameters, potentially limiting the study's applicability to broader, real-world populations. The authors should discuss how this may affect generalizability and potential bias in the results.

      We appreciate the reviewer’s comment regarding the potential impact of strict participant selection criteria on the broader applicability of our findings. We acknowledge that extending validation to more diverse populations would improve the generalizability of our findings.

      Our validation strategy included multiple cohorts from different regions, specifically 64 Japanese, 53 American and 100 Chinese individuals. These cohorts represent a clinically diverse population, including both healthy individuals and those with diabetes, allowing for validation across a broad spectrum of metabolic conditions. However, we recognize that further validation in additional populations and clinical settings would strengthen our conclusions. To address this, we conducted a large follow-up study of over 8,000 individuals with two years of follow-up (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which confirmed our main finding that glucose dynamics consist of mean, variance, and autocorrelation. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper; however, it provides further support for the clinical relevance and generalizability of our findings.

      We have added the following text to the Discussion section to address these considerations (lines 409-414, 354-361):

      Although our analysis included four datasets with a total of 270 individuals, and our sample size of 53 met the required threshold based on power calculations with a type I error of 0.05, a power of 0.8, and an expected correlation coefficient of 0.4, we acknowledge that the sample size may still be considered relatively small for a comprehensive assessment of these relationships. To further validate these findings, larger prospective studies with diverse populations are needed.

      Although our LASSO and factor analysis indicated that CGM-derived measures were strong predictors of %NC, this does not mean that other clinical parameters, such as lipids and blood pressure, are irrelevant in T2DM complications. Our study specifically focused on characterizing glucose dynamics, and we analyzed individuals with well-controlled serum cholesterol and blood pressure to reduce confounding effects. While we anticipate that inclusion of a more diverse population would not alter our primary findings regarding glucose dynamics, it is likely that a broader data set would reveal additional predictive contributions from lipid and blood pressure parameters.

      (4) The study effectively highlights the potential of CGM-derived indices as a tool for CAD risk assessment, a concept that aligns with contemporary advancements in personalized medicine. Despite its potential, the complexity of CGM-derived indices like AC_Var and ADRR may hinder their routine clinical adoption. Providing simplified models or actionable guidelines would facilitate their integration into everyday practice.

      We appreciate the reviewer’s concern about the complexity of CGM-derived indices such as AC_Var and ADRR for routine clinical use. We recognize that for these indices to be of practical use, they must be both interpretable and easily accessible to healthcare providers.

      To address this, we have developed an easy-to-use web application that automatically calculates these measures, including AC_Var, mean glucose levels, and glucose variability. By eliminating the need for manual calculations, this tool streamlines the process and makes these indices more practical for clinical use.

      Regarding interpretability, we acknowledge that establishing specific clinical guidelines would enhance the practical utility of these measures. For example, defining a cut-off value for AC_Var above which the risk of diabetes complications increases significantly would provide clearer clinical guidance. However, given our current sample size limitations and our predefined objective of investigating correlations among indices, we have taken a conservative approach by focusing on the correlation between AC_Var and %NC rather than establishing definitive cutoffs. This approach intentionally avoids problematic statistical practices like phacking. It is not realistic to expect a single study to accomplish everything from proposing a new concept to conducting large-scale clinical trials to establishing clinical guidelines. Establishing clinical guidelines typically requires the accumulation of multiple studies over many years. Recognizing this reality, we have been careful in our manuscript to make modest claims about the discovery of new “correlations” rather than exaggerated claims about immediate routine clinical use.

      To address this limitation, we conducted a large follow-up study of over 8,000 individuals in the next study (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which proposed clinically relevant cutoffs and reference ranges for AC_Var and other CGM-derived indices. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper; however, by integrating automated calculation tools with clear clinical thresholds, we expect to make these measures more accessible for clinical use.

      We have added the following text to the Discussion section to address these considerations (lines 415-419):

      While CGM-derived indices such as AC_Var and ADRR hold promise for CAD risk assessment, their complexity may present challenges for routine clinical implementation. To improve usability, we have developed a web-based calculator that automates these calculations. However, defining clinically relevant thresholds and reference ranges requires further validation in larger cohorts.

      (5) The exclusion of TIR from the main analysis is noted, but its relevance in diabetes management warrants further exploration. Integrating TIR as an outcome measure could provide additional clinical insights.

      We appreciate the reviewer’s comment regarding the potential role of time in range (TIR) as an outcome measure in our study. Because TIR is primarily influenced by the mean and variance of glucose levels, it does not fully capture the distinct role of glucose autocorrelation, which was the focus of our investigation.

      To clarify this point, we have expanded the Discussion section as follows (lines 380-388):

      Although time in range (TIR) was not included in the main analyses due to the relatively small number of T2DM patients and the predominance of participants with TIR >70%, our results demonstrate that CGM-derived indices outperformed conventional markers such as FBG, HbA1c, and PG120 in predicting %NC. Furthermore, multiple regression analysis between factor scores and TIR revealed that only factor 1 (mean) and factor 2 (variance) were significantly associated with TIR (Fig. S8C, D). This finding confirms the presence of three distinct components in glucose dynamics and highlights the added value of examining AC_Var as an independent glycemic feature beyond conventional CGM-derived measures.

      (6) While the study reflects a commitment to understanding CAD risks in a global context by including datasets from Japan, America, and China, the authors should provide demographic details (e.g., age, gender, socioeconomic status) and discuss how these factors might influence glucose dynamics and coronary plaque vulnerability.

      We appreciate the reviewer’s comment regarding the potential influence of demographic factors on glucose dynamics and coronary plaque vulnerability. We examined these relationships and found that age and sex had minimal effects on glucose dynamics characteristics, as shown in Figure S8A and S8B. These findings suggest that our primary conclusions regarding glucose dynamics and coronary risk remain robust across demographic groups within our data set.

      To address the reviewer’s suggestion, we have added the following discussion (lines 361-368):

      In our analysis of demographic factors, we found that age and gender had minimal influence on glucose dynamics characteristics (Fig. S8A, B), suggesting that our findings regarding the relationship between glucose dynamics and coronary risk are robust across different demographic groups within our dataset. Future studies involving larger and more diverse populations would be valuable to comprehensively elucidate the potential influence of age, gender, and other demographic factors on glucose dynamics characteristics and their relationship to cardiovascular risk.

      (7) While the article shows CGM-derived indices outperform traditional markers (e.g., HbA1c, FBG, PG120), it does not compare these indices against existing advanced risk models (e.g., Framingham Risk Score for CAD). A direct comparison would strengthen the claim of superiority.

      We appreciate the reviewer’s comment regarding the comparison of CGMderived indices with existing CAD risk models. Given that our study population consisted of individuals with well-controlled total cholesterol and blood pressure levels, a direct comparison with the Framingham Risk Score for Hard Coronary Heart Disease (Wilson, Peter WF, et al. “Prediction of coronary heart disease using risk factor categories.” Circulation 97.18 (1998): 1837-1847.) may introduce inherent bias, as these factors are key components of the score.

      Nevertheless, to further assess the predictive value of the CGM-derived indices, we performed additional analyses using linear regression to predict %NC. Using the Framingham Risk Score, we obtained an R² of 0.04 and an Akaike Information Criterion (AIC) of 330. In contrast, our proposed model incorporating the three glycemic parameters - CGM_Mean, CGM_Std, and AC_Var - achieved a significantly improved R² of 0.36 and a lower AIC of 321, indicating superior predictive accuracy. We have updated the Result section as follows (lines 115-122):

      The regression model including CGM_Mean, CGM_Std and AC_Var to predict %NC achieved an R<sup>2</sup> of 0.36 and an Akaike Information Criterion (AIC) of 321. Each of these indices showed statistically significant independent positive correlations with %NC (Fig. 1A). In contrast, the model using conventional glycemic markers (FBG, HbA1c, and PG120) yielded an R² of only 0.05 and an AIC of 340 (Fig. 1B). Similarly, the model using the Framingham Risk Score for Hard Coronary Heart Disease (Wilson et al., 1998) showed limited predictive value, with an R² of 0.04 and an AIC of 330 (Fig. 1C).

      (8) The study mentions varying CGM sampling intervals across datasets (5-minute vs. 15minute). Authors should employ sensitivity analysis to assess the impact of these differences on the results. This would help clarify whether higher-resolution data significantly improves predictive performance.

      We appreciate the reviewer’s comment regarding the potential impact of different CGM sampling intervals on our results. To assess the robustness of our findings across different sampling frequencies, we performed a down sampling analysis by converting our 5minute interval data to 15-minute intervals. The AC_Var value calculated from 15-minute intervals was significantly correlated with that calculated from 5-minute intervals (R = 0.99, 95% CI: 0.97-1.00). Consequently, the main findings remained consistent across both sampling frequencies, indicating that our results are robust to variations in temporal resolution. We have added this analysis to the Result section (lines 122-126):

      The AC_Var computed from 15-minute CGM sampling was nearly identical to that computed from 5-minute sampling (R = 0.99, 95% CI: 0.97-1.00) (Fig. S1A), and the regression using the 15‑min features yielded almost the same performance (R<sup>2</sup>  = 0.36; AIC = 321; Fig. S1B).

      (9) The identification of actionable components in glucose dynamics lays the groundwork for clinical stratification. The authors could explore the use of CGM-derived indices to develop a simple framework for stratifying risk into certain categories (e.g., low, moderate, high). This could improve clinical relevance and utility for healthcare providers.

      We appreciate the reviewer’s suggestion regarding the potential for CGMderived indices to support clinical stratification. We completely agree with the idea that establishing risk categories (e.g., low, moderate, high) based on specific thresholds would enhance the clinical utility of these measures. However, given our current sample size limitations and our predefined objective of investigating correlations among indices, we have taken a conservative approach by focusing on the correlation between AC_Var and %NC rather than establishing definitive cutoffs. This approach intentionally avoids problematic statistical practices like p-hacking. It is not realistic to expect a single study to accomplish everything from proposing a new concept to conducting large-scale clinical trials to establishing clinical thresholds. Establishing clinical thresholds typically requires the accumulation of multiple studies over many years. Recognizing this reality, we have been careful in our manuscript to make modest claims about the discovery of new “correlations” rather than exaggerated claims about immediate routine clinical use.

      To address this limitation, we conducted a large follow-up study of over 8,000 individuals in the next study (Sugimoto, Hikaru, et al. “Stratification of individuals without prior diagnosis of diabetes using continuous glucose monitoring” medRxiv (2025)), which proposed clinically relevant cutoffs and reference ranges for AC_Var and other CGM-derived indices. As this large study was beyond the scope of the present manuscript due to differences in primary objectives and analytical approaches, it was not included in this paper. However, we expect to make these measures more actionable in clinical use by integrating automated calculation tools with clear clinical thresholds.

      We have added the following text to the Discussion section to address these considerations (lines 415-419):

      While CGM-derived indices such as AC_Var and ADRR hold promise for CAD risk assessment, their complexity may present challenges for routine clinical implementation. To improve usability, we have developed a web-based calculator that automates these calculations. However, defining clinically relevant thresholds and reference ranges requires further validation in larger cohorts.

      (10) While the study acknowledges several limitations, authors should also consider explicitly addressing the potential impact of inter-individual variability in glucose metabolism (e.g., age-related changes, hormonal influences) on the findings.

      We appreciate the reviewer’s comment regarding the potential impact of interindividual variability in glucose metabolism, including age-related changes and hormonal influences, on our results. In our analysis, we found that age had minimal effects on glucose dynamics characteristics, as shown in Figure S8A. In addition, CGM-derived measures such as ADRR and AC_Var significantly contributed to the prediction of %NC independent of insulin secretion (I.I.) and insulin sensitivity (Composite index) (Fig. 2). These results suggest that our primary conclusions regarding glucose dynamics and coronary risk remain robust despite individual differences in glucose metabolism.

      To address the reviewer’s suggestion, we have added the following discussion (lines 186-188, 361-368):

      Conventional indices, including FBG, HbA1c, PG120, I.I., Composite index, and Oral DI, did not contribute significantly to the prediction compared to these CGM-derived indices.

      In our analysis of demographic factors, we found that age and gender had minimal influence on glucose dynamics characteristics (Fig. S8A, B), suggesting that our findings regarding the relationship between glucose dynamics and coronary risk are robust across different demographic groups within our dataset. Future studies involving larger and more diverse populations would be valuable to comprehensively elucidate the potential influence of age, gender, and other demographic factors on glucose dynamics characteristics and their relationship to cardiovascular risk.

      (11) It's unclear whether the identified components (value, variability, and autocorrelation) could serve as proxies for underlying physiological mechanisms, such as beta-cell dysfunction or insulin resistance. Please clarify.

      We appreciate the reviewer’s comment regarding the physiological underpinnings of the glucose components we identified. The mean, variance, and autocorrelation components we identified likely reflect specific underlying physiological mechanisms related to glucose regulation. In our previous research (Sugimoto, Hikaru, et al. “Improved detection of decreased glucose handling capacities via continuous glucose monitoring-derived indices.” Communications Medicine 5.1 (2025): 103.), we explored the relationship between glucose dynamics characteristics and glucose control capabilities using clamp tests and mathematical modelling. These investigations revealed that autocorrelation specifically shows a significant correlation with the disposition index (the product of insulin sensitivity and insulin secretion) and insulin clearance parameters.

      Furthermore, our current study demonstrates that CGM-derived measures such as ADRR and AC_Var significantly contributed to the prediction of %NC independent of established metabolic parameters including insulin secretion (I.I.) and insulin sensitivity (Composite index), as shown in Figure 2. These results suggest that the components we identified capture distinct physiological aspects of glucose metabolism beyond traditional measures of beta-cell function and insulin sensitivity. Further research is needed to fully characterize these relationships, but our results imply that these characteristics of glucose dynamics offer supplementary insight into the underlying beta-cell dysregulation that contributes to coronary plaque vulnerability.

      To address the reviewer’s suggestion, we have added the following discussion to the Result section (lines 186-188):

      Conventional indices, including FBG, HbA1c, PG120, I.I., Composite index, and Oral DI, did not contribute significantly to the prediction compared to these CGM-derived indices.

      Minor Comments:

      (1) The use of LASSO and PLS regression is appropriate, but the rationale for choosing these methods over others (e.g., Ridge regression) should be explained in greater detail.

      We appreciate the reviewer’s comment and have added the following discussion to the Methods section (lines 578-585):

      LASSO regression was chosen for its ability to perform feature selection by identifying the most relevant predictors. Unlike Ridge regression, which simply shrinks coefficients toward zero without reaching exactly zero, LASSO produces sparse models, which is consistent with our goal of identifying the most critical features of glucose dynamics associated with coronary plaque vulnerability. In addition, we implemented PLS regression as a complementary approach due to its effectiveness in dealing with multicollinearity, which was particularly relevant given the high correlation among several CGM-derived measures.

      (2) While figures are well-designed, adding annotations to highlight key findings (e.g., significant contributors in factor analysis) would improve clarity.

      We appreciate the reviewer’s suggestion to improve the clarity of our figures. In the factor analysis, we decided not to include annotations because indicators such as ADRR and J-index can be associated with multiple factors, which could lead to misleading or confusing interpretations. However, in response to the suggestion, we have added annotations to the PLS analysis, specifically highlighting items with VIP values greater than 1 (Fig. 2D, S2D) to emphasize key contributors.

      (3) The term "value" as a component of glucose dynamics could be clarified. For instance, does it strictly refer to mean glucose levels, or does it encompass other measures?

      We appreciate the reviewer’s question regarding the term “value” in the context of glucose dynamics. Factor 1 was predominantly influenced by CGM_Mean, with a factor loading of 0.99, indicating that it primarily represents mean glucose levels. Given this strong correlation, we have renamed Factor 1 to “Mean” (Fig. 3A) to more accurately reflect its role in glucose dynamics.

      (4) The concept of autocorrelation may be unfamiliar to some readers. A brief, intuitive explanation with a concrete example of how it manifests in glucose dynamics would enhance understanding.

      We appreciate the reviewer’s suggestion. Autocorrelation refers to the relationship between a variable and its past values over time. In the context of glucose dynamics, it reflects how current glucose levels are influenced by past levels, capturing patterns such as sustained hyperglycemia or recurrent fluctuations. For example, if an individual experiences sustained high glucose levels after a meal, the strong correlation between successive glucose readings indicates high autocorrelation. We have included this explanation in the revised manuscript (lines 519-524) to improve clarity for readers unfamiliar with the concept. Additionally, Figure 4A shows an example of glucose dynamics with different autocorrelation.

      (5) Ensure consistent use of terms like "glucose dynamics," "CGM-derived indices," and "plaque vulnerability." For instance, sometimes indices are referred to as "components," which might confuse readers unfamiliar with the field.

      We appreciate the reviewer’s comment about ensuring consistency in terminology. To avoid confusion, we have reviewed and standardized the use of terms such as “CGM-derived indices,” and “plaque vulnerability” throughout the manuscript. Additionally, while many of our measures are strictly CGM-derived indices, several “components” in our analysis include fasting blood glucose (FBG) and glucose waveforms during the OGTT. For these measures, we retained the descriptors “glucose dynamics” and “components” rather than relabelling them as CGM-derived indices.

      (6) Provide a more detailed overview of the supplementary materials in the main text, highlighting their relevance to the key findings.

      We appreciate the reviewer’s suggestion. We revised the manuscript by integrating the supplementary text into the main text (lines 129-160), which provides a clearer overview of the supplementary materials. Consequently, the Supplementary Information section now only contains supplementary figures, while their relevance and key details are described in the main text. 

      Reviewer #3 (Recommendations for the authors):

      Other Concerns:

      (1) The text states the significance of tests, however, no p-values are listed: Lines 118-119: Significance is cited between CGM indices and %NC, however, neither the text nor supplementary text have p-values. Need p-values for Figure 3C, Figure S10. When running the https://cgm-basedregression.streamlit.app/ multiple regression analysis, a p-value should be given as well. Do the VIP scores (Line 142) change with the inclusion of SBP, DBP, TG, LDL, and HDL? Do the other datasets have the same well-controlled serum cholesterol and BP levels?

      We appreciate the reviewer’s concern regarding statistical significance and the documentation of p values.

      First, given the multiple comparisons in our study, we used q values rather than p values, as shown in Figure 1D. Q values provide a more rigorous statistical framework for controlling the false discovery rate in multiple testing scenarios, thereby reducing the likelihood of false positives.

      Second, our statistical reporting follows established guidelines, including those of the New England Journal of Medicine (Harrington, David, et al. “New guidelines for statistical reporting in the journal.” New England Journal of Medicine 381.3 (2019): 285-286.), which recommend that “reporting of exploratory end points should be limited to point estimates of effects with 95% confidence intervals” and that “replace p values with estimates of effects or association and 95% confidence intervals”. According to these guidelines, p values should not be reported in this type of study. We determined significance based on whether these 95% confidence intervals excluded zero - a statistical method for determining whether an association is significantly different from zero (Tan, Sze Huey, and Say Beng Tan. “The correct interpretation of confidence intervals.” Proceedings of Singapore Healthcare 19.3 (2010): 276-278.).

      For the sake of transparency, we provide p values for readers who may be interested, although we emphasize that they should not be the basis for interpretation, as discussed in the referenced guidelines. Specifically, in Figure 1A-B, the p values for CGM_Mean, CGM_Std, and AC_Var were 0.02, 0.02, and <0.01, respectively, while those for FBG, HbA1c, and PG120 were 0.83, 0.91, and 0.25, respectively. In Figure 3C, the p values for factors 1–5 were 0.03, 0.03, 0.03, 0.24, and 0.87, respectively, and in Figure S8C, the p values for factors 1–3 were <0.01, <0.01, and 0.20, respectively. We appreciate the opportunity to clarify our statistical methodology and are happy to provide additional details if needed.

      We confirmed that the results of the variable importance in projection (VIP) analysis remained stable after including additional covariates, such as systolic blood pressure (SBP), diastolic blood pressure (DBP), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C). The VIP values for ADRR, MAGE, AC_Var, and LI consistently exceeded one even after these adjustments, suggesting that the primary findings are robust in the presence of these clinical variables. We have added the following sentences in the Results and Methods section (lines 188-191, 491-494):

      Even when SBP, DBP, TG, LDL-C, and HDL-C were included as additional input variables, the results remained consistent, and the VIP scores for ADRR, AC_Var, MAGE, and LI remained greater than 1 (Fig. S2D).

      Of note, as the original reports document, the validation datasets did not specify explicit cutoffs for blood pressure or cholesterol. Consequently, they included participants with suboptimal control of these parameters.

      (2) Negative factor loadings have not been addressed and consistency in components: Figure 3, Figure S7. All the main features for value in Figure 3A are positive. However, MVALUE in S7B is very negative for value whereas the other features highlighted for value are positive. What is driving this difference? Please explain if the direction is important. Line 480 states that variables with factor loadings >= 0.30 were used for interpretation, but it appears in the text (Line 156, Figure 3) that oral DI was used for value, even though it had a -0.61 loading. Figure 3, Figure S7. HBGI falls within two separate components (value and variability). There is not a consistent component grouping. Removal of MAG (Line 185) and only MAG does not seem scientific. Did the removal of other features also result in similar or different Cronbach's ⍺? It is unclear what Figure S8B is plotting. What does each point mean?

      We appreciate the reviewer’s comment regarding the classification of CGMderived measures into the three components: value, variability, and autocorrelation. As the reviewer correctly points out, some measures may load differently between the value and variability components in different datasets. However, we believe that this variability reflects the inherent mathematical properties of these measures rather than a limitation of our study.

      For example, the HBGI clusters differently across datasets due to its dependence on the number of glucose readings above a threshold. In populations where mean glucose levels are predominantly below this threshold, the HBGI is more sensitive to glucose variability (Fig. S3A). Conversely, in populations with a wider range of mean glucose levels, HBGI correlates more strongly with mean glucose levels (Fig. 3A). This context-dependent behaviour is expected given the mathematical properties of these measures and does not indicate an inconsistency in our classification approach.

      Importantly, our main findings remain robust: CGM-derived measures systematically fall into three components-value, variability, and autocorrelation. Traditional CGM-derived measures primarily reflect either value or variability, and this categorization is consistently observed across datasets. While specific indices such as HBGI may shift classification depending on population characteristics, the overall structure of CGM data remains stable.

      With respect to negative factor loadings, we agree that they may appear confusing at first. However, in the context of exploratory factor analysis, the magnitude, or absolute value, of the loading is most critical for interpretation, rather than its sign. Following established practice, we considered variables with absolute loadings of at least 0.30 to be meaningful contributors to a given component. Accordingly, although the oral DI had a negative loading of –0.61, its absolute magnitude exceeded the threshold of 0.30, so it was considered in our interpretation of the “value” component. Regarding the reviewer’s observation that MVALUE in Figure S7B shows a strongly negative loading while other indices in the same component show positive loadings, we believe this reflects the relative orientation of the factor solution rather than a substantive difference in interpretation. In factor analysis, the direction of factor loadings is arbitrary: multiplying all the loadings for a given factor by –1 would not change the factor’s statistical identity. Therefore, the important factor is not whether a variable loads positively or negatively but rather the strength of its association with the latent component (i.e., the absolute value of the loading).

      The rationale for removing MAG was based on statistical and methodological considerations. As is common practice in reliability analyses, we examined whether Cronbach’s α would improve if we excluded items with low factor loadings or weak item–total correlations. In the present study, we recalculated Cronbach’s α after removing the MAG item because it had a low loading. Its exclusion did not substantially affect the theoretical interpretation of the factor, which we conceptualize as “secretion” (without CGM). MAG’s removal alone is scientifically justified because it was the only item whose exclusion improved Cronbach's α while preserving interpretability. In contrast, removing other items would have undermined the conceptual clarity of the factor or would not have meaningfully improved α. Furthermore, the MAG item has a high factor 2 loading.

      Each point in Figure S8B (old version) corresponds to an individual participant.

      To address these considerations, we have added the following text to the Discussion, Methods, (lines 388-396, 600-601) and Figure S6B (current version) legend:

      Some indices, such as HBGI, showed variation in classification across datasets, with some populations showing higher factor loadings in the “mean” component and others in the “variance” component. This variation occurs because HBGI calculations depend on the number of glucose readings above a threshold. In populations where mean glucose levels are predominantly below this threshold, the HBGI is more sensitive to glucose variability (Fig. S5A). Conversely, in populations with a wider range of mean glucose levels, the HBGI correlates more strongly with mean glucose levels (Fig. 3A). Despite these differences, our validation analyses confirm that CGM-derived indices consistently cluster into three components: mean, variance, and autocorrelation.

      Variables with absolute factor loadings of ≥ 0.30 were used in interpretation.

      Box plots comparing factors 1 (Mean), 2 (Variance), and 3 (Autocorrelation) between individuals without (-) and with (+) diabetic macrovascular complications. Each point corresponds to an individual. The boxes represent the interquartile range, with the median shown as a horizontal line. Mann–Whitney U tests were used to assess differences between groups, with P values < 0.05 considered statistically significant.

      Minor Concerns:

      (1) NGT is not defined.

      We appreciate the reviewer for pointing out that the term “NGT” was not clearly defined in the original manuscript. We have added the following text to the Methods section (lines 447-451):

      T2DM was defined as HbA1c ≥ 6.5%, fasting plasma glucose (FPG) ≥ 126 mg/dL or 2‑h plasma glucose during a 75‑g OGTT (PG120) ≥ 200 mg/dL. IGT was defined as HbA1c 6.0– 6.4%, FPG 110–125 mg/dL or PG120 140–199 mg/dL. NGT was defined as values below all prediabetes thresholds (HbA1c < 6.0%, FPG < 110 mg/dL and PG120 < 140 mg/dL).

      (2) Is it necessary to list the cumulative percentage (Line 173), it could be clearer to list the percentage explained by each factor instead.

      We appreciate the reviewer’s suggestion to list the percentage explained by each factor rather than the cumulative percentage for improved clarity. According to the reviewer’s suggestion, we have revised the results to show the individual contribution of each factor (39%, 21%, 10%, 5%, 5%) rather than the cumulative percentages (39%, 60%, 70%, 75%, 80%) that were previously listed (lines 220-221).

      (3) Figure S10. How were the coefficients generated for Figure S10? No methods are given.

      We conducted a multiple linear regression analysis in which time in range (TIR) was the dependent variable and the factor scores corresponding to the first three latent components (factor 1 representing the mean, factor 2 representing the variance, and factor 3 representing the autocorrelation) were the independent variables. We have added the following text to the figure legend (Fig. S8C) to provide a more detailed description of how the coefficients were generated:

      Comparison of predicted Time in range (TIR) versus measured TIR using multiple regression analysis between TIR and factor scores in Figure 3. In this analysis, TIR was the dependent variable, and the factor scores corresponding to the first three latent components (factor 1 representing the mean, factor 2 representing the variance, and factor 3 representing the autocorrelation) were the independent variables. Each point corresponds to the values for a single individual.

      (4) In https://cgm-basedregression.streamlit.app/, more explanation should be given about the output of the multiple regression. Regression is spelled incorrectly on the app.

      We appreciate the reviewer for pointing out the need for a clearer explanation of the multiple regression analysis presented in the online tool

      (https://cgmregressionapp2.streamlit.app/). We have added the description about the regression and corrected the typographical error in the spelling of “regression” within the app. 

      (5) The last section of results (starting at line 225) appears to be unrelated to the goal of predicting %NC.

      We appreciate the reviewer’s feedback regarding the relevance of the simulation component of our manuscript. The primary contribution of our study goes beyond demonstrating correlations between CGM-derived measures and %NC; it highlights three fundamental components of glycemic patterns-mean, variance, and autocorrelation-and their independent relationships with coronary plaque characteristics. The simulations are included to illustrate how glycemic patterns with identical means and variability can have different autocorrelation structures. As reviewer 2 pointed out in minor comment #4, temporal autocorrelation can be difficult to interpret, so these visualizations were intended to provide intuitive examples for readers.

      However, we agree with the reviewer’s concern about the coherence of the manuscript. In response, we have streamlined the simulation section by removing technical simulations that do not directly support our primary conclusions (old version of the manuscript, lines 239-246, 502-526), while retaining only those that enhance understanding of the three glycemic components (Fig. 4A).

      (6) Figure S2. The R2 should be reported.

      We appreciate the reviewer for suggesting that we report R² in Figure S2. In the revised version, we have added the correlation coefficients and their 95% confidence intervals to Figure 1E.

      (7) Multiple panels have a correlation line drawn with a slope of 1 which does not reflect the data or r^2 listed. this should be fixed.

      We appreciate the reviewer’s concern that several panels included regression lines with a fixed slope of one that did not reflect the associated R² values. We have corrected Figures 1A–C and 3C to display regression lines representing the estimated slopes derived from the regression analyses.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public Review):

      Areas of improvement and suggestions:

      (1) "These results suggest the SP targets interneurons in the brain that feed into higher processing centers from different entry points likely representing different sensory input" and "All together, these data suggest that the abdominal ganglion harbors several distinct type of neurons involved in directing PMRs"

      The characterization of the post-mating circuitry has been largely described by the group of Barry Dickson and other labs. I suggest ruling out a potential effect of mSP in any of the well-known post-mating neuronal circuitry, i.e: SPSN, SAG, pC1, vpoDN or OviDNs neurons. A combination of available split-Gal4 should be sufficient to prove this.

      We agree that this information is important to distinguish neurons which are direct SP targets from neurons which are involved in directing reproductive behaviors. We have now tested drivers for these neurons and added these data in Fig 3 (SAG neurons) and as Suppl Figs S4 (SPSN and genital tract neuron drivers SPR3 and SPR21), Suppl Fig S6 (overlap in single cell expression atlas), Suppl Fig S7 (overlap of SPSN split drivers with SPR8, fru11/12 and dsx split drivers in the brain inducing PMRs) and Suppl Fig S9 (pC1, OviDNs, OviENs, OviINs and vpoDN).  

      The newly added data are in full support of our conclusion that SP targets central nervous system neurons, which we termed SP Response Inducing Neurons (SPRINz). In particular, we find lines that express in genital tract neurons, but do not induce an SP response (Supp Figs S4, S7 and S10) or do not express in genital tract neurons and induce an SP response (Fig 2 and Supp Fig S2).

      We have analysed the expression of SPSN in the brain and VNC and find expression in few neurons (Suppl Fig S4). This result is consistent with expression of the genes driving SPSN expression in the single cell expression atlas indicating overlap of expression in very few neurons (Suppl Fig S6). We have already shown that FD6 (VT003280) which is part of the SPSN splitGal4 driver, expresses in the brain and VNC and can induce PMRs from SP expression (Fig 4).

      We have taken this further to test another SPSN driver (VT058873) in combination with SPR8, fru11/12 and dsx and find PMRs induced by mSP expression (Suppl Fig S7). Moreover, if we restrict expression of mSP to the brain with otdflp we can induce PMRs from mSP expression and obtain the same response by activating these brain neurons (Suppl Fig S7). We note that the VT058873 ∩ fru11/12 intersection in combination with otdflp stopmSP or stopTrpA1 in the head, did not result in PMRs. Here, PMR inducing neurons likely reside in the VNC, but currently no tools are available to test this further.

      We further tested pC1, OviDNs, OviENs, OviINs and vpoDN for induction of PMRs from expression of mSP. We are pleased to see that OviEN-SS2s, OviIN-SS1 and vpoDN splitGAl4 drivers can reduce receptivity, but not induce oviposition (Suppl Fig S8). We predicted such drivers based on previously published data (Haussmann et al. 2013), which we now validated.

      (2) Authors must show how specific is their "head" (elav/otd-flp) and "trunk" (elav/tsh) expression of mSP by showing images of the same constructs driving GFP.

      The expression pattern for tshGAL, which expresses in the trunk is already published (Soller et al., 2006). We have added images for “head” expression for tshGAL and adjusted our statement to be pre-dominantly expressed in the VNC in Suppl Fig 1.

      (3) VT3280 is termed as a SAG driver. However, VT3280 is a SPSN specific driver (Feng et al., 2014; Jang et al., 2017; Scheunemann et al., 2019; Laturney et al., 2023). The authors should clarify this.

      According to the reviewers suggestion, we have clarified the specificity of VT003280 and now say that this is FD6.

      (4) Intersectional approaches must rule out the influence of SP on sex-peptide sensing neurons (SPSN) in the ovary by combining their constructs with SPSN-Gal80 construct. In line with this, most of their lines targets the SAG circuit (4I, J and K). Again, here they need to rule out the involvement of SPSN in their receptivity/egg laying phenotypes. Especially because "In the female genital tract, these split-Gal4 combinations show expression in genital tract neurons with innervations running along oviduct and uterine walls (Figures S3A-S3E)".

      We agree with this reviewer that we need a higher resolution of expression to only one cell type. However, this is a major task that we will continue in follow up studies.

      In principal, use of GAL80 is a valid approach to restrict expression, if levels of GAL80 are higher than those of GAL4, because GAL80 binds GAL4 to inhibit its activity. Hence, if levels of GAL80 are lower, results could be difficult to interpret.

      (5) The authors separate head (brain) from trunk (VNC) responses, but they don't narrow down the neural circuits involved on each response. A detailed characterization of the involved circuits especially in the case of the VNC is needed to (a) show that the intersectional approach is indeed labelling distinct subtypes and (b) how these distinct neurons influence oviposition.

      Again, we agree with this reviewer that we need a higher resolution of expression to only one cell type. However, this is a major task that we will continue in follow up studies.

      Reviewer #2 (Public Review):

      Strength:

      The intersectional approach is appropriate and state-of-the art. The analysis is a very comprehensive tour-de-force and experiments are carefully performed to a high standard. The authors also produced a useful new transgenic line (UAS-FRTstopFRT mSP). The finding that neurons in the brain (head) mediate the SP effect on receptivity, while neurons in the abdomen and thorax (ventral nerve cord or peripheral neurons) mediate the SP effect on oviposition, is a significant step forward in the endavour to identify the underlying neuronal networks and hence a mechanistic understanding of SP action. Though this result is not entirely unexpected, it is novel as it was not shown before.

      We thank reviewer 2 for recognizing the advance of our work.

      Weakness:

      Though the analysis identifies a small set of neurons underlying SP responses, it does not go the last step to individually identify at least a few of them. The last paragraph in the discussion rightfully speculates about the neurochemical identity of some of the intersection neurons (e.g. dopaminergic P1 neurons, NPF neurons). At least these suggested identities could have been confirmed by straight-forward immunostainings agains NPF or TH, for which antisera are available. Moreover, specific GAL4 lines for NPF or P1 or at least TH neurons are available which could be used to express mSP to test whether SP activation of those neurons is sufficient to trigger the SP effect.

      We appreciate this reviewers recognition of our previous work showing that receptivity and oviposition are separable. As pointed out we have now gone one step further and identified in a tour de force approach subsets of neurons in the brain and VNC.

      We agree with this reviewer that we need a higher resolution of expression to only one cell type. As pointed out by this reviewer, the neurochemical identity is an excellent suggestions and will help to further restrict expression to just one type of neuron. However, this is a major task that we will continue in follow up studies.

      Reviewer #3 (Public Review):

      Strengths:

      Besides the main results described in the summary above, the authors discovered the following:

      (1) Reduction of receptivity and induction of egg-laying are separable by restricting the expression of membrane-tethered SP (mSP): head-specific expression of mSP induces reduction of receptivity only, whereas trunk-specific expression of mSP induces oviposition only. Also, they identified a GAL4 line (SPR12) that induced egg laying but did not reduce receptivity.

      (2) Expression of mSP in the genital tract sensory neurons does not induce PMR. The authors identified three GAL4 drivers (SPR3, SPR 21, and fru9), which robustly expressed mSP in genital tract sensory neurons but did not induce PMRs. Also, SPR12 does not express in genital tract neurons but induces egg laying by expressing mSP.

      We thank reviewer 2 for recognizing these two important points regarding the SP response that point to a revised model for how the underlying circuitry induces the post-mating response. To further substantiate these findings we now have added a splitGal4 nSyb ∩ ppk which expresses in genital tract neurons, but does not induce PMRs from mSP expression.

      Weaknesses:

      (1) Intersectional expression involving ppk-GAL4-DBD was negative in all GAL4AD lines (Supp. Fig.S5). As the authors mentioned,   neurons may not intersect with SPR, fru, dsx, and FD6 neurons in inducing PMRs by mSP. However, since there was no PMR induction and no GAL4 expression at all in any combination with GAL4-AD lines used in this study, I would like to have a positive control, where intersectional expression of mSP in ppk-GAL4-DBD and other GAL4-AD lines (e.g., ppk-GAL4-AD) would induce PMR.

      We have added a positive control for ppk expression by combining the ppk-DBD line with a nSyb-AD which expresses in all neurons in Supp Fig S8. This experiment confirms our previous observations that ppk splitGal4 in combination with other drivers does not induce an SP response despite driving expression in genital tract neurons. We have expanded the discussion section to point out that we have identified additional cells in the brain expressing ppkGAL4, but expression of split-GAL4 ppk is absent in these cells. Part of this work has previously been published (Nallasivan et al. 2021). Accordingly, we amended the text to say when expression was achieved with ppkGAL or ppk splitGAL4.

      (2) The results of SPR RNAi knock-down experiments are inconclusive (Figure 5). SPR RNAi cancelled the PMR in dsx ∩ fru11/12 and partially in SPR8 ∩ fru 11/12 neurons. SPR RNAi in dsx ∩ SPR8 neurons turned virgin females unreceptive; it is unclear whether SPR mediates the phenotype in SPR8 ∩ fru 11/12 and dsx ∩ SPR8 neurons.

      We agree with this reviewer that the interpretation of the SPR RNAi results are complicated by the fact that SP has additional receptors (Haussmann et al 2013). The results are conclusive for all three intersections when expressing UAS mSP in SPR RNAi with respect to oviposition, e.g. egg laying is not induced in the absence of SPR. For receptivity, the results are conclusive for dsx ∩ fru11/12 and partially for SPR8 ∩ fru 11/12.

      Potentially, SPR RNAi knock-down does not sufficiently reduce SPR levels to completely reduce receptivity in some intersection patterns, likely also because splitGal4 expression is less efficient.

      Why SPR RNAi in dsx ∩ SPR8 neurons turned virgin females unreceptive is unclear, but we anticipate that we need a higher resolution of expression to only one cell type to resolve this unexpected result. However, this is a major task that we will continue in follow up studies.

      SPR RNAi knock-down experiments may also help clarify whether mSP worked autocrine or juxtacrine to induce PMR. mSP may produce juxtacrine signaling, which is cell non-autonomous.

      Whether membrane-tethered SP induces the response in a autocrine manner is an import aspect in the interpretation of the results from mSP expression.

      Removing SPR by SPR RNAi and expression of mSP in the same neurons did not induce egg laying for all three intersection and did not reduce receptivity for dsx ∩ fru11/12 and for SPR8 ∩ fru 11/12. Accordingly, we can conclude that for these neurons the response is induced in an autocrine manner.

      We have added this aspect to the discussion section.

  3. Dec 2025
    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      The manuscript by Shan et al seeks to define the role of the CHI3L1 protein in macrophages during the progression of MASH. The authors argue that the Chil1 gene is expressed highly in hepatic macrophages. Subsequently, they use Chil1 flx mice crossed to Clec4F-Cre or LysM-Cre to assess the role of this factor in the progression of MASH using a high-fat, high-cholesterol diet (HFHC). They found that loss of Chil1 in KCs (Clec4F Cre) leads to enhanced KC death and worsened hepatic steatosis. Using scRNA seq, they also provide evidence that loss of this factor promotes gene programs related to cell death. From a mechanistic perspective, they provide evidence that CHI3L serves as a glucose sink and thus loss of this molecule enhances macrophage glucose uptake and susceptibility to cell death. Using a bone marrow macrophage system and KCs they demonstrate that cell death induced by palmitic acid is attenuated by the addition of rCHI3L1. While the article is well written and potentially highlights a new mechanism of macrophage dysfunction in MASH, there are some concerns about the current data that limit my enthusiasm for the study in its current form. Please see my specific comments below.

      (1) The authors' interpretation of the results from the KC (Clec4F) and MdM KO (LysM-Cre) experiments is flawed. For example, in Figure 2 the authors present data that knockout of Chil1 in KCs using Clec4f Cre produces worse liver steatosis and insulin resistance. However, in supplemental Figure 4, they perform the same experiment in LysM-Cre mice and find a somewhat different phenotype. The authors appear to be under the impression that LysM-Cre does not cause recombination in KCs and therefore interpret this data to mean that Chil1 is relevant in KCs and not MdMs. However, LysM-Cre DOES lead to efficient recombination in KCs and therefore Chil1 expression will be decreased in both KCs and MdM (along with PMNs) in this line.

      Therefore, a phenotype observed with KC-KO should also be present in this model unless the authors argue that loss of Chil1 from the MdMs has the opposite phenotype of KCs and therefore attenuates the phenotype. The Cx3Cr1 CreER tamoxifen inducible system is currently the only macrophage Cre strategy that will avoid KC recombination. The authors need to rethink their results with the understanding that Chil1 is deleted from KCs in the LysM-Cre experiment. In addition, it appears that only one experiment was performed, with only 5 mice in each group for both the Clec4f and LysM-Cre data. This is generally not enough to make a firm conclusion for MASH diet experiments.

      We thank the reviewer for raising this important point regarding our data interpretation. We have carefully examined the deletion efficiency of Chi3l1 in primary Kupffer cells (KCs) from Lyz2<sup>∆Chil1</sup> (LysM-Cre) mice. Our results show roughly a 40% reduction in Chi3l1 expression at both the mRNA and protein levels (Revised Manuscript, Figure S7B and C). Given this modest decrease, Chi3l1 deletion in KCs of Lyz2<sup>∆Chil1</sup> mice was incomplete, which likely accounts for the phenotypic differences observed between Clec4f<sup>∆Chil1</sup> and Lyz2<sup>∆Chil1</sup> mice in the MASLD model.

      Furthermore, we have increased the sample size in both the Clec4f- and LysM-Cre experiments to 9–12 mice per group following the HFHC diet, thereby strengthening the statistical power and reliability of our findings (Revised Figures 2 and S8).

      (2) The mouse weight gain is missing from Figure 2 and Supplementary Figure 4. This data is critical to interpret the changes in liver pathology, especially since they have worse insulin resistance.

      We thank the reviewer for this valuable comment. We have now included the mouse body weight data in the revised manuscript (Figure 2A, B and Figures S8A, B). Compared with mice on a normal chow diet (NCD), all groups exhibited progressive weight gain during HFHC diet feeding. Notably, Clec4f<sup>∆Chil1</sup> mice gained significantly more body weight than Chil1<sup>fl/fl</sup> controls, whereas Lyz2<sup>∆Chil1</sup> mice showed a similar weight gain trajectory to Chil1<sup>fl/fl</sup> mice under the same conditions.

      (3) Figure 4 suggests that KC death is increased with KO of Chil1. However, this data cannot be concluded from the plots shown. In Supplementary Figure 6 the authors provide a more appropriate gating scheme to quantify resident KCs that includes TIM4. The TIM4 data needs to be shown and quantified in Figure 4. As shown in Supplementary Figure 6, the F4/80 hi population is predominantly KCs at baseline; however, this is not true with MASH diets. Most of the recruited MoMFs also reside in the F4/80 hi gate where they can be identified by their lower expression of TIM4. The MoMF gate shown in this figure is incorrect. The CD11b hi population is predominantly PMNs, monocytes, and cDC,2 not MoMFs (PMID:33997821). In addition, the authors should stain the tissue for TIM4, which would also be expected to reveal a decrease in the number of resident KCs.

      We thank the reviewer for raising this critical point regarding the gating strategy and interpretation of KC death. We have now refined our flow cytometry gating based on the reviewer’s suggestion. Specifically, we analyzed TIM4 expression and attempted to identify TIM4<sup>low</sup> MoMFs populations in our model. However, we did not detect a distinct TIM4<sup>low</sup> population, likely because our mice were fed the HFHC diet for only 16 weeks and had not yet developed liver fibrosis. We therefore reason that MoMFs have not fully acquired TIM4 expression at this stage.

      To improve our analysis, we referred to published strategies (PMID: 41131393; PMID: 32562600) and gated KCs as CD45<sup>+</sup>CD11b<sup>+</sup>F4/80<sup>hi</sup> TIM4<sup>hi</sup> and MoMFs as CD45<sup>+</sup>Ly6G<sup>-</sup>CD11b<sup>+</sup>F4/80<sup>low</sup> TIM4<sup>low/-</sup>. Using this approach, we observed a gradual reduction of KCs and a corresponding increase in MoMFs in WT mice, with a significantly faster loss of KCs in Chil1<sup>-/-</sup> mice (Revised Figure 4C, D; Figure S10A).

      Furthermore, immunofluorescence staining for TIM4 combined with TUNEL or cleaved caspase-3 confirmed an increased number of dying KCs in Chil1<sup>-/-</sup> mice compared to WT following HFHC diet feeding (Revised Figure 4E; Figure S10B).

      (4) While the Clec4F Cre is specific to KCs, there is also less data about the impact of the Cre system on KC biology. Therefore, when looking at cell death, the authors need to include some mice that express Clec4F cre without the floxed allele to rule out any effects of the Cre itself. In addition, if the cell death phenotype is real, it should also be present in LysM Cre system for the reasons described above. Therefore, the authors should quantify the KC number and dying KCs in this mouse line as well.

      We thank the reviewer for raising this important point. During our study, we indeed observed an increased number of KCs in Clec4f-Cre mice compared to WT controls, suggesting that the Clec4f-Cre system itself may modestly affect KC homeostasis. To address this, we compared KCs numbers between Clec4f<sup>∆Chil1</sup> and Clec4f-Cre mice and found that Clec4f<sup>∆Chil1</sup> mice displayed a significant reduction in KCs numbers following HFHC diet feeding. Moreover, co-staining for TIM4 and TUNEL revealed a marked increase in KCs death in Clec4f<sup>∆Chil1</sup> mice relative to Clec4f-Cre mice, indicating that the observed phenotype is attributable to Chil1 deletion rather than Cre expression alone. These data have been reported in our related manuscript (He et al., bioRxiv, 2025.09.26.678483; doi: 10.1101/2025.09.26.678483).

      In addition, we quantified KCs numbers and KCs death in the Lyz2-Cre line. TIM4/TUNEL co-staining showed comparable levels of KCs death between Chil1<sup>fl/fl</sup> and Lyz2<sup>∆Chil1</sup> mice (Revised Figure S11B). Consistently, flow cytometry analyses revealed no significant differences in KCs numbers between these two groups before (0 weeks) or after (20 weeks) HFHC diet feeding (Revised Figures S11C, D). As discussed in our response to Comment 1, this may be due to the incomplete deletion of Chi3l1 in KCs (<50%) in the Lyz2-Cre line, which likely attenuates the phenotype.

      (5) I am somewhat concerned about the conclusion that Chil1 is highly expressed in liver macrophages. Looking at our own data and those from the Liver Atlas it appears that this gene is primarily expressed in neutrophils. At a minimum, the authors should address the expression of Chil1 in macrophage populations from other publicly available datasets in mouse MASH to validate their findings (several options include - PMID: 33440159, 32888418, 32362324). If expression of Chil1 is not present in these other data sets, perhaps an environmental/microbiome difference may account for the distinct expression pattern observed. Either way, it is important to address this issue.

      We thank the reviewer for this insightful comment and agree that analysis of scRNA-seq data, including our own and those reported in the Liver Atlas as well as in the referenced studies (PMID: 33440159, 32888418, 32362324), indicates that Chil1 is predominantly expressed in neutrophils.

      However, our immunofluorescence staining under normal physiological conditions revealed that Chi3l1 protein is primarily localized in Kupffer cells (KCs), as demonstrated by strong co-staining with TIM4 (Revised Figure 1E). In MASLD mouse models induced by HFHC or MCD diets, we observed that both KCs and monocyte-derived macrophages (MoMFs) express Chi3l1, with particularly high levels in MoMFs.

      We speculate that the apparent discrepancy between scRNA-seq datasets and our in situ findings may reflect differences in cellular proportions and detection sensitivity. Since hepatic macrophages (particularly KCs and MoMFs) constitute a larger proportion of total liver immune cells compared with neutrophils, their contribution to total Chi3l1 protein levels in tissue staining may appear dominant, despite lower transcript abundance per cell in sequencing datasets. We have included a discussion of this point in the revised manuscript to clarify this distinction (Revised manuscript, page 8,line 341-350 ).

      Minor points:

      (1) Were there any changes in liver fibrosis or liver fibrosis markers present in these experiments?

      We assessed liver fibrosis using Sirius Red staining and α-SMA Western blot analysis.

      We found no induction of liver fibrosis in our HFHC-induced MASLD model (Revised Figure S1A, B), but a clear elevation of fibrosis markers in the MCD-induced MASH model (Revised Figure S6A, B).

      (2) In Supplementary Figure 3, the authors do a western blot for CHI3L1 in BMDMs. This should also be done for KCs isolated from these mice. Does this antibody work for immunofluorescence? Staining liver tissue would provide valuable information on the expression patterns.

      We have included qPCR and western blot for Chi3l1 in isolated primary KCs from Lyz2<sup>∆Chil1</sup> mice. The data show a slight, non-significant reduction in both mRNA and protein levels in KCs (Revised Figure S7B, C). The immunofluorescence staining on liver tissue showed that Chi3l1 is more likely expressed in the plasma membranes of TIM4<sup>+</sup> F4/80<sup>+</sup> KCs both under NCD and HFHC diet (Revised Figure 1E).

      (3) What is the impact of MASH diet feeding on Chil1 expression in KCs or in the liver in general?

      In both our MASLD and MASH models, diet feeding consistently upregulates Chi3l1 in KCs or in the liver in general (Revised Figure 1F, G, S6C,D).

      (4) In Figure S1 the authors show tSNE plots of various monocyte and macrophage genes in the liver. Are these plots both diets together? How do things look when comparing these markers between the STD and HFHC diet? The population of recruited LAMs seems very small for 16 weeks of diet. Moreover, Chil1 should also be shown on these tSNE plots as well.

      Yes, these plots are both diets together. When compared separately, the core marker expression is consistent between NCD and HFHC diets. However, the HFHC diet induces a relative increase in KC marker expression within the MoMF cluster, suggesting phenotypic adaptation (Author response image 1A, below). Moreover, Chil1 expression on the t-SNE plot was shown (Author response image 1B, below). However, compared to lineage-specific marker genes, Chi3l1 expression is rather low.

      Author response image 1.

      Gene expression levels of lineage-specific marker genes in monocytes/macrophages clusters between NCD and HFHC diets. (A) UMAP plots show the scaled expression changes of lineage-specific markers in KCs/monocyte/macrophage clusters from mice under NCD and HFHC diets. Color represents the level of gene expression. (B) UMAP plots show the scaled expression changes of Chil1 in KCs/monocyte/macrophage clusters from mice under NCD and HFHC diets. Color represents the level of gene expression.

      (5) In Figure 5, the authors demonstrate that CHI3L1 binds to glucose. However, given that all chitin molecules bind to carbohydrates, is this a new finding? The data showing that CHI3L is elevated in the serum after diet is interesting. What happens to serum levels of this molecule in KC KO or total macrophage KO mice? Do the authors think it primarily acts as a secreted molecule or in a cell-intrinsic manner?

      We thank the reviewer for these insightful comments, which helped us clarify the novelty of our findings.

      (1) Novelty of CHI3L1-Glucose Binding:

      While chitin-binding domains are known to interact with carbohydrate polymers, our key discovery is that CHI3L1 (YKL-40)—a mammalian chitinase-like protein lacking enzymatic activity—specifically binds to glucose, a simple monosaccharide. This differs fundamentally from canonical binding to insoluble polysaccharides such as chitin and reveals a potential role for CHI3L1 in monosaccharide recognition, linking it to glucose metabolism and energy sensing. We clarified this point in the revised manuscript (page 9, line374-379).

      (2) Serum CHI3L1 in Knockout Models:

      Consistent with the reviewer’s suggestion, serum Chi3l1 levels are altered in our knockout models:

      KC-specific KO (Clec4f<sup>ΔChil1</sup>): Under normal chow, serum CHI3L1 is markedly reduced compared to controls and remains lower following HFHC feeding (Author response image 2A, below), indicating that Kupffer cells are the main source of circulating CHI3L1 under basal and disease conditions.

      Macrophage KO (Lyz2<sup>ΔChil1</sup>): No significant changes were observed between Chil1<sup>fl/fl</sup> and Lyz2<sup>ΔChil1</sup> mice under either diet (Author response image 2B, below), likely due to minimal monocyte-derived macrophage recruitment in this HFHC model (see Revised Figure 4C,D).

      (3) Secreted vs. Cell-Intrinsic Role:

      CHI3L1 predominantly localizes to the KC plasma membrane, consistent with a secreted role, and its serum reduction in KC-specific knockouts supports the physiological relevance of its secreted role. While cell-intrinsic effects have been reported elsewhere, our current data do not address this in KCs and warrant future investigation.

      Author response image 2.

      Chi3l1 expression in serum before and after HFHC in CKO mice. (A) Western blot to detect Chi3l1 expression in serum of Chil1<sup>fl/fl</sup> and Clec4f<sup>ΔChil1</sup> mice before and after 16 weeks’ HFHC diet. n=3 mice/group. (B) Western blot to detect Chi3l1 expression in serum of Chil1<sup>fl/fl</sup> and Lyz2ΔChil1 before and after 16 weeks’ HFHC diet. n=3 mice/group.

      Reviewer #2 (Public review):

      The manuscript from Shan et al., sets out to investigate the role of Chi3l1 in different hepatic macrophage subsets (KCs and moMFs) in MASLD following their identification that KCs highly express this gene. To this end, they utilise Chi3l1KO, Clec4f-CrexChi3l1fl, and Lyz2-CrexChi3l1fl mice and WT controls fed a HFHC for different periods of time.

      Major:

      Firstly, the authors perform scRNA-seq, which led to the identification of Chi3l1 (encoded by Chil1) in macrophages. However, this is on a limited number of cells (especially in the HFHC context), and hence it would also be important to validate this finding in other publicly available MASLD/Fibrosis scRNA-seq datasets. Similarly, it would be important to examine if cells other than monocytes/macrophages also express this gene, given the use of the full KO in the manuscript. Along these lines, utilisation of publicly available human MASLD scRNA-seq datasets would also be important to understand where the increased expression observed in patients comes from and the overall relevance of macrophages in this finding.

      We thank the reviewer for this valuable suggestion and acknowledge the limited number of cells analyzed under the HFHC condition in our original dataset. To strengthen our findings, we have now examined four additional publicly available scRNA-seq datasets— two from mouse models and two from human MASLD patients (Revised Figure S3, manuscript page 4, line 164-172). Across these datasets, the specific cell type showing the highest Chil1 expression varied somewhat between studies, likely reflecting model differences and disease stages. Nevertheless, Chil1 expression was consistently enriched in hepatic macrophage populations, including both Kupffer cells and infiltrating macrophages, in mouse and human livers. Notably, Chil1 expression was higher in infiltrating macrophages compared to resident Kupffer cells, supporting its upregulation during MASLD progression. These additional analyses confirm the robustness and crossspecies relevance of our finding that macrophages are the primary Chil1-expressing cell type in the liver.

      Next, the authors use two different Cre lines (Clec4f-Cre and Lyz2-Cre) to target KCs and moMFs respectively. However, no evidence is provided to demonstrate that Chil1 is only deleted from the respective cells in the two CRE lines. Thus, KCs and moMFs should be sorted from both lines, and a qPCR performed to check the deletion of Chil1. This is especially important for the Lyz2-Cre, which has been routinely used in the literature to target KCs (as well as moMFs) and has (at least partial) penetrance in KCs (depending on the gene to be floxed). Also, while the Clec4f-Cre mice show an exacerbated MASLD phenotype, there is currently no baseline phenotype of these animals (or the Lyz2Cre) in steady state in relation to the same readouts provided in MASLD and the macrophage compartment. This is critical to understand if the phenotype is MASLD-specific or if loss of Chi3l1 already affects the macrophages under homeostatic conditions.

      We thank the reviewer for raising this important point.

      (1) Chil1 deletion efficiency in Clec4f-Cre and Lyz2-Cre lines:

      We have assessed the efficiency of Chil1 deletion in both Lyz2<sup>∆Chil1</sup> and Clec4f<sup>∆Chil1</sup> mice by evaluating mRNA and protein levels of Chi3l1. For the Lyz2<sup>∆Chil1</sup> mice, we measured Chi3l1 expression in bone marrow-derived macrophages (BMDMs) and primary Kupffer cells (KCs). Both qPCR (for mRNA) and Western blotting (for protein) reveal that Chi3l1 is almost undetectable in BMDMs from Lyz2<sup>∆Chil1</sup> mice when compared to Chil1<sup>fl/fl</sup> controls. In contrast, we observe no significant reduction in Chi3l1 expression in KCs from these animals (Revised Figure S7B, C), suggesting Chil1 is deleted in BMDMs but not in KCs in Lyz2-Cre line.

      For the Clec4f<sup>∆Chil1</sup> mice, both mRNA and protein levels of Chi3l1 are barely detectable in BMDMs and primary KCs when compared to Chil1<sup>fl/fl</sup> controls (Revised Figure S4B, C). However, we did observe a faint Chi3l1 band in KCs of Clec4f<sup>∆Chil1</sup> mice, which we suspect is due to contamination from LSECs during the KC isolation process, given that the TIM4 staining for KCs was approximately 90%. Overall, Chil1 is deleted in both KCs and BMDMs in Clec4f-Cre line.

      Notably, since we observed a pronounced MASLD phenotype in Clec4f-Cre mice but not in Lyz2-Cre mice, these findings further underscore the critical role of Kupffer cells in the progression of MASLD.

      (2) Whether the phenotype is MASLD-specific or whether loss of Chi3l1 already affects the macrophages under homeostatic conditions: We now included phenotypic data of Clec4f<sup>ΔChil1</sup> mice (KC-specific KO) and Lyz2<sup>∆Chil1</sup> mice (MoMFs-specific KO) fed with NCD 16w (Revised Figure 2A-F, S8A-F). Shortly speaking, there is no baseline difference between Chil1<sup>fl/fl</sup> and Clec4f<sup>ΔChil1</sup> or Lyz2<sup>∆Chil1</sup> mice in steady state in relation to the same readouts provided in MASLD.

      Next, the authors suggest that loss of Chi3l1 promotes KC death. However, to examine this, they use Chi3l1 full KO mice instead of the Clec4f-Cre line. The reason for this is not clear, because in this regard, it is now not clear whether the effects are regulated by loss of Chi3l1 from KCs or from other hepatic cells (see point above). The authors mention that Chi3l1 is a secreted protein, so does this mean other cells are also secreting it, and are these needed for KC death? In that case, this would not explain the phenotype in the CLEC4F-Cre mice. Here, the authors do perform a basic immunophenotyping of the macrophage populations; however, the markers used are outdated, making it difficult to interpret the findings. Instead of F4/80 and CD11b, which do not allow a perfect discrimination of KCs and moMFs, especially in HFHC diet-fed mice, more robust and specific markers of KCs should be used, including CLEC4F, VSIG4, and TIM4.

      We thank the reviewer for raising this important point. We performed experiments in Clec4f<sup>∆Chil1</sup> (KC-specific KO) model. The phenotype in these mice closely mirrors that of the full KO: we observed a significant reduction in KC numbers and a concurrent increase in KC cell death following an HFHC diet in Clec4f<sup>∆Chil1</sup> mice post HFHC diet compared to Clec4f-cre mice. We have reported these data in the following related manuscript (Figure 6 D-G). This confirms that the loss of CHI3L1 specifically from KCs is sufficient to drive this effect.

      Hyperactivated Glycolysis Drives Spatially-Patterned Kupffer Cell Depletion in MASLD Jia He, Ran Li, Cheng Xie, Xiane Zhu, Keqin Wang, Zhao Shan bioRxiv 2025.09.26.678483; doi: https://doi.org/10.1101/2025.09.26.678483

      While other hepatic cells (e.g., neutrophils and liver sinusoidal endothelial cells) also express Chi3l1, our data indicate that KC-secreted Chi3l1 plays a dominant and cellautonomous role in maintaining KCs viability. The potential contribution of other cellular sources to this phenotype remains an interesting direction for future study.

      We apologize for the lack of clarity in our initial immunophenotyping. We have revised the flow cytometry data to clearly show that KCs are rigorously defined as TIM4+ cells (Revised Figure 4C, D).

      Additionally, while the authors report a reduction of KCs in terms of absolute numbers, there are no differences in proportions. Thus, coupled with a decrease also in moMF numbers at 16 weeks (when one would expect an increase if KCs are decreased, based on previous literature) suggests that the differences in KC numbers may be due to differences in total cell counts obtained from the obese livers compared with controls. To rule this out, total cell counts and total live CD45+ cell counts should be provided. Here, the authors also provide tunnel staining in situ to demonstrate increased KC death, but as it is typically notoriously difficult to visualise dying KCs in MASLD models, here it would be important to provide more images. Similarly, there appear to be many more Tunel+ cells in the KO that are not KCs; thus, it would be important to examine this in the CLEC4F-Cre line to ascertain direct versus indirect effects on cell survival.

      We thank the reviewer for raising this important point. We have now included the total cell counts and total live CD45<sup>+</sup> cell counts, which showed similar numbers between WT and Chil1<sup>-/-</sup> mice post HFHC diet (Figure 3A, below).

      Moreover, we included cleavaged caspase 3 and TIM4 co-staining in WT and Chil1<sup>-/-</sup> mice before and after HFHC diets, which confirmed increased KCs death in Chil1<sup>-/-</sup> mice (Revised Figure S10B). We have compared KCs number and KCs death between Clec4fcre and Clec4f<sup>∆Chil1</sup> mice under NCD and HFHC diet in the following manuscript (Figure 6 D-G). The data showed similar KCs number under NCD and reduced KCs number in Clec4f<sup>∆Chil1</sup> mice compared to Clec4f-cre mice, which confirms direct effects of Chi3l1 on cell survival but not because of cre insertion.

      Hyperactivated Glycolysis Drives Spatially-Patterned Kupffer Cell Depletion in MASLD Jia He, Ran Li, Cheng Xie, Xiane Zhu, Keqin Wang, Zhao Shan bioRxiv 2025.09.26.678483; doi: https://doi.org/10.1101/2025.09.26.678483

      Author response image 3.

      Number of total cells and total live CD45+ cells in liver of WT and Chil1<sup>-/-</sup> mice. (A) Number of total cells and total live CD45+ cells/liver were statistically analyzed. n= 3-4 mice per group.

      Finally, the authors suggest that Chi3l1 exerts its effects through binding glucose and preventing its uptake. They use ex vivo/in vitro models to assess this with rChi3l1; however, here I miss the key in vivo experiment using the CLEC4F-Cre mice to prove that this in KCs is sufficient for the phenotype. This is critical to confirm the take-home message of the manuscript.

      We agree that it is essential to confirm the in vivo relevance of Chi3l1-mediated glucose regulation in Kupffer cells (KCs). Our data suggest that KCs undergo cell death not because they express Chi3l1 per se, but because they exhibit a glucose-hungry metabolic phenotype that makes them uniquely dependent on Chi3l1-mediated regulation of glucose uptake. To directly assess this mechanism in vivo, we injected 2-NBDG, a fluorescent glucose analog, into overnight-fasted and refed mice and quantified its uptake in hepatic KCs. Notably, Chi3l1-deficient KCs exhibited significantly increased 2-NBDG uptake compared with controls, and this effect was markedly suppressed by co-treatment with recombinant Chi3l1 (rChi3l1) (Revised Figure 6G, H). These findings demonstrate that Chi3l1 regulates glucose uptake by KCs in vivo, supporting our proposed mechanism that Chi3l1 controls KC metabolic homeostasis through modulation of glucose availability.

      Minor points:

      (1) Some key references of macrophage heterogeneity in MASLD are not cited: PMID: 32362324 and PMID: 32888418.

      We thank the reviewer for highlighting these critical references and have included them in the introduction (Revised manuscript, page 2, line 64-73).

      (2) In the discussion, Figure 3H is referenced (Serum data), but there is no Figure 3H. If the authors have this data (increased Chi3l1 in serum of mice fed HFHC diet), what happens in CLEC4F-Cre mice fed the diet? Is this lost completely? This comes back to the point regarding the specificity of expression.

      We apologize for the mistake. It should be Figure 5F now in the revised version, in which serum Chi3l1 was significantly upregulated after HFHC diet. Moreover, under a normal chow diet (NCD), serum CHI3L1 is significantly lower in Clec4f<sup>ΔChil1</sup> mice compared to controls (Chil1<sup>fl/fl</sup>). Following an HFHC diet, levels increase in both genotypes but remain relatively lower in the KC-KO mice (please see Figure 2A above). This data strongly suggests that Kupffer Cells (KCs) are the primary source of serum CHI3L1 under basal conditions and a major contributor during MASLD progression.

      Reviewer #3 (Public review):

      This paper investigates the role of Chi3l1 in regulating the fate of liver macrophages in the context of metabolic dysfunction leading to the development of MASLD. I do see value in this work, but some issues exist that should be addressed as well as possible.

      (1) Chi3l1 has been linked to macrophage functions in MASLD/MASH, acute liver injury, and fibrosis models before (e.g., PMID: 37166517), which limits the novelty of the current work. It has even been linked to macrophage cell death/survival (PMID: 31250532) in the context of fibrosis, which is a main observation from the current study.

      We thank the reviewer for this insightful comment regarding the novelty of our findings. We agree that Chi3l1 has previously been linked to macrophage survival and function in models of liver injury and fibrosis (e.g., PMID: 37166517, 31250532). However, our study focuses specifically on the early stage of MASLD, prior to the onset of fibrosis, revealing a distinct mechanistic role for CHI3L1 in this context.

      We demonstrate that CHI3L1 directly interacts with extracellular glucose to regulate its cellular uptake—a previously unrecognized biochemical function. Furthermore, we show that CHI3L1’s protective role is metabolically dependent, safeguarding glucose-dependent Kupffer cells (KCs) but not monocyte-derived macrophages (MoMFs). This metabolic dichotomy and the direct link between CHI3L1 and glucose sensing represent conceptual advances beyond previous studies of CHI3L1 in fibrotic or injury models.

      (2) The LysCre-experiments differ from experiments conducted by Ariel Feldstein's team (PMID: 37166517). What is the explanation for this difference? - The LysCre system is neither specific to macrophages (it also depletes in neutrophils, etc), nor is this system necessarily efficient in all myeloid cells (e.g., Kupffer cells vs other macrophages). The authors need to show the efficacy and specificity of the conditional KO regarding Chi3l1 in the different myeloid populations in the liver and the circulation.

      We thank the reviewer for this important comment and the opportunity to clarify both the efficiency and specificity of our conditional knockouts, as well as the differences from the study by Feldstein’s group (PMID: 37166517).

      (1) Chil1 deletion efficiency in Clec4f-Cre and Lyz2-Cre lines:

      We have assessed the efficiency of Chil1 deletion in both Lyz2<sup>∆Chil1</sup> and Clec4f<sup>∆Chil1</sup> mice by evaluating mRNA and protein levels of Chi3l1. For the Lyz2<sup>∆Chil1</sup> mice, we measured Chi3l1 expression in bone marrow-derived macrophages (BMDMs) and primary Kupffer cells (KCs). Both qPCR (for mRNA) and Western blotting (for protein) reveal that Chi3l1 is almost undetectable in BMDMs from Lyz2<sup>∆Chil1</sup> mice when compared to Chil1<sup>fl/fl</sup> controls. In contrast, we observe no significant reduction in Chi3l1 expression in KCs from these animals (Revised Figure S7B, C), suggesting that Chil1 is deleted in BMDMs but not in KCs in Lyz2-Cre line.

      For the Clec4f<sup>∆Chil1</sup> mice, both mRNA and protein levels of Chi3l1 are barely detectable in BMDMs and primary KCs when compared to Chil1<sup>fl/fl</sup> controls (Revised Figure S4B, C). However, we did observe a faint Chi3l1 band in KCs of Clec4f<sup>∆Chil1</sup> mice, which we suspect is due to contamination from LSECs during the KC isolation process, given that the TIM4 staining for KCs was approximately 90%. Overall, Chil1 is deleted in both KCs and BMDMs in Clec4f-Cre line.

      Notably, since we observed a pronounced MASLD phenotype in Clec4f-Cre mice but not in Lyz2-Cre mice, these findings further underscore the critical role of Kupffer cells in the progression of MASLD.

      (2) Explanation for Differences from Feldstein et al. (PMID: 37166517):

      Our findings differ from those reported by Feldstein’s group primarily due to differences in disease stage and model. We used a high-fat, high-cholesterol (HFHC) diet to model earlystage MASLD characterized by steatosis and inflammation without fibrosis (Revised Figure S1A,B). In this context, we observed KC death but minimal MoMF infiltration (Revised Figure 4D). Accordingly, deletion of Chi3l1 in MoMFs (Lyz2<sup>∆Chil1</sup>) had no measurable effect on insulin resistance or steatosis, consistent with limited MoMF involvement at this stage. In contrast, the Feldstein study employed a CDAA-HFAT diet that models later-stage MASH with fibrosis. In that setting, Lyz2<sup>∆Chil1</sup> mice showed reduced recruitment of neutrophils and MoMFs, which likely underlies the attenuation of fibrosis and disease severity reported. Together, these data support a model in which KCs and MoMFs play temporally distinct roles during MASLD progression: KCs primarily drive early lipid accumulation and metabolic dysfunction, whereas MoMFs contribute more substantially to inflammation and fibrosis at later stages.

      (3) The conclusions are exclusively based on one MASLD model. I recommend confirming the key findings in a second, ideally a more fibrotic, MASH model.

      We thank the reviewer for this valuable suggestion to validate our findings in an additional MASH model. We have now included data from a methionine- and choline-deficient (MCD) diet–induced MASH model, which exhibits pronounced hepatic lipid accumulation and fibrosis (Revised Figure S6A,B). Consistent with our HFHC results, Clec4f<sup>∆Chil1</sup> mice displayed exacerbated MASH progression in this model, including increased lipid deposition, inflammation, and fibrosis (Revised Figure S6E-G).These findings confirm that CHI3L1 deficiency in Kupffer cells promotes hepatic lipid accumulation and disease progression across distinct MASLD/MASH models.

      (4) Very few human data are being provided (e.g., no work with own human liver samples, work with primary human cells). Thus, the translational relevance of the observations remains unclear.

      We thank the reviewer for this important comment regarding translational relevance. We fully agree that validation in human liver samples would further strengthen our study. However, obtaining tissue from early-stage steatotic livers is challenging due to the asymptomatic nature of this disease stage. Nonetheless, multiple studies have consistently reported Chi3l1 upregulation in human fibrotic and steatotic liver disease (PMID: 31250532, 40352927, 35360517), supporting the clinical significance of our mechanistic findings. We have now expanded the Discussion to highlight these human data and better contextualize our results within the spectrum of human MASLD/MASH progression (Revised manuscript, page 9, line390-394).

      Minor points:

      The authors need to follow the new nomenclature (e.g., MASLD instead of MAFLD, e.g., in Figure 1).

      "MASLD" used throughout.

      We thank the reviewers for their rigorous critique again. We thank eLife for fostering an environment of fairness and transparency that enables authors to communicate openly and present their data honestly.

      Reference

      (1) Tran, S. Baba I, Poupel L, et al(2020) Impaired Kupffer Cell Self-Renewal Alters the Liver Response to Lipid Overload during Non-alcoholic Steatohepatitis. Immunity 53, 627-640.

    1. Author response:

      The following is the authors’ response to the original reviews.

      We are grateful for the insightful and constructive feedback received from reviewers. As outlined in our previous response to the public reviews of the manuscript, we have made only minor changes to the manuscript to clarify some points noted by Reviewers 1 and 3. Firstly, we identify the DUB shown in the correlation plot (Fig 3B) - whose knockdown enhances PROTAC sensitivity without significantly altering cell cycle progression - as BAP1. Secondly, we explain in more detail how we selected DUB hits for further study, and thirdly, we acknowledge that the result in Figure 5G is unexpected given prevailing knowledge in the field.

      Please see below the detailed list of changes we have made to the manuscript.

      In response to Reviewer 1 (Point 2 of public review and Point 2 in recommendations to author)

      We have labelled one of the hits (as BAP1) in Figure 3B

      In response to Reviewer 1 (Point 2 of public review and Point 2 in recommendations to author) and Reviewer 3 (Point 6 in recommendations to authors)

      We have rewritten our description of Figure 3 in order to make clarifications about how we selected which hits to take forwards in our study

      In response to Reviewer 3 (Point 1 in the recommendation to authors)

      We corrected a typo in the first subtitle of the results section

      In response to Reviewer 3 (Point 2 in the recommendation to authors)

      We added information requested about how we selected our top hits

      In response to Reviewer 1 (Point 4 in public review and Point 4 in recommendation to authors)

      We pointed out the seemingly contradictory nature of the UCHL5 result in Figure 5G for the reader

      All of the changes have been aimed at clarifying our narrative, without any change to data content, analysis or interpretation, and we hope these improvements can be agreed by editorial review.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Wang, Po-Kai, et al., utilized the de novo polarization of MDCK cells cultured in Matrigel to assess the interdependence between polarity protein localization, centrosome positioning, and apical membrane formation. They show that the inhibition of Plk4 with Centrinone does not prevent apical membrane formation, but does result in its delay, a phenotype the authors attribute to the loss of centrosomes due to the inhibition of centriole duplication. However, the targeted mutagenesis of specific centrosome proteins implicated in the positioning of centrosomes in other cell types (CEP164, ODF2, PCNT, and CEP120) did not affect centrosome positioning in 3D cultured MDCK cells. A screen of proteins previously implicated in MDCK polarization revealed that the polarity protein Par-3 was upstream of centrosome positioning, similar to other cell types.

      Strengths:

      The investigation into the temporal requirement and interdependence of previously proposed regulators of cell polarization and lumen formation is valuable to the community. Wang et al., have provided a detailed analysis of many of these components at defined stages of polarity establishment. Furthermore, the generation of PCNT, p53, ODF2, Cep120, and Cep164 knockout MDCK cell lines is likely valuable to the community.

      Weaknesses:

      Additional quantifications would highly improve this manuscript, for example it is unclear whether the centrosome perturbation affects gamma tubulin levels and therefore microtubule nucleation, it is also not clear how they affect the localization of the trafficking machinery/polarity proteins. For example, in Figure 4, the authors measure the intensity of Gp134 at the apical membrane initiation site following cytokinesis, but there is no measure of Gp134 at the centrosome prior to this.

      We thank the reviewer for this important suggestion. Previous studies have shown that genes encoding appendage proteins and CEP120 do not regulate γ-tubulin recruitment to centrosomes (Betleja, Nanjundappa, Cheng, & Mahjoub, 2018; Vasquez-Limeta & Loncarek, 2021). Although the loss of PCNT reduces γ-tubulin levels, this reduction is partially compensated by AKAP450. Even in the case of PCNT/AKAP450 double knockouts, low levels of γ-tubulin remain at the centrosome (Gavilan et al., 2018), suggesting that it is difficult to completely eliminate γ-tubulin by perturbing centrosomal genes alone.

      To directly address this question, in the revised manuscript (Page 8, Paragraph 4; Figure 4—figure supplement 3), we employed a recently reported method to block γ-tubulin recruitment by co-expressing two constructs: the centrosome-targeting carboxy-terminal domain (C-CTD) of CDK5RAP2 and the γ-tubulin-binding domain of NEDD1 (N-gTBD). This approach effectively depleted γ-tubulin and abolished microtubule nucleation at the centrosome (Vinopal et al., 2023). Interestingly, despite the reduced efficiency of apical vesicle trafficking, these cells were still able to establish polarity, with centrioles positioned apically. These results suggest that microtubule nucleation at the centrosomes (centrosomal microtubules) facilitates—but is not essential for—polarity establishment.

      Regarding Figure 4, we assume the reviewer was referring to Gp135 rather than Gp134. In the revised manuscript (Page 8, Paragraph 2; Figure 4I), we observed a slight decrease in Gp135 intensity near PCNT-KO centrosomes at the pre-Abs stage. However, its localization at the AMIS following cytokinesis remained unaffected. These results suggest that the loss of PCNT has a limited impact on Gp135 localization. 

      Reviewer #2 (Public review):

      Summary:

      The authors decoupled several players that are thought to contribute to the establishment of epithelial polarity and determined their causal relationship. This provides a new picture of the respective roles of junctional proteins (Par3), the centrosome, and endomembrane compartments (Cdc42, Rab11, Gp135) from upstream to downstream.

      Their conclusions are based on live imaging of all players during the early steps of polarity establishment and on the knock-down of their expression in the simplest ever model of epithelial polarity: a cell doublet surrounded by ECM.

      The position of the centrosome is often taken as a readout for the orientation of the cell polarity axis. There is a long-standing debate about the actual role of the centrosome in the establishment of this polarity axis. Here, using a minimal model of epithelial polarization, a doublet of daugthers MDCK cultured in Matrigel, the authors made several key observations that bring new light to our understanding of a mechanism that has been studied for many years without being fully explained:

      (1) They showed that centriole can reach their polarized position without most of their microtubule-anchoring structures. These observations challenge the standard model according to which centrosomes are moved by the production and transmission of forces along microtubules.

      (2) However) they showed that epithelial polarity can be established in the absence of a centriole.

      (3) (Somehow more expectedly) they also showed that epithelial polarity can't be established in the absence of Par3.

      (4) They found that most other polarity players that are transported through the cytoplasm in lipid vesicles, and finally fused to the basal or apical pole of epithelial cells, are moved along an axis which is defined by the position of centrosome and orientation of microtubules.

      (5) Surprisingly, two non-daughter cells that were brought in contact (for 6h) could partially polarize by recruiting a few Par3 molecules but not the other polarity markers.

      (6) Even more surprisingly, in the absence of ECM, Par 3 and centrosomes could move to their proper position close to the intercellular junction after cytokinesis but other polarity markers (at least GP135) localized to the opposite, non-adhesive, side. So the polarity of the centrosome-microtubule network could be dissociated from the localisation of GP135 (which was believed to be transported along this network).

      Strengths:

      (1) The simplicity and reproducibility of the system allow a very quantitative description of cell polarity and protein localisation.

      (2) The experiments are quite straightforward, well-executed, and properly analyzed.

      (3) The writing is clear and conclusions are convincing.

      Weaknesses:

      (1) The simplicity of the system may not capture some of the mechanisms involved in the establishment of cell polarity in more physiological conditions (fluid flow, electrical potential, ion gradients,...).

      We agree that certain mechanisms may not be captured by this simplified system. However, the model enables us to observe intrinsic cellular responses, minimize external environmental variables, and gain new insights into how epithelial cells position their centrosomes and establish polarity. 

      (2) The absence of centriole in centrinone-treated cells might not prevent the coalescence of centrosomal protein in a kind of MTOC which might still orient microtubules and intracellular traffic. How are microtubules organized in the absence of centriole? If they still form a radial array, the absence of a centriole at the center of it somehow does not conflict with classical views in the field.

      Previous studies have shown that in the absence of centrioles, centrosomal proteins can relocate to alternative microtubule-organizing centers (MTOCs), such as the Golgi apparatus (Gavilan et al., 2018). Furthermore, centriole loss leads to increased nucleation of non-centrosomal microtubules (Martin, Veloso, Wu, Katrukha, & Akhmanova, 2018). However, these microtubules typically do not form the classical radial array or a distinct star-like organization. 

      While this non-centrosomal microtubule network can still support polarity establishment, it does so less efficiently—similar to what is observed in p53-deficient cells undergoing centriole-independent mitosis (Meitinger et al., 2016). Thus, although the absence of centrioles does not completely prevent microtubule-based organization or polarity establishment, it impairs their spatial coordination and reduces overall efficiency compared to a centriole-centered microtubule-organizing center (MTOC). 

      (3) The mechanism is still far from clear and this study shines some light on our lack of understanding. Basic and key questions remain:

      (a) How is the centrosome moved toward the Par3-rich pole? This is particularly difficult to answer if the mechanism does not imply the anchoring of MTs to the centriole or PCM.

      Previous studies have shown that Par3 interacts with dynein, potentially anchoring it at the cell cortex (Schmoranzer et al., 2009). This interaction enables dynein, a minus-enddirected motor, to exert pulling forces on microtubules, thereby promoting centrosome movement toward the Par3-enriched pole.

      In our experiments (Figure 4), we attempted to disrupt centrosomal microtubule nucleation by knocking out multiple genes involved in centrosome structure and function, including ODF2 and PCNT. Under these perturbations, γ-tubulin still remained detectable at the centrosome, and we were unable to completely eliminate centrosomal microtubules. 

      To address this question more directly, we employed a strategy to deplete γ-tubulin from centrosomes by co-expressing the centrosome-targeting C-terminal domain (C-CTD) of CDK5RAP2 and the γ-tubulin-binding domain of NEDD1 (N-gTBD). As shown in the new data of the revised manuscript (Page 8, Paragraph 4; Figure 4—figure supplement 3), this approach effectively depleted γ-tubulin from centrosomes, thereby abolishing microtubule nucleation at the centrosome. 

      Surprisingly, even under these conditions, centrioles remained apically positioned (Page 8, Paragraph 4; Figure 4—figure supplement 3), indicating that centrosomal microtubules are not essential for centrosome movement during polarization.

      Given these findings, we agree that the precise mechanism by which the Par3-enriched cortex attracts or guides centrosome movement remains unclear. Although dynein–Par3 interactions may contribute, further studies are needed to elucidate how centrosome repositioning occurs in the absence of microtubule-based pulling forces from the centrosome itself.

      (b) What happens during cytokinesis that organises Par3 and intercellular junction in a way that can't be achieved by simply bringing two cells together? In larger epithelia cells have neighbours that are not daughters, still, they can form tight junctions with Par3 which participates in the establishment of cell polarity as much as those that are closer to the cytokinetic bridge (as judged by the overall cell symmetry). Is the protocol of cell aggregation fully capturing the interaction mechanism of non-daughter cells?

      We speculate that a key difference between cytokinesis and simple cell-cell contact lies in the presence or absence of actomyosin contractility during the process of cell division. Specifically, contraction of the cytokinetic ring generates mechanical forces between the two daughter cells, which are absent when two non-daughter cells are simply brought together. While adjacent epithelial cells can indeed form tight junctions and recruit Par3, the lack of shared cortical tension and contractile actin networks between non-daughter cells may lead to differences in how polarity is initiated. This mechanical input during cytokinesis may serve as an organizing signal for centrosome positioning. This idea is supported by recent work showing that the actin cytoskeleton can influence centrosome positioning (Jimenez et al., 2021), suggesting that contractile actin structures formed during cytokinesis may contribute to spatial organization in a manner that cannot be replicated by simple aggregation. 

      In our experiments, we simply captured two cells that were in contact within Matrigel. We cannot say for sure that it captures all the interaction mechanisms of non-daughter cells, but it does provide a contrast to daughter cells produced by cytokinesis. 

      Reviewer #3 (Public review):

      Here, Wang et al. aim to clarify the role of the centrosome and conserved polarity regulators in apical membrane formation during the polarization of MDCK cells cultured in 3D. Through well-presented and rigorous studies, the authors focused on the emergence of polarity as a single MDCK cell divided in 3D culture to form a two-cell cyst with a nascent lumen. Focusing on these very initial stages, rather than in later large cyst formation as in most studies, is a real strength of this study. The authors found that conserved polarity regulators Gp135/podocalyxin, Crb3, Cdc42, and the recycling endosome component Rab11a all localize to the centrosome before localizing to the apical membrane initiation site (AMIS) following cytokinesis. This protein relocalization was concomitant with a repositioning of centrosomes towards the AMIS. In contrast, Par3, aPKC, and the junctional components E-cadherin and ZO1 localize directly to the AMIS without first localizing to the centrosome. Based on the timing of the localization of these proteins, these observational studies suggested that Par3 is upstream of centrosome repositioning towards the AMIS and that the centrosome might be required for delivery of apical/luminal proteins to the AMIS.

      To test this hypothesis, the authors generated numerous new cell lines and/or employed pharmacological inhibitors to determine the hierarchy of localization among these components. They found that removal of the centrosome via centrinone treatment severely delayed and weakened the delivery of Gp135 to the AMIS and single lumen formation, although normal lumenogenesis was apparently rescued with time. This effect was not due to the presence of CEP164, ODF2, CEP120, or Pericentrin. Par3 depletion perturbed the repositioning of the centrosome towards the AMIS and the relocalization of the Gp135 and Rab11 to the AMIS, causing these proteins to get stuck at the centrosome. Finally, the authors culture the MDCK cells in several ways (forced aggregation and ECM depleted) to try and further uncouple localization of the pertinent components, finding that Par3 can localize to the cell-cell interface in the absence of cell division. Par3 localized to the edge of the cell-cell contacts in the absence of ECM and this localization was not sufficient to orient the centrosomes to this site, indicating the importance of other factors in centrosome recruitment.

      Together, these data suggest a model where Par3 positions the centrosome at the AMIS and is required for the efficient transfer of more downstream polarity determinants (Gp135 and Rab11) to the apical membrane from the centrosome. The authors present solid and compelling data and are well-positioned to directly test this model with their existing system and tools. In particular, one obvious mechanism here is that centrosome-based microtubules help to efficiently direct the transport of molecules required to reinforce polarity and/or promote lumenogenesis. This model is not really explored by the authors except by Pericentrin and subdistal appendage depletion and the authors do not test whether these perturbations affect centrosomal microtubules. Exploring the role of microtubules in this process could considerably add to the mechanisms presented here. In its current state, this paper is a careful observation of the events of MCDK polarization and will fill a knowledge gap in this field. However, the mechanism could be significantly bolstered with existing tools, thereby elevating our understanding of how polarity emerges in this system.

      We agree that further exploration of microtubule dynamics could strengthen the mechanistic framework of our study. In our initial experiments, we disrupted centrosome function through genetic perturbations (e.g., knockout of PCNT, CEP120, CEP164, and ODF2). However, consistent with previous reports (Gavilan et al., 2018; Tateishi et al., 2013), we found that single-gene deletions did not completely eliminate centrosomal microtubules. Furthermore, imaging microtubule organization in 3D culture presents technical challenges. Due to the increased density of microtubules during cell rounding, we were unable to obtain clear microtubule filament structures—either using α-tubulin staining in fixed cells or SiR-tubulin labeling in live cells. Instead, the signal appeared diffusely distributed throughout the cytosol.

      To overcome this, we employed a recently reported approach by co-expressing the centrosome-targeting carboxy-terminal domain (C-CTD) of CDK5RAP2 and the γtubulin-binding domain (gTBD) of NEDD1 to completely deplete γ-tubulin and abolish centrosomal microtubule nucleation (Vinopal et al., 2023). In our new data presented in the revised manuscript (Page 8, Paragraph 4; Figure 4—figure supplement 3), we found that cells lacking centrosomal microtubules were still able to polarize and position the centrioles apically. However, the efficiency of polarized transport of Gp135 vesicles to the apical membrane was reduced. These findings suggest that centrosomal microtubules are not essential for polarity establishment but may contribute to efficient apical transport. 

      Reference

      Betleja, E., Nanjundappa, R., Cheng, T., & Mahjoub, M. R. (2018). A novel Cep120-dependent mechanism inhibits centriole maturation in quiescent cells. Elife, 7. doi:10.7554/eLife.35439

      Gavilan, M. P., Gandolfo, P., Balestra, F. R., Arias, F., Bornens, M., & Rios, R. M. (2018). The dual role of the centrosome in organizing the microtubule network in interphase. EMBO Rep, 19(11). doi:10.15252/embr.201845942

      Jimenez, A. J., Schaeffer, A., De Pascalis, C., Letort, G., Vianay, B., Bornens, M., . . . Thery, M. (2021). Acto-myosin network geometry defines centrosome position. Curr Biol, 31(6), 1206-1220 e1205. doi:10.1016/j.cub.2021.01.002

      Martin, M., Veloso, A., Wu, J., Katrukha, E. A., & Akhmanova, A. (2018). Control of endothelial cell polarity and sprouting angiogenesis by non-centrosomal microtubules. Elife, 7. doi:10.7554/eLife.33864

      Meitinger, F., Anzola, J. V., Kaulich, M., Richardson, A., Stender, J. D., Benner, C., . . . Oegema, K. (2016). 53BP1 and USP28 mediate p53 activation and G1 arrest after centrosome loss or extended mitotic duration. J Cell Biol, 214(2), 155-166. doi:10.1083/jcb.201604081

      Schmoranzer, J., Fawcett, J. P., Segura, M., Tan, S., Vallee, R. B., Pawson, T., & Gundersen, G. G. (2009). Par3 and dynein associate to regulate local microtubule dynamics and centrosome orientation during migration. Curr Biol, 19(13), 1065-1074. doi:10.1016/j.cub.2009.05.065

      Tateishi, K., Yamazaki, Y., Nishida, T., Watanabe, S., Kunimoto, K., Ishikawa, H., & Tsukita, S. (2013). Two appendages homologous between basal bodies and centrioles are formed using distinct Odf2 domains. J Cell Biol, 203(3), 417-425. doi:10.1083/jcb.201303071

      Vasquez-Limeta, A., & Loncarek, J. (2021). Human centrosome organization and function in interphase and mitosis. Semin Cell Dev Biol, 117, 30-41. doi:10.1016/j.semcdb.2021.03.020

      Vinopal, S., Dupraz, S., Alfadil, E., Pietralla, T., Bendre, S., Stiess, M., . . . Bradke, F. (2023). Centrosomal microtubule nucleation regulates radial migration of projection neurons independently of polarization in the developing brain. Neuron, 111(8), 1241-1263 e1216. doi:10.1016/j.neuron.2023.01.020.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Figures:

      (1) Figure 3 B+C - Although in comparison to Figure 2 it appears the p53 mutation does not affect θN-C, or Lo-c. the figure would benefit from direct comparison to control cells.

      We appreciate your suggestion to improve the clarity of the figure. In response, we have revised Figure 3B+C to include control cell data, allowing for clearer side-by-side comparisons in the updated figures. 

      (2) Figure 3D - Clarify if both were normalized to time point 0:00 of the p53 KO. The image used appears that Gp135 intensity increases substantially between 0:00 and 0:15 in the figure, but the graph suggests that the intensity is the same if not slightly lower.

      Figure 3D – The data were normalized to the respective 0:00 time point for each condition. Because the intensity profile was measured along a line connecting the two nuclei, Gp135 signal could only be detected if it appeared along this line. However, the images shown are maximum-intensity projections, meaning that Gp135 signals from peripheral regions are projected onto the center of the image. This may create the appearance of increased intensity at certain time points (e.g., Figure 3A, p53-KO + CN, 0:00–0:15). 

      (3) Figure 4A: The diagram does not accurately represent the effect of the mutations, for example, PCNT mutation likely doesn't completely disrupt PCM (given gamma-tubulin is still visible in the staining), but instead results in its disorganization, Cep164 also wouldn't be expected to completely ablate distal appendages.

      Thank you for your comment. We have modified the figure in the revised manuscript (Figure 4A) to more clearly depict the defective DAs. 

      (4) Figure 4 + Supplements: A more in-depth characterization of the mutations would help address the previous comment and strengthen the manuscript. Especially as these components have previously been implicated in centrosome transport.

      Thank you for your valuable suggestion. As noted in previous studies, CEP164 is essential for distal appendage function and basal body docking, with its loss resulting in blocked ciliogenesis (Tanos et al., 2013); CEP120 is required for centriole elongation and distal appendage formation, and its loss also results in blocked ciliogenesis (Comartin et al., 2013; Lin et al., 2013; Tsai, Hsu, Liu, Chang, & Tang, 2019); ODF2 functions upstream in the formation of subdistal appendages, and its loss eliminates these structures and impairs microtubule anchoring (Tateishi et al., 2013); and PCNT functions as a PCM scaffold, necessary for the recruitment of PCM components and for microtubule nucleation at the centrosome (Fong, Choi, Rattner, & Qi, 2008; Zimmerman, Sillibourne, Rosa, & Doxsey, 2004). 

      Given that the phenotypes of these mutants have been well characterized in the literature. Here, we further focus on their roles in centrosome migration and polarized vesicle trafficking within the specific context of our study. 

      (5) Figure 4: It would be interesting to measure the Gp135 intensity at the centrosomes, given that the model proposes it is trafficked from the centrosomes to the AMIS.

      Thank you for your suggestion. We have included measurements of Gp135 intensity at the centrosomes during the Pre-Abs stage in the revised figure (Figure 4I). Our data show no significant differences in Gp135 intensity between wild-type (WT) and CEP164-, ODF2-, or CEP120-knockout (KO) cell lines. However, a slight decrease in Gp135 intensity was observed in PCNT-KO cells. 

      (6) Figure 6F shows that in suspension culture polarity is reversed, however, in Figure 6G gp135 still localizes to the cytokinetic furrow prior to polarity reversal. Given this paper demonstrates Par-3 is upstream of centrosome positioning, it would be important to have temporal data of how Par-3 localizes prior to the ring observed in 6F.

      Thank you for your comment. We have included a temporal analysis of Par3 localization using fixed-cell staining in the revised figure (Figure 6—figure supplement 1D). This analysis shows that Par3 also localizes to the cytokinesis site during the Pre-Abs stage, prior to ring formation observed during the Post-CK stage (Figure 6F). Interestingly, during the Pre-Abs stage, the centrosomes also migrate toward the center of the cell doublets in suspension culture, and Gp135 surrounding the centrosomes is also recruited to a region near the center (Figure 6—figure supplement 1E). These data suggest that Par3 also is initially recruited to the cytokinesis site before polarity reversal, potentially promoting centrosome migration. The main difference from Matrigel culture is the peripheral localization of Par3 and Gp135 in suspension, which is likely due to the lack of external ECM signaling. 

      Results:

      (1) Page 7 Paragraph 1 - consistently use AMIS (Apical membrane initiation site) rather than "the apical site".

      Thank you for your helpful comment. We have revised the manuscript (Page 7, Paragraph 1) and will now use "AMIS" (Apical Membrane Initiation Site) instead of "the apical site" throughout the text. 

      (2) Page 7 Paragraph 4 - A single sentence explaining why the p53 background had to be used for the Cep120 deletion would be beneficial. Did the cell line have a reduced centrosome number? Does this effect apical membrane initiation similar to centrinone?

      We have revised the text (Page 7, Paragraph 4) to clarify that we were unable to generate a CEP120 KO line in p53-WT cells for unknown reasons. CEP120-KO cells have a normal number of centrosome, but their centrioles are shorter. Because this KO line still contains centrioles, the effect is different from centrinone treatment, which results in a complete loss of centrioles. 

      (3) Page 10 paragraph 4 - This paragraph is confusing to read. I understand that in the cysts and epithelial sheet the cytokinetic furrow is apical, therefore a movement towards the AMIS could be due to its coincidence with the furrow. However, the phrasing "....we found that centrosomes move towards the apical membrane initiation site direction before bridge abscission. Taken together these findings indicate the position is strongly associated with the site of cytokinesis but not with the apical membrane" is confusing to the reader.

      We have revised the manuscript (Page 11, paragraph 4) to change the AMIS as the center of the cell doublet. During de novo epithelial polarization, the apical membrane has not yet formed at the Pre-Abs stage. However, at the Pre-Abs stage, the centrosome has already migrated toward the site of cytokinesis, suggesting that centrosome positioning is correlated with the site of cell division. A similar phenomenon occurs in fully polarized epithelial cysts and sheets, where the centrosomes also migrate before bridge abscission. Thus, we propose that the position of the centrosome is closely associated with the site of cytokinesis and is independent of apical membrane formation. 

      Discussion

      (1) Page 11, Paragraph 2 - citations needed when discussing previous studies.

      Thank you for your suggestion. We have included the necessary references to the discussion of the previous studies in the revised manuscript (Page 12, Paragraph 2). 

      (2) Page 12, Paragraph 2 - This section of the discussion would be strengthened by discussing the role of the actomyosin network in defining centrosome position (Jimenez et al., 2021). It seems plausible that the differences observed in the different conditions could be due to altered actomyosin architecture. Especially where the cells haven't undergone cytokinesis.

      We appreciate the suggestion of a role for the actomyosin network in determining centrosome positioning. Recent studies have indeed highlighted the role of the actomyosin network in regulating centrosome centering and off-centering (Jimenez et al., 2021). During the pre-abscission stage of cell division, the actomyosin network undergoes significant dynamic changes, with the contractile ring forming at the center and actin levels decreasing at the cell periphery. In contrast, under aggregated cell conditions—meaning cells that have not undergone division—the actomyosin network does not exhibit such dynamic changes. The loss of actomyosin remodeling may therefore influence whether the centrosome moves. Thus, alterations in actomyosin architecture may contribute to the differences observed under various conditions, particularly when cells have not yet completed cytokinesis. We have revised Paragraph 2 on Page 13 to briefly mention the referenced study and to propose that the actomyosin network may influence centrosome positioning, contributing to our observed results. This addition strengthens the discussion and clarifies our findings. 

      (3) Page 12 paragraph 3 - Given that centrosome translocation during cytokinesis in MDCK cells (this study) appears to be similar to that observed in HeLa cells and the zebrafish Kupffers vesicle (Krishnan et al., 2022) it would be interesting to discuss why Rab11a and PCNT may not be essential to centrosome positioning in MDCK cells.

      Thank you for your insightful comment. We agree that it is interesting that centrosome translocation during cytokinesis in MDCK cells (as observed in our study) is similar to that observed in HeLa cells and zebrafish Kupffer's vesicle (Krishnan et al., 2022). However, there are notable differences between these systems that may help explain why Rab11a and PCNT are not essential for centrosome positioning in MDCK cells.

      Our study used 3D culture of MDCK cells, while the reference study examined adherent culture of HeLa cells. In the adherent culture, cells attached to the culture surface form large actin stress fibers on their basal side, which weakens the actin networks in the apical and intercellular regions. In contrast, the 3D culture system used in our study better preserves cell polarity and the integrity of the actin network, which might contribute to centrosome positioning independent of Rab11a and PCNT. Differences in culture conditions and actin network architecture may explain why Rab11a and PCNT are not required for centrosome positioning in MDCK cells.

      Furthermore, the referenced study focused on Rab11a and PCNT in zebrafish embryos at 3.3–5 hours post-fertilization (hpf), a time point before the formation of the Kupffer’s vesicle. At this stage, the cells they examined may not yet have become epithelial cells, which may also influence the requirement of Rab11a and PCNT for centrosome positioning. We hypothesize that during the pre-abscission stage, centrosome migration toward the cytokinetic bridge occurs primarily in epithelial cells, and that the polarity and centrosome positioning mechanisms in these cells may differ from those in other cell types, such as zebrafish embryos.

      Furthermore, data from Krishnan et al. (2022) suggest that cytokinesis failure in pcnt+/- heterozygous embryos and Rab11a functional-blocked embryos may be due to the presence of supernumerary centrosomes. Consistent with this, our data show that blocking cytokinesis inhibits centrosome movement in MDCK cells. However, in our MDCK cell lines with PCNT or Rab11a knockdown, we did not observe significant cytokinesis failure, and centrosome migration proceeded normally. 

      Reviewer #2 (Recommendations for the authors):

      Suggestions for experiments:

      (1) A description of the organization of microtubules in the absence of centriole, or in the absence of ECM would be interesting to understand how polarity markers end up where you observed them. This easy experiment may significantly improve our understanding of this system.

      Previous studies have shown that in the absence of centrioles, microtubule organization undergoes significant changes. Specifically, the number of non-centrosomal microtubules increases, and these microtubules are not radially arranged, leading to the absence of focused microtubule organizing centers in centriolar-deficient cells (Martin, Veloso, Wu, Katrukha, & Akhmanova, 2018). This disorganized microtubule network reduces the efficiency of vesicle transport during de novo epithelial polarization at the mitotic preabscission stage. 

      In contrast, the organization of microtubules under ECM-free conditions remains less well characterized. Here, we show that while the ECM plays a critical role in establishing the direction of epithelial polarity, it does not influence the positioning of the centrosome, the microtubule-organizing center (MTOC).  

      (2) Would it be possible to knock down ODF2 and pericentrin to completely disconnect the centrosome from microtubules?

      ODF2 is the base of subdistal appendages. When ODF2 is knocked out, it affects the recruitment of all downstream proteins to the subdistal appendages (Mazo, Soplop, Wang, Uryu, & Tsou, 2016). One study has shown that ODF2 knockout cells almost completely lost subdistal appendage structures and significantly reduced the microtubule asters surrounding the centrioles (Tateishi et al., 2013). However, although pericentrin (PCNT) is the main scaffold of the pericentriolar matrix (PCM) of centrosomes, the microtubule organization ability of centrosomes can be compensated by AKAP450, a paralog of PCNT, after PCNT knockout. A previous study has even shown that in cells with a double knockout of PCNT and AKAP450, γ-tubulin can still be recruited to the centrosomes, and centrosomes can still nucleate microtubules (Gavilan et al., 2018). This suggests that there are other proteins or pathways that promote microtubule nucleation on centrosomes. We are unsure whether the triple knockout of ODF2, PCNT, and AKAP450 can completely disconnect the centrosome from microtubules. However, a recent study reported a simpler approach involving the expression of dominant-negative fragments of the γ-tubulinbinding protein NEDD1 and the activator CDK5RAP2 at the centrosome (Vinopal et al., 2023). In our revised manuscript (Page 8, Paragraph 4; Figure 4—figure supplement 3), we applied this strategy, which resulted in the depletion of nearly all γ-tubulin from the centrosome. This indicates a strong suppression of centrosomal microtubule nucleation and an effective disconnection of the centrosome from the microtubule network. 

      (3) The study does not distinguish the role of cytokinesis from the role of tight junctions, which form only after cytokinesis and not simply by bringing cells into contact. Would it be feasible and interesting to study the polarization after cytokinesis in cells that could not form tight junctions (due to the absence of Ecad or ZO1 for example)?

      Studying cell polarization after cytokinesis in cells unable to form tight junctions is a promising area of research.

      Recent studies have shown that mouse embryonic stem cells (mESCs) cultured in Matrigel can form ZO-1-labelled tight junctions at the midpoint of cell–cell contact even in the absence of cell division. However, in the absence of E-cadherin, ZO-1 localization is significantly impaired. Interestingly, despite the loss of E-cadherin, the Golgi apparatus and centrosomes remain oriented toward the cell–cell interface (Liang, Weberling, Hii, Zernicka-Goetz, & Buckley, 2022). These findings suggest that cell polarity can be maintained independently of tight junction formation, highlighting the potential value of studying cell polarization that lack tight junctions.

      Furthermore, while studies have explored the effects of knocking down tight junction components such as JAM-A and Cingulin on lumen formation in MDCK 3D cultures (Mangan et al., 2016; Tuncay et al., 2015), the role of ZO-1 in this context remains underexplored. Cingulin knockdown has been shown to disrupt endosome targeting and the formation of the AMIS, while both JAM-A and Cingulin knockdown result in actin accumulation at multiple points, leading to the formation of multi-lumen structures rather than a reversal of polarity. However, previous research has not specifically investigated centrosome positioning in JAM-A and Cingulin knockdown cells, an area that could provide valuable insights into how polarity is maintained in the absence of tight junctions. 

      Writing details:

      (1) The migration of the centrosome in the absence of appendages or PCM is proposed to be ensured by compensatory mechanisms ensuring the robustness of microtubule anchoring to the centrosome. It could also be envisaged that the centrosome motion does not require this anchoring and that other yet unknown moving mechanisms, based on an actin network for example, might exist.

      Thank you for your valuable comments. We agree that there may indeed be some unexpected mechanisms that allow centrosomes to move independently of microtubule anchoring to the centrosome, such as mechanisms based on actin filaments or noncentrosomal microtubules; these mechanisms are worth further investigation.

      In response to your suggestion, in the Paragraph 5 of the discussion section, we further clarified that while a microtubule anchoring mechanism might be one explanation, other mechanisms could also influence centrosome movement in the absence of appendages or PCM. Additionally, we revised the Paragraph 4 regarding the possibility of actin network-driven centrosome movement and emphasized the importance of future research for a deeper understanding of these processes. 

      (2) The actual conclusion of the study of Martin et al (eLife 2018) is not simply that centrosome is not involved in cell polarization but that it hinders cell polarization!

      Thank you for your valuable feedback. We agree with the findings of Martin et al. (eLife 2018) that centrosome is not irrelevant to cell polarity, but rather they inhibit cell polarization. Therefore, we have revised the manuscript (Page 2, Paragraph 2) to more accurately reflect this viewpoint. 

      (3) This study recalls some conclusions of the study by Burute et al (Dev Cell 2017), in particular the role of Par3 in driving centrosome toward the intercellular junction of daughter cells after cytokinesis. It would be welcome to comment on the results of this study in light of their work.

      Thank you for your valuable feedback. The study by Burute et al. (Dev Cell, 2017) showed that in micropattern-cultures of MCF10A cells, the cells exhibit polarity and localize their centrosomes towards the intercellular junction, while downregulation of Par3 gene expression disrupts this centrosome positioning. This result is similar to our findings in 3D cultured MDCK cells and consistent with previous studies in C. elegans intestinal cells and migrating NIH 3T3 cells (Feldman & Priess, 2012; Schmoranzer et al., 2009), indicating that Par3 indeed influences centrosome positioning in different cellular systems. However, Par3 does not directly localize to the centrosome; rather, it localizes to the cell cortex or cell-cell junctions. Therefore, Par3 likely regulates centrosome positioning through other intermediary molecules or mechanisms, but the specific mechanism remains unclear and requires further investigation. 

      (4) Could the term apico-basal be used in the absence of a basement membrane to form a basal pole?

      We understand that using the term "apico-basal" in the absence of a basement membrane might raise some questions. Traditionally, the apico-basal axis refers to the polarity of epithelial cells, where the apical surface faces the lumen or external environment, and the basal surface is oriented toward the basement membrane. However, in the absence of a basement membrane, such as in certain in vitro systems or under specific experimental conditions, polarity along a similar axis can still be observed. In such cases, the term "apico-basal" can still be used to describe the polarity between the apical domain and the region where it contacts the substrate or adjacent cells. 

      (5) The absence of centrosome movement to the intercellular bridge in spread cells in culture is not so surprising considering the work of Lafaurie-Janvore et al (Science 2018) about the role of cell spreading in the regulation of bridge tension and abscission delay.

      Thank you for your valuable comment. Indeed, previous studies have shown that in some cell types, the centrosome does move toward the intercellular bridge in spread cells (Krishnan et al., 2022; Piel, Nordberg, Euteneuer, & Bornens, 2001), but other studies have suggested that this movement may not be significant and it may not occur in universally observed across all cell types (Jonsdottir et al., 2010). In our study, we aim to demonstrate that this phenomenon is more pronounced in 3D culture systems compared to 2D spread cell culture systems. Previous studies and our work have observed that centrosome migration occurs during the pre-abscission stage, but whether this migration is directly related to cytokinetic bridge tension or the time of abscission remains an open question. Further research is needed to explore the potential relationship between centrosome positioning, cytokintic bridge tension, and the timing of abscission. 

      (6) GP135 (podocalyxin) has been proposed to have anti-adhesive/lubricant properties (hence its pro-invasive effect). Could it be possible that once localized at the cell surface it is systematically moved away from regions that are anchored to either the ECM or adjacent cells? So its localization away from the centrosome in an ECM-free experiment would not be a consequence of defective targeting but relocalization after reaching the plasma membrane?

      Thank you for your valuable comment. We agree that GP135 may indeed move directly across the cell surface, away from the region where it interacts with the ECM or adjacent cells. This re-localization could be due to its anti-adhesive or lubricating properties, which may facilitate its displacement from these adhesive sites. To validate this, it is necessary to employ higher-resolution real-time imaging system to observe the dynamic behavior of GP135 on the cell surface.

      However, this does not contradict our main conclusion. Under suspension culture conditions without ECM, the centrosome positioning in cell doublets is indeed decoupled from apical membrane orientation. This suggests that the localization of the centrosome and the apical membrane is regulated by different mechanisms. Specifically, the GP135 protein tends to accumulate away from areas of contact with the ECM or adjacent cells, possibly through movement within the cell membrane or by recycling endosome transport. In contrast, centrosome positioning is closely related to the cytokinesis site. Our study clearly elucidates the differences between these two polarity properties. 

      Reviewer #3 (Recommendations for the authors):

      Major:

      (1) To me, a clear implication of these studies is that Gp135, Rab11, etc. are delivered to the AMIS on centrosomal microtubules. The authors do not explore this model except to say that depletion of SD appendage or pericentrin has no effect on the protein relocalization to the AMIS. However, the authors do not observe microtubule association with the centrosome in these KO conditions. This analysis is imperative to interpret existing results since these are new KO conditions in this cell/culture system and parallel pathways (e.g. CDK5RAP2) are known to contribute to microtubule association with the centrosome. An ability to comment on the mechanism by which the centrosome contributes to the efficiency of polarization would greatly enhance the paper.

      Microtubule requirement could also be tested in numerous additional ways requiring varying degrees of new experiments:

      (a) faster live cell imaging at abscission to see if the deposition of those components appears to traffic on MTs;

      (b) live cell imaging with microtubules (e.g. SPY-tubulin) and/or EB1 to determine the origin and polarity of microtubules at the pertinent stages;

      For (a) and (b), because the cells were cultured in Matrigel, they tended to be round up, with a dense internal structure that made observation difficult. In contrast, under adherent culture conditions, the cells were flattened with a more dispersed internal structures, making them easier to observe. We had previously used SPY-tubulin to label microtubules for live cell imaging; however, due to the dense microtubule structure in 3D culture, the image contrast was reduced, and we could not clearly observe the microtubule network within the cells. 

      (c) acute nocodazole treatment at abscission to determine the effect on protein localization.

      Regarding the method of using nocodazole to study microtubule requirements at the abscission stage, we believe that nocodazole treatment may lead to cytokinesis failure. Cell division failure results in the formation of binucleated cells, which are unable to establish cell polarity. Furthermore, nocodazole treatment cannot distinguish between centrosomal and non-centrosomal microtubules, making it unsuitable for studying the specific role of centrosomal microtubules in this process.

      In our new data (Figure 4-figure supplementary 3) presented in the revised manuscript, we employed a recently reported method by co-expressing of the centrosome-targeting carboxy-terminal domain (C-CTD) of CDK5RAP2 and the γ-tubulin-binding domain (gTBD) of NEDD1 to completely deplete γ-tubulin and abolish centrosomal microtubule nucleation (Vinopal et al., 2023). We found that cells lacking centrosomal microtubules were still able to polarize and position the centrioles apically. However, the efficiency of polarized transport of Gp135 vesicles to the apical membrane was reduced. These findings suggest that centrosomal microtubules are not essential for polarity establishment but may contribute to facilitate efficient apical transport. 

      (2) Similar to the expanded analysis of the role of microtubules in this system, it would be excellent if the author could expand on the role of Par3 and the centrosome, although this reviewer recognizes that the authors have already done substantial work. For example, what are the consequences of Gp135 and/or Rab11 getting stuck at the centrosome? Do the authors have any later images to determine when and if these components ever leave the centrosome? Existing literature focuses on the more downstream consequence of Par3 removal on single-lumen formation. 

      Similarly, could the authors expand on the description of polarity disruption following centrinone treatment? It is clear that Gp135 recruitment is disrupted, but how and when do things get fixed and what else is disrupted at the very earliest stages of AMIS formation? The authors have an excellent opportunity to really expand on what is known about the requirements for these conserved components.

      Regarding the use of centrinone in treatment, we speculate that Gp135 can still accumulate at the AMIS over time, although the efficiency of its recruitment may be reduced.

      Furthermore, under similar conditions, other apical membrane components (such as the Crumbs3 protein) may exhibit similar characteristics to Gp135 protein. 

      (3) Perhaps satisfying both of the above asks, could the authors do a faster time-lapse at the relevant time points, i.e. as proteins are being recruited to the AMIS (time points between 1Aiv and v)? This type of imaging again might help shed light on the mechanism.

      We believe the above questions are very important and may require further experimental verification in the future. 

      Minor:

      (1) What is the green patch of Gp135 in Figure 2A that does not colocalize with the centrosome? Is this another source of Gp135 that is being delivered to the AMIS? This type of patch is also visible in Figure 3A 15 and 30-minute panels.

      During mitosis, membrane-composed organelles such as the Golgi apparatus are typically dispersed throughout the cytoplasm. However, during the pre-abscission stage, these organelles begin to reassemble and cluster around the centrosome. Furthermore, they also accumulate in the region between the nucleus and the cytokinetic bridge, corresponding to the “patch” mentioned in Figure 2A. 

      Live cell imaging results showed that this Gp135 patch initially appears in a region not associated with the centrosome. Subsequently, they were either directly transported to the AMIS or fused with the centrosome-associated Gp135 and transported together. Notably, this patch was only observed when Gp135 was overexpressed in cells. No such distinct protein patches were observed when staining endogenous Gp135 protein (Figure 1A), suggesting that overexpression of Gp135 protein may lead to a localized increase in its concentration in that region. 

      (2) I am confused by the "polarity index" quantification as this appears to just be a nucleus centrosome distance measurement and wouldn't, for example, distinguish if the centrosomes separated from the nucleus but were on the basal side of the cell.

      The position of the centrosome within the cell (i.e., its distance from the nucleus) can indeed serve as an indicator of cell polarity (Burute et al., 2017). We acknowledge that this quantitative method does not directly capture the specific direction in which the centrosome deviates from the cell center. To address this limitation, we have incorporated information about the angle between the nucleus and the centrosome, which allows for a more accurate description of changes in cell polarity (Rodriguez-Fraticelli, Auzan, Alonso, Bornens, & Martin-Belmonte, 2012). 

      (3) How is GP135 "at AMIS" measured? Is an arbitrary line drawn? This is important later when comparing to centrinone treatment in Figure 3D where the quantification does not seem to accurately capture the enrichment of Gp135 that is seen in the images.

      To measure the expression level of Gp135 in the "AMIS" region of the cell, we first connected the centers of the two cell nuclei in three-dimensional space to form a straight line. Then, we used the Gp135 expression intensity at the midpoint of this line as the representative value for the AMIS region. This method is based on the assumption that the AMIS region is most likely located between the centers of the two cell nuclei. Therefore, this quantitative method provides a standardized assessment tool for comparing Gp135 expression levels under different conditions. 

      (4) The authors reference cell height (p.7) but no data for this measurement are shown

      Thank you for the comment. Although we did not perform quantitative measurements, the differences in cell height are clearly visible in Figure 3E (p53-KO + CN), which visually illustrates this phenomenon. 

      (5) Can the authors comment on the seeming reduction of Par3 in p53 KO cells?

      We did not observe a reduction of Par3 in p53-KO cells in our experiments.

      (6) Can the authors make sense of the E-cad localization: Figure 5, Supplement 2.

      Our study revealed that E-cadherin begins to accumulate at the cell-cell contact sites during the pre-abscission stage. Its appearance is similar to that of ZO-1, which also appears near the cell division site during this phase. Therefore, the behavior of E-cadherin contrasts sharply with that of Gp135, further highlighting the unique trafficking mechanisms of apical membrane proteins during this process. 

      (7) I find the results in Figure 6G puzzling. Why is ECM signaling required for Gp135 recruitment to the centrosome. Could the authors discuss what this means?

      We appreciate the reviewer’s valuable comments and thank you for the opportunity to clarify this point. The data in Figure 6G do not indicate that ECM signaling is required for the recruitment of Gp135 to the centrosome. Rather, our findings suggest that even in the absence of ECM, the centrosomes can migrate to a polarized position similar to that in Matrigel culture. This suggests that centrosome migration and the orientation of the nucleus–centrosome axis may be independent of ECM signaling and are primarily driven by cytokinesis alone. 

      Regarding the localization of Gp135, previous studies have shown that ECM signaling through integrin promotes endocytosis, which is crucial for the internalization of Gp135 from the cell membrane and its subsequent transport to the AMIS (Buckley & St Johnston, 2022). Our study found that, prior to its accumulation at the AMIS, Gp135 transiently localizes around the centrosome. In the absence of ECM, due to reduced endocytosis, Gp135 primarily remains on the cell membrane and does not undergo intracellular trafficking.  

      (8) The authors end the Discussion stating that these studies may have implication for in vivo settings, yet do not discuss the striking similarities to the C. elegans and Drosophila intestine or the findings from any other more observational studies of tubular epithelial systems in vivo (e.g. mouse kidney polarization, zebrafish neuroepithelium, etc.). These models should be discussed.

      Thank you for your valuable comment. Indeed, all types of epithelial tissues or tubular epithelial systems in vivo share some common features during cell division, which have been well-documented across various species. 

      These features include: during interphase, the centrosome is located at the apical surface of the cells; after the cell enters mitosis, the centrosome moves to the lateral side of the cell to regulate spindle orientation; and during cytokinesis, the cleavage furrow ingresses asymmetrically from the basal to the apical side, with the cytokinetic bridge positioned at the apical surface. Our study using MDCK 3D culture and transwell culture systems successfully mimicked these key features, demonstrating that these in vitro models are of significant value for studying cell polarization dynamics. 

      Based on our observations, we speculate that the centrosome may return to the apical surface after anaphase, just before bridge abscission. This is consistent with our findings from studies using MDCK 3D cultures and transwell systems, which showed that the centrosome relocates prior to the final stages of cytokinesis.

      Additionally, we propose that de novo polarization of the kidney tubule in vivo may not solely depend on the aggregation and mesenchymal-epithelial transition (MET) of the metanephric mesenchyme. It may also be related to the cell division process, which triggers centrosome migration and polarized vesicle trafficking. These processes likely contribute to enhancing cell polarization, as we observed in our in vitro models.

      We hope this will further clarity the potential implications of our findings for in vivo model studies, as well as and their broader impact on the field of tubular epithelial cell polarization research. 

      (9) There are several grammatical issues/typos throughout the paper. A careful readthrough is required. For example:

      this sentence makes no sense "that the centrosome acts as a hub of apical recycling endosomes and centrosome migration during cytokinetic pre-abscission before apical membrane components are targeted to the AMIS"

      We carefully reviewed the paper and made necessary revisions to address the issues raised. In particular, we revised certain sentences to improve clarity and readability (Page 5, Paragraph 3). 

      (10) P.8: have been previously reported [to be] involved in MDCK...

      We appreciate the reviewer's valuable suggestions. We have revised the sentence accordingly (Page 9, Paragraph 2). 

      (11) This sentence seems misplaced: "Cultured conditions influence cellular polarization preferences."

      The sentence itself is fine, but to improve the coherence and clarity of the paragraph, we adjusted the paragraph structure and added some transitional phrases (Page 13, Paragraph 1).  

      (12) "Play a downstream role in Par3 recruitment" doesn't make sense, this should just be downstream of Par3 recruitment.

      Thank you for your suggestion. We have revised the wording accordingly, changing it to "downstream of Par3 recruitment" (Page 10, Paragraph 2).  

      Reference

      Buckley, C. E., & St Johnston, D. (2022). Apical-basal polarity and the control of epithelial form and function. Nat Rev Mol Cell Biol, 23(8), 559-577. doi:10.1038/s41580-022-00465-y

      Burute, M., Prioux, M., Blin, G., Truchet, S., Letort, G., Tseng, Q., . . . Thery, M. (2017). Polarity Reversal by Centrosome Repositioning Primes Cell Scattering during Epithelial-to-Mesenchymal Transition. Dev Cell, 40(2), 168-184. doi:10.1016/j.devcel.2016.12.004

      Comartin, D., Gupta, G. D., Fussner, E., Coyaud, E., Hasegan, M., Archinti, M., . . . Pelletier, L. (2013). CEP120 and SPICE1 cooperate with CPAP in centriole elongation. Curr Biol, 23(14), 13601366.

      doi:10.1016/j.cub.2013.06.002

      Feldman, J. L., & Priess, J. R. (2012). A role for the centrosome and PAR-3 in the hand-off of MTOC function during epithelial polarization. Curr Biol, 22(7), 575-582. doi:10.1016/j.cub.2012.02.044

      Fong, K. W., Choi, Y. K., Rattner, J. B., & Qi, R. Z. (2008). CDK5RAP2 is a pericentriolar protein that functions in centrosomal attachment of the gamma-tubulin ring complex. Mol Biol Cell, 19(1), 115-125. doi:10.1091/mbc.e07-04-0371

      Gavilan, M. P., Gandolfo, P., Balestra, F. R., Arias, F., Bornens, M., & Rios, R. M. (2018). The dual role of the centrosome in organizing the microtubule network in interphase. EMBO Rep, 19(11). doi:10.15252/embr.201845942

      Jimenez, A. J., Schaeffer, A., De Pascalis, C., Letort, G., Vianay, B., Bornens, M., . . . Thery, M. (2021). Acto-myosin network geometry defines centrosome position. Curr Biol, 31(6), 1206-1220 e1205. doi:10.1016/j.cub.2021.01.002

      Jonsdottir, A. B., Dirks, R. W., Vrolijk, J., Ogmundsdottir, H. M., Tanke, H. J., Eyfjord, J. E., & Szuhai, K. (2010). Centriole movements in mammalian epithelial cells during cytokinesis. BMC Cell Biol, 11, 34. doi:10.1186/1471-2121-11-34

      Krishnan, N., Swoger, M., Rathbun, L. I., Fioramonti, P. J., Freshour, J., Bates, M., . . . Hehnly, H. (2022). Rab11 endosomes and Pericentrin coordinate centrosome movement during preabscission in vivo. Life Sci Alliance, 5(7). doi:10.26508/lsa.202201362

      Liang, X., Weberling, A., Hii, C. Y., Zernicka-Goetz, M., & Buckley, C. E. (2022). E-cadherin mediates apical membrane initiation site localisation during de novo polarisation of epithelial cavities. EMBO J, 41(24), e111021. doi:10.15252/embj.2022111021

      Lin, Y. N., Wu, C. T., Lin, Y. C., Hsu, W. B., Tang, C. J., Chang, C. W., & Tang, T. K. (2013). CEP120 interacts with CPAP and positively regulates centriole elongation. J Cell Biol, 202(2), 211219. doi:10.1083/jcb.201212060

      Mangan, A. J., Sietsema, D. V., Li, D., Moore, J. K., Citi, S., & Prekeris, R. (2016). Cingulin and actin mediate midbody-dependent apical lumen formation during polarization of epithelial cells. Nat Commun, 7, 12426. doi:10.1038/ncomms12426

      Martin, M., Veloso, A., Wu, J., Katrukha, E. A., & Akhmanova, A. (2018). Control of endothelial cell polarity and sprouting angiogenesis by non-centrosomal microtubules. Elife, 7. doi:10.7554/eLife.33864

      Mazo, G., Soplop, N., Wang, W. J., Uryu, K., & Tsou, M. F. (2016). Spatial Control of Primary Ciliogenesis by Subdistal Appendages Alters Sensation-Associated Properties of Cilia. Dev Cell, 39(4), 424-437. doi:10.1016/j.devcel.2016.10.006

      Piel, M., Nordberg, J., Euteneuer, U., & Bornens, M. (2001). Centrosome-dependent exit of cytokinesis in animal cells. Science, 291(5508), 1550-1553. doi:10.1126/science.1057330

      Rodriguez-Fraticelli, A. E., Auzan, M., Alonso, M. A., Bornens, M., & Martin-Belmonte, F. (2012). Cell confinement controls centrosome positioning and lumen initiation during epithelial morphogenesis. J Cell Biol, 198(6), 1011-1023. doi:10.1083/jcb.201203075

      Schmoranzer, J., Fawcett, J. P., Segura, M., Tan, S., Vallee, R. B., Pawson, T., & Gundersen, G. G. (2009). Par3 and dynein associate to regulate local microtubule dynamics and centrosome orientation during migration. Curr Biol, 19(13), 1065-1074. doi:10.1016/j.cub.2009.05.065

      Tanos, B. E., Yang, H. J., Soni, R., Wang, W. J., Macaluso, F. P., Asara, J. M., & Tsou, M. F. (2013). Centriole distal appendages promote membrane docking, leading to cilia initiation. Genes Dev, 27(2), 163-168. doi:10.1101/gad.207043.112

      Tateishi, K., Yamazaki, Y., Nishida, T., Watanabe, S., Kunimoto, K., Ishikawa, H., & Tsukita, S. (2013). Two appendages homologous between basal bodies and centrioles are formed using distinct Odf2 domains. J Cell Biol, 203(3), 417-425. doi:10.1083/jcb.201303071

      Tsai, J. J., Hsu, W. B., Liu, J. H., Chang, C. W., & Tang, T. K. (2019). CEP120 interacts with C2CD3 and Talpid3 and is required for centriole appendage assembly and ciliogenesis. Sci Rep, 9(1), 6037. doi:10.1038/s41598-019-42577-0

      Tuncay, H., Brinkmann, B. F., Steinbacher, T., Schurmann, A., Gerke, V., Iden, S., & Ebnet, K. (2015). JAM-A regulates cortical dynein localization through Cdc42 to control planar spindle orientation during mitosis. Nat Commun, 6, 8128. doi:10.1038/ncomms9128

      Vinopal, S., Dupraz, S., Alfadil, E., Pietralla, T., Bendre, S., Stiess, M., . . . Bradke, F. (2023). Centrosomal microtubule nucleation regulates radial migration of projection neurons independently of polarization in the developing brain. Neuron, 111(8), 1241-1263 e1216. doi:10.1016/j.neuron.2023.01.020

      Zimmerman, W. C., Sillibourne, J., Rosa, J., & Doxsey, S. J. (2004). Mitosis-specific anchoring of gamma tubulin complexes by pericentrin controls spindle organization and mitotic entry. Mol Biol Cell, 15(8), 3642-3657. doi:10.1091/mbc.e03-11-0796.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Chengjian Zhao et al. focused on the interactions between vascular, biliary, and neural networks in the liver microenvironment, addressing the critical bottleneck that the lack of high-resolution 3D visualization has hindered understanding of these interactions in liver disease.

      Strengths:

      This study developed a high-resolution multiplex 3D imaging method that integrates multicolor metallic compound nanoparticle (MCNP) perfusion with optimized CUBIC tissue clearing. This method enables the simultaneous 3D visualization of spatial networks of the portal vein, hepatic artery, bile ducts, and central vein in the mouse liver. The authors reported a perivascular structure termed the Periportal Lamellar Complex (PLC), which is identified along the portal vein axis. This study clarifies that the PLC comprises CD34⁺Sca-1⁺ dual-positive endothelial cells with a distinct gene expression profile, and reveals its colocalization with terminal bile duct branches and sympathetic nerve fibers under physiological conditions.<br />

      Weaknesses:

      This manuscript is well-written, organized, and informative. However, there are some points that need to be clarified.

      (1) After MCNP-dye injection, does it remain in the blood vessels, adsorb onto the cell surface, or permeate into the cells? Does the MCNP-dye have cell selectivity?

      The experimental results showed that after injection, the MCNP series nanoparticles predominantly remained within the lumens of blood vessels and bile ducts, with their tissue distribution determined by physical perfusion. No diffusion of the dye signal into the surrounding parenchymal tissue was observed, nor was there any evidence of adsorption onto the cell surface or entry into cells. The newly added Supplementary Figure S2A–H further confirmed this feature, demonstrating that the dye signals were strictly confined to the luminal space, clearly delineating the continuous course of blood vessels and the branching morphology of bile ducts. These findings strongly support the conclusion that “MCNP dyes are distributed exclusively within the luminal compartments.”

      Therefore, the MCNP dyes primarily serve as intraluminal tracers within the tissue rather than as labels for specific cell types.

      (2) All MCNP-dyes were injected after the mice were sacrificed, and the mice's livers were fixed with PFA. After the blood flow had ceased, how did the authors ensure that the MCNP-dyes were fully and uniformly perfused into the microcirculation of the liver?

      Thank you for the reviewer’s valuable comments. Indeed, since all MCNP dyes were perfused after the mice were euthanized and blood circulation had ceased, we cannot fully ensure a homogeneous distribution of the dye within the hepatic microcirculation. The vascular labeling technique based on metallic nanoparticle dyes used in this study offers clear imaging, stable fluorescence intensity, and multiplexing advantages; however, it also has certain limitations. The main issue is that the dye distribution within the hepatic parenchyma can be affected by factors such as lobular overlap, local tissue compression, and variations in vascular pathways, resulting in regional inhomogeneity of dye perfusion. This is particularly evident in areas where multiple lobes converge or where anatomical structures are complex, leading to local dye accumulation or over-perfusion.

      In our experiments, we attempted to minimize local blockage or over-perfusion by performing PBS pre-flushing and low-pressure, constant-speed perfusion. Nevertheless, localized dye accumulation or uneven distribution may still occur in lobe junctions or structurally complex regions. Such variation represents one of the methodological limitations. Overall, the dye signals in most samples remained confined to the vascular and biliary lumens, and the distribution pattern was highly reproducible.

      We have addressed this issue in the Discussion section but would like to emphasize here that, although this system has clear advantages, it remains sensitive to anatomical variability in the liver—such as lobular overlap and vascular heterogeneity. At vascular junctions, local perfusion inhomogeneity or dye accumulation may occur; therefore, injection strategies and perfusion parameters should be adjusted according to liver size and vascular condition to improve reproducibility and imaging quality. It should also be noted that the results obtained using this method primarily aim to visualize the overall and fine anatomical structures of the hepatic vascular system rather than to quantitatively reflect hemodynamic processes. In the future, we plan to combine in vivo perfusion or dynamic fluid modeling to further validate the diffusion characteristics of the dyes within the hepatic microcirculation.

      (3) It is advisable to present additional 3D perspective views in the article, as the current images exhibit very weak 3D effects. Furthermore, it would be better to supplement with some videos to demonstrate the 3D effects of the stained blood vessels.

      Thank you for the reviewer’s valuable comments. In response to the suggestion, we have added perspective-rendered images generated from the 3D staining datasets to provide a more intuitive visualization of the spatial morphology of the hepatic vasculature. These images have been included in Figure S2A–J. In addition, we have prepared supplementary videos (available upon request) that dynamically display the three-dimensional distribution of the stained vessels, further enhancing the spatial perception and visualization of the results.

      (4) In Figure 1-I, the authors used MCNP-Black to stain the central veins; however, in addition to black, there are also yellow and red stains in the image. The authors need to explain what these stains are in the legend.

      Thank you for the reviewer’s constructive comment. In Figure 1I, MCNP-Black labels the central vein (black), MCNP-Yellow labels the portal vein (yellow), MCNP-Pink labels the hepatic artery (pink), and MCNP-Green labels the bile duct (green). We have revised the Figure 1 legend to include detailed descriptions of the color signals and their corresponding structures to avoid any potential confusion.

      (5) There is a typo in the title of Figure 4F; it should be "stem cell".

      Thank you for the reviewer’s careful correction. We have corrected the spelling error in the title of Figure 4F to “stem cell” and updated it in the revised manuscript.

      (6) Nuclear staining is necessary in immunofluorescence staining, especially for Figure 5e. This will help readers distinguish whether the green color in the image corresponds to cells or dye deposits.

      We thank the reviewer for the valuable suggestion. We understand that nuclear staining can help determine the origin of fluorescence signals. However, in our three-dimensional imaging system, the deep signal acquisition range after tissue clearing often causes nuclear dyes such as DAPI to generate highly dense and widespread fluorescence, especially in regions rich in vascular structures, which can obscure the fine vascular and perivascular details of interest. Therefore, this study primarily focuses on high-resolution visualization of the spatial architecture of the vascular and biliary systems. We have added an explanation regarding this point in Figures S2I–J.

      Reviewer #2 (Public review):

      Summary:

      The present manuscript of Xu et al. reports a novel clearing and imaging method focusing on the liver. The authors simultaneously visualized the portal vein, hepatic artery, central vein, and bile duct systems by injecting metal compound nanoparticles (MCNPs) with different colors into the portal vein, heart left ventricle, inferior vena cava, and the extrahepatic bile duct, respectively. The method involves: trans-cardiac perfusion with 4% PFA, the injection of MCNPs with different colors, clearing with the modified CUBIC method, cutting 200 micrometer thick slices by vibratome, and then microscopic imaging. The authors also perform various immunostaining (DAB or TSA signal amplification methods) on the tissue slices from MCNP-perfused tissue blocks. With the application of this methodical approach, the authors report dense and very fine vascular branches along the portal vein. The authors name them as 'periportal lamellar complex (PLC)' and report that PLC fine branches are directly connected to the sinusoids. The authors also claim that these structures co-localize with terminal bile duct branches and sympathetic nerve fibers, and contain endothelial cells with a distinct gene expression profile. Finally, the authors claim that PLC-s proliferate in liver fibrosis (CCl4 model) and act as a scaffold for proliferating bile ducts in ductular reaction and for ectopic parenchymal sympathetic nerve sprouting.

      Strengths:

      The simultaneous visualization of different hepatic vascular compartments and their combination with immunostaining is a potentially interesting novel methodological approach.

      Weaknesses:

      This reviewer has several concerns about the validity of the microscopic/morphological findings as well as the transcriptomics results. In this reviewer's opinion, the introduction contains overstatements regarding the potential of the method, there are severe caveats in the method descriptions, and several parts of the Results are not fully supported by the documentation. Thus, the conclusions of the paper may be critically viewed in their present form and may need reconsideration by the authors.

      We sincerely thank the reviewer for the thorough evaluation and constructive comments on our study. We fully understand and appreciate the reviewer’s concerns regarding the methodological validity and interpretation of the results. In response, we have made comprehensive revisions and additions to the manuscript as follows:

      First, we have carefully revised the Introduction and Discussion sections to provide a more balanced description of the methodological potential, removing statements that might be considered overstated, and clarifying the applicable scope and limitations of our approach (see the revised Introduction and Discussion).

      Second, we have substantially expanded the Methods section with detailed information on model construction, imaging parameters, data processing workflow, and technical aspects of the single-cell transcriptomic reanalysis, to enhance the transparency and reproducibility of the study.

      Third, we have added additional references and explanatory notes in the Results section to better support the main conclusions (see Section 6 of the Results).

      Finally, we have rechecked and validated all experimental data, and conducted a verification analysis using an independent single-cell RNA-seq dataset (Figure S6). The results confirm that the morphological observations and transcriptomic findings are consistent and reproducible across independent experiments.

      We believe these revisions have greatly strengthened the reliability of our conclusions and the overall scientific rigor of the manuscript. Once again, we sincerely appreciate the reviewer’s valuable comments, which have been very helpful in improving the logic and clarity of our work.

      Reviewer #3 (Public review):

      Summary:

      In the reviewed manuscript, researchers aimed to overcome the obstacles of high-resolution imaging of intact liver tissue. They report successful modification of the existing CUBIC protocol into Liver-CUBIC, a high-resolution multiplex 3D imaging method that integrates multicolor metallic compound nanoparticle (MCNP) perfusion with optimized liver tissue clearing, significantly reducing clearing time and enabling simultaneous 3D visualization of the portal vein, hepatic artery, bile ducts, and central vein spatial networks in the mouse liver. Using this novel platform, the researchers describe a previously unrecognized perivascular structure they termed Periportal Lamellar Complex (PLC), regularly distributed along the portal vein axis. The PLC originates from the portal vein and is characterized by a unique population of CD34⁺Sca-1⁺ dual-positive endothelial cells. Using available scRNAseq data, the authors assessed the CD34⁺Sca-1⁺ cells' expression profile, highlighting the mRNA presence of genes linked to neurodevelopment, biliary function, and hematopoietic niche potential. Different aspects of this analysis were then addressed by protein staining of selected marker proteins in the mouse liver tissue. Next, the authors addressed how the PLC and biliary system react to CCL4-induced liver fibrosis, implying PLC dynamically extends, acting as a scaffold that guides the migration and expansion of terminal bile ducts and sympathetic nerve fibers into the hepatic parenchyma upon injury.

      The work clearly demonstrates the usefulness of the Liver-CUBIC technique and the improvement of both resolution and complexity of the information, gained by simultaneous visualization of multiple vascular and biliary systems of the liver at the same time. The identification of PLC and the interpretation of its function represent an intriguing set of observations that will surely attract the attention of liver biologists as well as hepatologists; however, some claims need more thorough assessment by functional experimental approaches to decipher the functional molecules and the sequence of events before establishing the PLC as the key hub governing the activity of biliary, arterial, and neuronal liver systems. Similarly, the level of detail of the methods section does not appear to be sufficient to exactly recapitulate the performed experiments, which is of concern, given that the new technique is a cornerstone of the manuscript.

      Nevertheless, the work does bring a clear new insight into the liver structure and functional units and greatly improves the methodological toolbox to study it even further, and thus fully deserves the attention of readers.

      Strengths:

      The authors clearly demonstrate an improved technique tailored to the visualization of the liver vasulo-biliary architecture in unprecedented resolution.

      This work proposes a new biological framework between the portal vein, hepatic arteries, biliary tree, and intrahepatic innervation, centered at previously underappreciated protrusions of the portal veins - the Periportal Lamellar Complexes (PLCs).

      Weaknesses:

      Possible overinterpretation of the CD34+Sca1+ findings was built on re-analysis of one scRNAseq dataset.

      Lack of detail in the materials and methods section greatly limits the usefulness of the new technique to other researchers.

      We thank the reviewer for this important comment. We agree that when conclusions are mainly based on a single dataset, overinterpretation should be avoided. In response to this concern, we have carefully re-evaluated and clearly limited the scope of our interpretation of the scRNA-seq analysis. In addition, we performed a validation analysis using an independent single-cell RNA-seq dataset (see new Figure S6), which consistently confirmed the presence and characteristic transcriptional profile of the periportal CD34⁺Sca1⁺ endothelial cell population. These supplementary analyses strengthen the robustness of our findings and address the reviewer’s concern regarding potential overinterpretation.

      In the revised manuscript, we have also greatly expanded the Materials and Methods section by providing detailed information on sample preparation, imaging parameters, data processing workflow, and single-cell reanalysis procedures. These revisions substantially improve the transparency and reproducibility of our methodology, thereby enhancing the usability and reference value of this technique for other researchers.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Introduction

      (1) In general, the Introduction is very lengthy and repetitive. It needs extensive shortening to a maximum of 2 A4 pages.

      We thank the reviewer for the valuable suggestions. We have thoroughly condensed and restructured the Introduction, removing redundant content and merging related paragraphs to make the theme more focused and the logic clearer. The revised Introduction has been shortened to within two A4 pages, emphasizing the scientific question, innovation, and technical approach of the study.

      (2) Please correct this erroneous sentence:

      '...the liver has evolved the most complex and densely n organized vascular network in the body, consisting primarily of the portal vein system, central vein system, hepatic artery system, biliary system, and intrahepatic autonomic nerve network [6, 7].'

      We thank the reviewer for pointing out this spelling error. The revised sentence is as follows:

      “…the liver has evolved the most complex and densely organized ductal-vascular network in the body, consisting primarily of the portal vein system, central vein system, hepatic artery system, biliary system, and intrahepatic autonomic nerve network [6, 7].”

      (3) '...we achieved a 63.89% improvement in clearing efficiency and a 20.12% increase in tissue transparency'

      Please clarify what you exactly mean by 'clearing efficiency' and 'increased tissue transparency'.

      We thank the reviewer for the valuable comments and have clarified the relevant terminology in the revised manuscript.

      “Clearing efficiency” refers to the improvement in the time required for the liver tissue to become completely transparent when treated with the optimized Liver-CUBIC protocol (40% urea + H₂O₂), compared with the conventional CUBIC method. In this study, the clearing time was reduced from 9 days to 3.25 days, representing a 63.89% increase in time efficiency.

      “Tissue transparency” refers to the ability of the cleared tissue to transmit visible light. We quantified the optical transparency by measuring light transmittance across the 400–900 nm wavelength range using a microplate reader. The results showed that the average transmittance increased by 20.12%, indicating that Liver-CUBIC treatment markedly enhanced the optical clarity of the liver tissue.

      (4) I am concerned about claiming this imaging method as real '3D imaging'. Namely, while the authors clear full lobes, they actually cut the cleared lobes into 200-micrometer-thick slices and perform further microscopy imaging on these slices. Considering that they focus on ductular structures of the liver (such as vasculature, bile duct system, and innervations), 200 micrometer allows a very limited 3D overview, particularly in comparison with the whole-mount immuno-imaging methods combined with light sheet microscopy (such as Adori 2021, Liu 2021, etc). In this context, I feel several parts of the Introduction to be an overstatement: besides of emphasizing the advantages of the technique (such as simultaneous visualization of different hepatic vascular compartments and the bile duct system by MCNPs, the combination with immunostainings), the authors must honestly discuss the limitations (such as limited tissue overview, potential dye perfusion problems - uneven distribution of the dye etc).

      We appreciate the reviewer’s insightful comments. It is true that most of the imaging depth in this study was limited to approximately 200 μm, and thus it could not achieve whole-liver three-dimensional imaging comparable to light-sheet microscopy. However, the primary focus of our study was to resolve the microscopic intrahepatic architecture, particularly the spatial relationships among blood vessels, bile ducts, and nerve fibers. Through high-resolution imaging of thick tissue sections, combined with MCNP-based multichannel labeling and immunofluorescence co-staining, we were able to accurately delineate the three-dimensional distribution of these microstructures within localized regions.

      In addition to thick-section imaging, we also obtained whole-lobe dye perfusion data (as shown in Figure S1F), which comprehensively depict the three-dimensional branching patterns and distribution of the vascular systems within the liver lobe. These images were acquired from intact liver lobes perfused with MCNP dyes, revealing a continuous vascular network extending from major trunks to peripheral branches, thereby demonstrating that our approach is also capable of achieving organ-level visualization.

      We have added this image and a corresponding description in the revised manuscript to more comprehensively present the coverage of our imaging system, and we have incorporated this clarification into the Discussion section.

      Method

      (5) More information may be needed about MCNPs:

      a) As reported, there are nanoparticles with different colors in brightfield microscopy, but the particles are also excitable in fluorescence microscopy. Would you please provide a summary about excitation/emission wavelengths of the different MCNPs? This is crucial to understand to what extent the method is compatible with fluorescence immunohistochemistry.

      We thank the reviewer for the careful attention and professional suggestion. We fully agree that this issue is critical for evaluating the compatibility of our method with fluorescent immunohistochemistry. Different types of metal compound nanoparticles (MCNPs) have clearly distinguishable spectral properties:

      - MCNP-Green and MCNP-Yellow: AF488-matched spectra, with excitation/emission wavelengths of 495/519 nm.

      - MCNP-Pink: Designed for far-red spectra, with excitation/emission wavelengths of 561/640 nm.

      - MCNP-Black: Non-fluorescent, appearing black under bright-field microscopy only.

      The above information has been added to the Materials and Methods section.

      b) Also, is there more systematic information available concerning the advantage of these particles compared to 'traditional' fluorescence dyes, such as Alexa fluor or Cy-dyes, in fluorescence microscopy and concerning their compatibility with various tissue clearing methods (e.g., with the frequently used organic-solvent-based methods)?

      We thank the reviewer for the detailed question. Compared with conventional organic fluorescent dyes, MCNP offers the following advantages:

      - Enhanced photostability: Its inorganic core-shell structure resists fading even after hydrogen peroxide bleaching.

      - High signal stability: Fluorescence is maintained during aqueous-based clearing (e.g., CUBIC) and multiple rounds of staining without quenching.

      We appreciate the reviewer’s suggestion. In our Liver-CUBIC system, MCNP nanoparticles exhibited excellent multi-channel labeling stability and fluorescence signal retention. Regarding compatibility with other clearing methods (e.g., SCAFE, SeeDB, CUBIC), since these methods have limited effectiveness for whole-liver clearing (see Figure 2 of Tainaka, et al. 2014) and cannot meet the requirements for high-resolution microstructural imaging in this study, we consider further testing of their compatibility unnecessary.

      In summary, MCNP dye demonstrates superior signal stability and spectral separation compared with conventional organic fluorescent dyes in multi-channel, long-term, high-transparency three-dimensional tissue imaging.

      c) When you perfuse these particles, to which structures do they bind inside the ducts (vessels, bile ducts)? Is the 48h post-fixation enough to keep them inside the tubes/bind them to the vessel walls? Is there any 'wash-out' during the complex cutting/staining procedure? E.g., in Figure 2D: the 'classical' hepatic artery in the portal triad is not visible - but the MCNP apparently penetrated to the adjacent sinusoids at the edge of the lobulus. Also, in Figure 3B, there is a significant mismatch between the MNCP-green (bile duct) signal and the CD19 (epithelium marker) immunostaining. Please discuss these.

      The experimental results showed that following injection, MCNP nanoparticles primarily remained within the vascular and biliary lumens, and their tissue distribution depended on physical perfusion. No dye signal was observed to diffuse into the surrounding parenchyma, nor did the particles adhere to cell surfaces or enter cells. The newly added Supplementary Figures S2A–H further confirm this feature: the dye signal is strictly confined within the lumens, clearly delineating continuous vascular paths and biliary branching patterns, strongly supporting the conclusion that “MCNP dye is distributed only within luminal spaces.”

      Thus, MCNP dye mainly serves as an intraluminal tracer rather than a label for specific cell types.

      We provide the following explanations and analyses regarding MCNP distribution in the hepatic vascular and biliary systems and its post-fixation stability:

      - Potential signal displacement during sectioning/immunostaining: During slicing and immunostaining, a small number of particles may be washed away due to mechanical cutting or washing steps; however, the overall three-dimensional structure retains high spatial fidelity.

      - Observation in Figure 2D: MCNP was seen entering the sinusoidal spaces at the lobule periphery, but hepatic arteries were not visible, likely due to limitations in section thickness. Although arteries were not apparent in this slice, arterial distribution around the portal vein is visible in Figure 2C. It should be noted that Figures 2C, D, and E do not represent whole-liver imaging, so not all regions necessarily contain visible hepatic arteries. For easier identification, the main hepatic artery trunk is highlighted in cyan in Figure 2E.

      - Incomplete biliary signal in Figure 3B: This may be because CK19 labeling only covers biliary epithelial cells, whereas MCNP-green distributes throughout the biliary lumen. In Figure 3B, the terminal MCNP-green signal exhibits irregular polygonal structures, which we interpret as the canalicular regions.

      (6) Which fixative was used for 48h of postfixation (step 6) after MCNP injections?

      After MCNP injection, mouse livers were post-fixed in 4% paraformaldehyde (PFA) for 48 hours. This fixation condition effectively “locks” the MCNP particles within the vascular and biliary lumens, maintaining their spatial positions, while also being compatible with subsequent sectioning and multi-channel immunostaining analyses.

      The above information has been added to the Materials and Methods section

      (7) What is the 'desired thickness' in step 7? In the case of immunostained tissue, a 200-micrometer slice thickness is mentioned. However, based on the Methods, it is not completely clear what the actual thickness of the tissue was that was examined ultimately in the microscopes, and whether or not the clearing preceded the cutting or vice versa.

      We appreciate the reviewer’s question. The “desired thickness” referred to in step 7 of the manuscript corresponds to the thickness of tissue sections used for immunostaining and high-resolution microscopic imaging, which is typically around 200 µm. We selected 200 µm because this thickness is sufficient to observe the PLC structure in its entirety, allows efficient staining, and preserves tissue architecture well. Other researchers may choose different section thicknesses according to their experimental needs.

      In this study, the processing order for immunostained tissue samples was sectioning followed by clearing, as detailed below:

      Section Thickness

      To ensure antibody penetration and preservation of three-dimensional structure, tissue sections were typically cut to ~200 µm. Thicker sections can be used if more complete three-dimensional structures are required, but adjustments may be needed based on antibody penetration and fluorescence detection conditions.

      Clearing Sequence

      After sectioning, slices were processed using the Liver-CUBIC aqueous-based clearing system.

      (8) More information is needed concerning the 'deep-focus microscopy' (Keyence), the applied confocal system, and the THUNDER 'high resolution imaging system': basic technical information, resolutions, objectives (N.A., working distance), lasers/illumination, filters, etc.

      In this study, all liver lobes (left, right, caudate, and quadrate lobes) were subjected to Liver-CUBIC aqueous-based clearing to ensure uniform visualization of MCNP fluorescence and immunolabeling throughout the three-dimensional imaging of the entire liver.

      The above information has been added to the Materials and Methods section.

      Imaging Systems and Settings

      VHX-6000 Extended Depth-of-Field Microscope: Objective: VH-Z100R, 100×–1000×; resolution: 1 µm (typical); illumination: coaxial reflected; transmitted illumination on platform: ON.

      Zeiss Confocal Microscope (980): Objectives: 20× or 40×; image size: 1024 × 1024. Fluorescence detection was set up in three channels:

      - Channel 1: 639 nm laser, excitation 650 nm, emission 673 nm, detection range 673–758 nm, corresponding to Cy5-T1 (red).

      - Channel 2: 561 nm laser, excitation 548 nm, emission 561 nm, detection range 547–637 nm, corresponding to Cy3-T2 (orange).

      - Channel 3: 488 nm laser, excitation 493 nm, emission 517 nm, detection range 490–529 nm, corresponding to AF488-T3 (green).

      Leica THUNDER Imager 3D Tissue: Fluorescence detection in two channels:

      - Channel 1: FITC channel (excitation 488 nm, emission ~520 nm).

      - Channel 2: Orange-red channel (excitation/emission 561/640 nm).<br /> Equipped with matching filter sets to ensure signal separation.

      The above information has been added to the Materials and Methods section.

      (9) Liver-CUBIC, step 2: which lobe(s) did you clear (...whole liver lobes...).

      In this study, all liver lobes (left, right, caudate, and quadrate lobes) were subjected to Liver-CUBIC aqueous-based clearing to ensure uniform visualization of MCNP fluorescence and immunolabeling throughout the three-dimensional imaging of the entire liver.

      The above information has been added to the Materials and Methods section.

      (10) For the DAB and TSA IHC stainings, did you use free-floating slices, or did you mount the vibratome sections and do the staining on mounted sections?

      In this study, fixed livers were first sectioned into thick slices (~200 µm) using a vibratome. Subsequently, DAB and TSA immunohistochemical (IHC) staining were performed on free-floating sections. During the entire staining process, the slices were kept floating in the solutions, ensuring thorough antibody penetration in the thick sections while preserving the three-dimensional tissue architecture, thereby facilitating multiple rounds of staining and three-dimensional imaging.

      (11) Regarding the 'transmission quantification': this was measured on 1 mm thick slices. While it is interesting to make a comparison between different clearing methods in general, one must note that it is relatively easy to clear 1mm thick tissue slices with almost any kind of clearing technique and in any tissues. The 'real' differences come with thicker blocks, such as >5mm in the thinnest dimension. Do you have such experiences (e.g., comparison in whole 'left lateral liver lobes')?

      In this study, we performed three-dimensional visualization of entire liver lobes to depict the distribution of MCNPs and the overall spatial architecture of the vascular and biliary systems (Figure S1F). However, due to the limitations of the plate reader and fluorescence imaging systems in terms of spatial resolution and light penetration depth, quantitative analyses were conducted only on tissue sections approximately 1 mm thick.

      Regarding the comparative quantification of different clearing methods, as the reviewer noted, nearly all aqueous- or organic solvent–based clearing techniques can achieve relatively uniform transparency in 1 mm-thick tissue sections, so differences at this thickness are limited. We have not yet conducted systematic comparisons on whole-lobe sections thicker than 5 mm and therefore cannot provide “true” difference data for thicker tissues.

      (12) There is no method description for the ELMI studies in the Methods.

      Transmission Electron Microscopy (TEM) Analysis of MCNPs

      Before imaging, the MCNP dye solution was centrifuged at 14,000 × g for 10 minutes at 4 °C to remove aggregates and impurities. The supernatant was collected, diluted 50-fold, and 3–4 μL of the sample was applied onto freshly glow-discharged Quantifoil R1.2/1.3 copper grids (Electron Microscopy Sciences, 300 mesh). The sample was allowed to sit for 30 seconds to enable particle adsorption, after which excess liquid was gently wicked away with filter paper and the grid was air-dried at room temperature. The sample was then negatively stained with 1% uranyl acetate for 30 seconds and air-dried again before imaging.

      Negative-stain TEM images were acquired using a JEOL JEM-1400 transmission electron microscope operating at 120 kV and equipped with a CCD camera. Data acquisition followed standard imaging conditions.

      The above information has been added to the Materials and Methods section.

      (13) Please, provide a method description for the applied CCl4 cirrhosis model. This is completely missing.

      (1) Under a fume hood, carbon tetrachloride (CCl₄) was dissolved in corn oil at a 1:3 volume ratio to prepare a working solution, which was filtered through a 0.2 μm filter into a 30 mL glass vial. In our laboratory, to mimic chronic injury, mice in the experimental group were intraperitoneally injected at a dose of 1 mL/kg body weight per administration.

      (2) Mice were carefully removed from the cage and placed on a scale to record body weight for calculation of the injection volume.

      (3) The needle cap was carefully removed, and the required volume of the pre-prepared CCl₄ solution was drawn into the syringe. The syringe was gently flicked to remove any air bubbles.

      (4) Mice were placed on a textured surface (e.g., wire cage) and restrained. When the mouse was properly positioned, ideally with the head lowered about 30°, the left lower or right lower abdominal quadrant was identified.

      (5) Holding the syringe at a 45° angle, with the bevel facing up, the needle was inserted approximately 4–5 mm into the abdominal wall, and the calculated volume of CCl₄ was injected.

      (6) Mice were returned to their cage and observed for any signs of discomfort.

      (7) Needles and syringes were disposed of in a sharps container without recapping. A new syringe or needle was used for each mouse.

      (8) To establish a progressive liver fibrosis model, injections were administered twice per week (e.g., Monday and Thursday) for 3 or 6 consecutive weeks (n=3 per group). Control mice were injected with an equal volume of corn oil for 3 or 6 weeks (n=3 per group).

      (9) Forty-eight hours after the last injection, mice were euthanized by cervical dislocation, and livers were rapidly harvested. Portions of the liver were processed for paraffin embedding and histological sectioning, while the remaining tissue was either immediately frozen or used for subsequent molecular biology analyses.

      The above information has been added to the Materials and Methods section.

      (14) Please provide a method description for the quantifications reported in Figures 5D, 5F, and 6E.

      ImageJ software was used to analyze 3D stained images (Figs. 5F, 6E), and the ultra-depth-of-field 3D analysis module was used to analyze 3D DAB images (Fig. 5D). The specific steps are as follows:

      Figure 5D: DAB-stained 3D images from the control group and the CCl<sub>4</sub> 6-week (CCl<sub>4</sub>-6W) group were analyzed. For each group, 20 terminal bile duct branch nodes were randomly selected, and the actual path distance along the branch to the nearest portal vein surface was measured. All measurements were plotted as scatter plots to reflect the spatial extension of bile ducts relative to the portal vein under different conditions.

      Figure 5F: TSA 3D multiplex-stained images from the control group, CCl<sub>4</sub> 3-week (CCl<sub>4</sub>-3W), and CCl<sub>4</sub> 6-week (CCl<sub>4</sub>-6W) groups were analyzed. For each group, 5 terminal bile duct branch nodes were randomly selected, and the actual path distance along the branch to the nearest portal vein surface was measured. Measurements were plotted as scatter plots to illustrate bile duct spatial extension.

      Figure 6E: TSA 3D multiplex-stained images from the control, CCl<sub>4</sub>-3W, and CCl<sub>4</sub>-6W groups were analyzed. For each group, 5 terminal nerve branch nodes were randomly selected, and the actual path distance along the branch to the nearest portal vein surface was measured. Scatter plots were generated to depict the spatial distribution of nerves under different treatment conditions.

      (15) Please provide a method description for the human liver samples you used in Figure S6. Patient data, fixation, etc...

      The human liver tissue samples shown in Figure S6 were obtained from adjacent non-tumor liver tissues resected during surgical operations at West China Hospital, Sichuan University. All samples used were anonymized archived tissues, which were applied for scientific research in accordance with institutional ethical guidelines and did not involve any identifiable patient information. After being fixed in 10% neutral formalin for 24 hours, the tissues were routinely processed for paraffin embedding (FFPE), and sectioned into 4 μm-thick slices for immunostaining and fluorescence imaging.

      Results

      (16) While it is stated in the Methods that certain color MCNPs were used for labelling different structures (i.e., yellow: hepatic artery; green: bile duct; portal vein: pink; central veins: black), in some figures, apparently different color MCNPs are used for the respective structures. E.g., in Figure 1J, the artery is pink and the portal vein is green. Please clarify this.

      The color assignment of MCNP dyes is not fixed across different experiments or schematic illustrations. MCNP dyes of different colors are fundamentally identical in their physical and chemical properties and do not exhibit specific binding or affinity for particular vascular structures. We select different colors based on experimental design and imaging presentation needs to facilitate distinction and visualization, thereby enhancing recognition in 3D reconstruction and image display. Therefore, the color labeling in Figure 1F is primarily intended to illustrate the distribution of different vascular systems, rather than indicating a fixed correspondence to a specific dye or injection color.

      (17) In Figure 1J, the hepatic artery is extremely shrunk, while the portal vein is extremely dilated - compared to the physiological situation. Does it relate to the perfusion conditions?

      We appreciate the reviewer’s attention. In fact, under normal physiological conditions, the hepatic arteries labeled by CD31 are naturally narrow. Therefore, the relatively thin hepatic arteries and thicker portal veins shown in Figure 1J are normal and unrelated to the perfusion conditions. See figure 1E of Adori et al., 2021.

      (18) Re: MCNP-black labelled 'oval fenestrae': the Results state 50-100 nm, while they are apparently 5-10-micron diameter in Figure 1I. Accordingly, the comparison with the ELMI studies in the subsequent paragraph is inappropriate.

      We thank the reviewer for the correction. The previous statement was a typographical error. In fact, the diameter of the “elliptical windows” marked by MCNP-black is 5–10 μm, so the diameter of 5–10 μm shown in Figure 1I is correct.

      (19) Please, correct this erroneous sentence: 'Pink marked the hepatic arterial system by injection extrahepatic duct (Figure 2B).'

      Original sentence: “The hepatic arterial system was labeled in pink by injection through the extrahepatic duct (Figure 2B).”

      Revised sentence: “The hepatic arterial system was labeled in pink by injection through the left ventricle (Figure 2B).”

      (20) How do you define the 'primary portal vein tract'?

      We thank the reviewer for the question. The term “primary portal vein tract” refers to the first-order branches of the portal vein that enter the liver from the hepatic hilum. These are the major branches arising directly from the main portal vein trunk and are responsible for supplying blood to the respective hepatic lobes. This definition corresponds to the concept of the first-order portal vein in hepatic anatomy.

      (21) I am concerned that the 'periportal lamellar complex (PLC)' that the Authors describe really exists as a distinct anatomical or functional unit. I also see these in 3D scans - in my opinion, these are fine, lower-order portal vein branches that connect the portal veins to the adjacent sinusoid. The strong MCNP-labelling of these structures may be caused by the 'sticking' of the perfused MCNP solutions in these 'pockets' during the perfusion process. What do these structures look like with SMA or CD31 immunostaining? Also, one may consider that the anatomical evaluation of these structures may have limitations in tissue slices. Have you ever checked MCNP-perfused, cleared full live lobes in light sheet microscope scans? I think this would be very useful to have a comprehensive morphological overview. Unfortunately, based on the presented documentation, I am also not convinced that PLCs are 'co-localize' with fine terminal bile duct branches (Figure 3E, S3C), or with TH+ 'neuronal bead chain networks' (Fig 6C). More detailed and more convincing documentation is needed here.

      We thank the reviewer for the detailed comments. Regarding the existence and function of the periportal lamellar complex (PLC), our observations are based on MCNP-Pink labeling of the portal vein, through which we were able to identify the PLC structure surrounding the portal branches. It should be noted that the PLC represents a very small anatomical structure. Although we have not yet performed light-sheet microscopy scanning, we anticipate that such imaging would primarily visualize larger portal vein branches. Nevertheless, this does not affect our overall conclusions.

      We also appreciate the reviewer’s suggestion that the observed structures might result from MCNP adherence during perfusion. To verify the structural characteristics of the PLC, we performed immunostaining for SMA and CD31, which revealed a specific arrangement pattern of smooth muscle and endothelial markers rather than simple perfusion-induced deposition (Figures 4F and S6B).

      Regarding the apparent colocalization of the PLC with terminal bile duct branches (Figures 3E and S3C) and TH⁺ neuronal bead-like networks (Figure 6C), we acknowledge that current literature evidence remains limited. Therefore, we have carefully described these observations as possible spatial associations rather than definitive conclusions. Future studies integrating high-resolution three-dimensional imaging with functional analyses will help to further clarify the anatomical and physiological significance of the PLC.

      (22) 'Extended depth-of-field three-dimensional bright-field imaging revealed a strict 1:1 anatomical association between the primary portal vein trunk (diameter 280 {plus minus} 32 μm) and the first-order bile duct (diameter 69 {plus minus} 8 μm) (Figures 3A and S3A)'.

      How do you define '1:1 anatomical association'? How do you define and identify the 'order' (primary, secondary) of vessel and bile duct branches in 200-micrometer slices?

      We thank the reviewer for the question. In this study, the term “1:1 anatomical correlation” refers to the stable paired spatial relationship between the main portal vein trunk and its corresponding primary bile duct within the same portal territory. In other words, each main portal vein branch is accompanied by a primary bile duct of matching branching order and trajectory, together forming a “vascular–biliary bundle.”

      The definitions of “primary” and “secondary” branches were based on extended-depth 3D bright-field reconstructions, considering both branching hierarchy and vessel/duct diameters: primary branches arise directly from the main trunk at the hepatic hilum and exhibit the largest diameters (averaging 280 ± 32 μm for the portal vein and 69 ± 8 μm for the bile duct), whereas secondary branches extend from the primary branches toward the lobular interior with smaller calibers.

      (23) In my opinion, the applied methodical approach in the single cell transcriptomics part (data mining in the existing liver single cell database and performing Venn diagram intersection analysis in hepatic endothelial subpopulations) is largely inappropriate and thus, all the statements here are purely speculative. In my opinion, to identify the molecular characteristics of such small and spatially highly organized structures like those fine radial portal branches, the only way is to perform high-resolution spatial transcriptomic.

      We thank the reviewer for the comment. We fully acknowledge the importance of high-resolution spatial transcriptomics in identifying the fine structural characteristics of portal vein branches. Due to current funding and technical limitations, we were unable to perform such high-resolution spatial transcriptomic analyses. However, we validated the molecular features of the PLC using another publicly available liver single-cell RNA-sequencing dataset, which provided preliminary supporting evidence (Figures S6B and S6C). In the manuscript, we have carefully stated that this analysis is exploratory in nature and have avoided overinterpretation. In future studies, high-resolution spatial omics approaches will be invaluable for more precisely delineating the molecular characteristics of these fine structures.

      (24) 'How the autonomic nervous system regulates liver function in mice despite the apparent absence of substantive nerve fiber invasion into the parenchyma remains unclear.'

      Please consider the role of gap junctions between hepatocytes (e.g., Miyashita, 1991; Seseke, 1992).

      In this study, we analyzed the spatial distribution of hepatic nerves in mice using immunofluorescence staining and found that nerve fibers were almost exclusively confined to the portal vein region (Figure S6A). Notably, this distribution pattern differs markedly from that in humans. Previous studies have shown that, in human livers, nerves are not only located around the portal veins but also present along the central veins, interlobular septa, and within the parenchymal connective tissue (Miller et al., 2021; Yi, la Fleur, Fliers & Kalsbeek, 2010).

      Further research has provided a physiological explanation for this interspecies difference: even among species with distinct sympathetic innervation patterns in the parenchyma—i.e., with or without direct sympathetic input—the sympathetic efferent regulatory functions may remain comparable (Beckh, Fuchs, Ballé & Jungermann, 1990). This is because signals released from aminergic and peptidergic nerve terminals can be transmitted to hepatocytes through gap junctions as electrical signals (Hertzberg & Gilula, 1979; Jensen, Alpini & Glaser, 2013; Seseke, Gardemann & Jungermann, 1992; Taher, Farr & Adeli, 2017).

      However, the scarcity of nerve fibers within the mouse hepatic parenchyma suggests that the mechanisms by which the autonomic nervous system regulates liver function in mice may differ from those in humans. This observation prompted us to further investigate the potential role of PLC endothelial cells in this process.

      (25) Please, correct typos throughout the text.

      We thank the reviewer for this comment. We have carefully proofread the entire manuscript and corrected all typographical errors and minor language issues throughout the text.

      Reviewer #3 (Recommendations for the authors):

      (1) A strong recommendation - the authors ought to challenge their scRNAsq- re-analysis with another scRNAseq dataset, namely a recently published atlas of adult liver endothelial, but also mesenchymal, immune, and parenchymal cell populations https://pubmed.ncbi.nlm.nih.gov/40954217/, performed with Smart-seq2 approach, which is perfectly suitable as it brings higher resolution data, and extensive cluster identity validation with stainings. Pietilä et al. indicate a clear distinction of portal vein endothelial cells into two populations that express Adgrg6, Jag1 (e2c), from Vegfc double-positive populations (e5c and e2c). Moreover, the dataset also includes the arterial endothelial cells that were shown to be part of the PLC, but were not followed up with the scRNAseq analysis. This distinction could help the authors to further validate their results, better controlling for cross-contaminations that may occur during scRNAseq preparation.

      We thank the reviewer for the valuable suggestion. As noted, we have further validated the molecular characteristics of the PLC using a recently published atlas of adult liver endothelial cells (Pietilä et al., 2023, PMID: 40954217). This dataset, generated using the Smart-seq2 technique, provides high-resolution transcriptomic profiles. By analyzing this dataset, we identified a CD34⁺LY6A⁺ portal vein endothelial cell population within the e2 cluster, which is localized around the portal vein. We then examined pathways and gene expression patterns related to hematopoiesis, bile duct formation, and neural signaling within these cells. The results revealed gene enrichment patterns consistent with those observed in our primary dataset, further supporting the robustness of our analysis of the PLC’s molecular characteristics.

      (2) Improving the methods section is highly recommended, this includes more detailed information for material and protocols used - catalog numbers; protocol details of the usage - rocking platforms, timing, and tubes used for incubations; GitHub or similar page with code used for the scRNA seq re-analysis.

      We thank the reviewer for the valuable suggestion. We have added more detailed information regarding the materials and experimental procedures in the Methods section, including catalog numbers, incubation conditions (such as the type of shaker, incubation time, and tube specifications), and other relevant parameters.

      (3) In Figure 2A, the authors claim the size of the nanoparticle is 100nm, while based on the image, the size is ~150-180nm. A more thorough quantification of the particle size would help users estimate the usability of their method for further applications.

      We thank the reviewer for the comment. In the TEM image shown in Figure 2A, the nanoparticles indeed appear to be approximately 150–200 nm in size. We have re-verified the particle dimensions and will update the corresponding description in the Methods section to allow readers to more accurately assess the applicability of this approach.

      (4) In Figure 3E, it is not clear what is labeled by the pink signal. Please consider labeling the structures in the figure.

      We thank the reviewer for the valuable comment. The pink signal in Figure 3E was originally intended to label the hepatic artery. However, a slight spatial misalignment occurred during the labeling process, making its position appear closer to the central vein rather than the portal vein in the image. To avoid misunderstanding, we will add clear annotations to the image and clarify this deviation in the figure legend in the revised version. It should also be noted that this figure primarily aims to illustrate the spatial relationship between the bile duct and the portal vein, and this minor deviation does not affect the reliability of our experimental conclusions.

      (5) The following statement is not backed by quantification as it ought to be „Dual-channel three-dimensional confocal imaging combined with CK19 immunostaining revealed that the sites of dye leakage did not coincide with the CK19-positive terminal bile duct epithelium, but instead were predominantly localized within regions adjacent to the PLC structures".

      We thank the reviewer for the valuable comment. We have added the corresponding quantitative analysis to support this conclusion. Quantitative assessment of the extended-depth imaging data revealed that dye leakage predominantly occurred in regions adjacent to the PLC structure, rather than in the perivenous sinusoidal areas. The corresponding results have been presented in the revised Figure 3G.

      (6) Similarly, Figure 4F is central to the Sca1CD34 cell type identification but lacks any quantification, providing it would strengthen the key statement of the article. A possible way to approach this is also by FACS sorting the double-positive cells and bluk/qRT validation.

      We thank the reviewer for raising this point. We agree that quantitative validation of the Sca1⁺CD34⁺ population by FACS sorting could further support our conclusions. However, the primary focus of this study is on the spatial localization and transcriptional features of PLC endothelial cells. The identification of the Sca1⁺CD34⁺ subset is robustly supported by multiple complementary approaches, including three-dimensional imaging, co-staining with pan-endothelial markers, and projection mapping analyses. Collectively, these lines of evidence provide a solid basis for characterizing this unique endothelial population.

      (7) The images in Figure S4D are not comparable, as the Sca1-stained image shows a longitudinal section of the PV, but the other stainings are cross-sections of PVs.

      We thank the reviewer for the careful comment. We agree that the original Sca1-stained image, being a longitudinal section of the portal vein, was not optimal for direct comparison with other cross-sectional images. We have replaced it with a cross-sectional image of the portal vein to ensure comparability across all images. The updated image has been included in the revised Supplementary Figure S4D.

      (8) I might be wrong, but Figure 4J is entirely missing, and only a cartoon is provided. Either remove the results part or provide the data.

      We appreciate the reviewer’s careful observation. Figure 4J was intentionally designed as a schematic illustration to summarize the structural relationships and spatial organization of the portal vein, hepatic artery, and PLC identified in the previous panels (Figures 4A–4I). It does not represent newly acquired experimental data, but rather serves to provide a conceptual overview of the findings.

      To avoid misunderstanding, we have clarified this point in the figure legend and the main text, stating that Figure 4J is a schematic summary rather than an experimental image. Therefore, we respectfully prefer to retain the schematic figure to aid readers’ interpretation of the preceding results.

      (9) The methods section lacks information about the CCL4concentration, and it is thus hard to estimate the dosage of CCL4 received (ml/kg). This is important for the interpretation of the severity of the fibrosis and presence of cirrhosis, as different doses may or may not lead to cirrhosis within the short regimen performed by the authors [PMID: 16015684 DOI: 10.3748/wjg.v11.i27.4167]. Validation of the fibrosis/cirrhosis severity is, in this case, crucial for the correct interpretation of the results. If the level of cirrhosis is not confirmed, only progressive fibrosis should be mentioned in the manuscript, as these two terms cannot be used interchangeably.

      Thank you for the reviewer’s comment. We indeed omitted the information on the concentration of carbon tetrachloride (CCl<sub>4</sub>) in the Methods section. In our experiments, mice received intraperitoneal injections of CCl<sub>4</sub> at a dose of 1 mL/kg body weight, twice per week, for a total of six weeks. We have revised the manuscript accordingly, using the term “progressive fibrosis” to avoid confusion between fibrosis and cirrhosis.

      (10) The following statement is not backed by any correlation analysis: "Particularly during liver fibrosis progression, the PLC exhibits dynamic structural extension correlating with fibrosis severity,.. ".

      We thank the reviewer for the comment. The original statement that the “PLC correlates with fibrosis severity” lacked support from quantitative analysis. To ensure a precise description, we have revised the sentence as follows: “During liver fibrosis progression, the PLC exhibits dynamic structural extension.”

      (11) Similarly, the following statement is not followed by data that would address the impact of innervation on liver function: "How the autonomic nervous system regulates liver function in mice despite the apparent absence of substantive nerve fiber invasion into the parenchyma remains unclear.".

      This section has been revised. In this study, we analyzed the spatial distribution of nerves in the mouse liver using immunofluorescence staining. The results showed that nerve fibers were almost entirely confined to the portal vein region (Figure S6A). Notably, this distribution pattern differs significantly from that in humans. Previous studies have demonstrated that in the human liver, nerves are not only distributed around the portal vein but also present in the central vein, interlobular septa, and connective tissue of the hepatic parenchyma (Miller et al., 2021; Yi, la Fleur, Fliers & Kalsbeek, 2010).

      Previous studies have further explained the physiological basis for this difference: even among species with differences in parenchymal sympathetic innervation (i.e., species with or without direct sympathetic input), their sympathetic efferent regulatory functions may still be similar (Beckh, Fuchs, Ballé & Jungermann, 1990). This is because signals released by adrenergic and peptidergic nerve terminals can be transmitted to hepatocytes as electrical signals through intercellular gap junctions (Hertzberg & Gilula, 1979; Jensen, Alpini & Glaser, 2013; Seseke, Gardemann & Jungermann, 1992; Taher, Farr & Adeli, 2017). However, the scarcity of nerve fibers in the mouse hepatic parenchyma suggests that the mechanism by which the autonomic nervous system regulates liver function in mice may differ from that in humans. This finding also prompts us to further explore the potential role of PLC endothelial cells in this process.

      (12) Could the authors discuss their interpretation of the results in light of the fact that the innervation is lower in cirrhotic patients? https://pmc.ncbi.nlm.nih.gov/articles/PMC2871629/. Also, while ADGRG6 (Gpr126) may play important roles in liver Schwann cells, it is likely not through affecting myelination of the nerves, as the liver nerves are not myelinated https://pubmed.ncbi.nlm.nih.gov/2407769/ and https://www.pnas.org/doi/10.1073/pnas.93.23.13280.

      We have revised the text to state that although most hepatic nerves are unmyelinated, GPR126 (ADGRG6) may regulate hepatic nerve distribution via non-myelination-dependent mechanisms. Studies have shown that GPR126 exerts both Schwann cell–dependent and –independent functions during peripheral nerve repair, influencing axon guidance, mechanosensation, and ECM remodeling (Mogha et al., 2016; Monk et al., 2011; Paavola et al., 2014).

      (13) The manuscript would benefit from text curation that would:

      a) Unify the language describing the PLC, so it is clear that (if) it represents protrusions of the portal veins.

      We have standardized the description of the PLC throughout the manuscript, clearly specifying its anatomical relationship with the portal vein. Wherever appropriate, we indicate that the PLC represents protrusions associated with the portal vein, avoiding ambiguous or inconsistent statements.

      b) Increase the accuracy of the statements.

      Examples: "bile ducts, and the central vein in adult mouse livers."

      We have refined all statements for accuracy.

      c) Reduce the space given to discussion and results in the introduction, moving them to the respective parts. The same applies to the results section, where discussion occurs at more places than in the Discussion part itself.

      We have edited the Introduction, removing detailed results and functional explanations, and retaining only a concise overview.

      Examples: "The formation of PLC structures in the adventitial layer may participate in local blood flow regulation, maintenance of microenvironmental homeostasis, and vascular-stem cell interactions."

      "This finding suggests that PLC endothelial cells not only regulate the periportal microcirculatory blood flow, but also establish a specialized microenvironment that supports periportal hematopoietic regulation, contributing to stem cell recruitment, vascular homeostasis, and tissue repair. "

      "Together, these findings suggest the PLC endothelium may act as a key regulator of bile duct branching and fibrotic microenvironment remodeling in liver cirrhosis. " This one in particular would require further validation with protein stainings and similar, directly in your model.

      d) Provide a clear reference for the used scRNA seq so it's clear that the data were re-analyzed.

      Example: "single-cell transcriptomic analysis revealed significant upregulation of bile duct-related genes in the CD34<sup>+</sup>Sca-1<sup>+</sup> endothelium of PLC in cirrhotic liver, with notably high expression of Lgals1 (Galectin-1) and HGF(Figure 5G) "

      When describing the transcriptional analysis of PLC endothelial cells, we explicitly cited the original scRNA-seq dataset (Su et al., 2021), clarifying that these data were reanalyzed rather than newly generated.

      e) Introducing references for claims that, in places, are crucial for further interpretation of experiments.

      Examples: "It not only guides bile duct branching during development but also"; the authors show no data from liver development.

      Thank you for pointing this out. We have revised the relevant statement to ensure that the claim is accurate and well-supported.

      f) Results sentence "Instead, bile duct epithelial cells at the terminal ducts extended partially along the canalicular network without directly participating in the formation of the bile duct lumen." Lacks a callout to the respective Figure.

      We would like to thank the reviewers for pointing out this issue. In the revised manuscript, the relevant image (Figure 3D) has been clearly annotated with white arrows to indicate the phenomenon of terminal cholangiocytes extending along the bile canaliculi network. Additionally, the schematic diagram on the right side clearly shows the bile canaliculi, cholangiocytes, and bile flow direction using arrows and color coding, thus intuitively corresponding to the textual description.

      (14) Formal text suggestions: The manuscript text contains a lot of missed or excessive spaces and several typos that ought to be fixed. A few examples follow:

      a) "densely n organized vascular network "

      b) "analysis, while offering high spatial "

      c) "specific differences, In the human liver, "

      d) Figure 4F has a typo in the description.

      e) "generation of high signal-to-noise ratio, multi-target " SNR abbreviation was introduced earlier.

      f) Canals of Hering, CoH abbreviation comes much later than the first mention of the Canals of Hering.

      We thank the reviewer for the helpful comment regarding textual consistency. We have carefully reviewed and revised the entire manuscript to improve the accuracy, clarity, and consistency of the text.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Domínguez-Rodrigo and colleagues make a moderately convincing case for habitual elephant butchery by Early Pleistocene hominins at Olduvai Gorge (Tanzania), ca. 1.8-1.7 million years ago. They present this at the site scale (the EAK locality, which they excavated), as well as across the penecontemporaneous landscape, analyzing a series of findspots that contain stone tools and large-mammal bones. The latter are primarily elephants, but giraffids and bovids were also butchered in a few localities. The authors claim that this is the earliest well-documented evidence for elephant butchery; doing so requires debunking other purported cases of elephant butchery in the literature, or in one case, reinterpreting elephant bone manipulation as being nutritional (fracturing to obtain marrow) rather than technological (to make bone tools). The authors' critical discussion of these cases may not be consensual, but it surely advances the scientific discourse. The authors conclude by suggesting that an evolutionary threshold was achieved at ca. 1.8 ma, whereby regular elephant consumption rich in fats and perhaps food surplus, more advanced extractive technology (the Acheulian toolkit), and larger human group size had coincided.

      The fieldwork and spatial statistics methods are presented in detail and are solid and helpful, especially the excellent description (all too rare in zooarchaeology papers) of bone conservation and preservation procedures. However, the methods of the zooarchaeological and taphonomic analysis - the core of the study - are peculiarly missing. Some of these are explained along the manuscript, but not in a standard Methods paragraph with suitable references and an explicit account of how the authors recorded bone-surface modifications and the mode of bone fragmentation. This seems more of a technical omission that can be easily fixed than a true shortcoming of the study. The results are detailed and clearly presented.

      By and large, the authors achieved their aims, showcasing recurring elephant butchery in 1.8-1.7 million-year-old archaeological contexts. Nevertheless, some ambiguity surrounds the evolutionary significance part. The authors emphasize the temporal and spatial correlation of (1) elephant butchery, (2) Acheulian toolkits, and (3) larger sites, but do not actually discuss how these elements may be causally related. Is it not possible that larger group size or the adoption of Acheulian technology have nothing to do with megafaunal exploitation? Alternative hypotheses exist, and at least, the authors should try to defend the causation, not just put forward the correlation. The only exception is briefly mentioning food surplus as a "significant advantage", but how exactly, in the absence of food-preservation technologies? Moreover, in a landscape full of aggressive scavengers, such excess carcass parts may become a death trap for hominins, not an advantage. I do think that demonstrating habitual butchery bears very significant implications for human evolution, but more effort should be invested in explaining how this might have worked.

      Overall, this is an interesting manuscript of broad interest that presents original data and interpretations from the Early Pleistocene archaeology of Olduvai Gorge. These observations and the authors' critical review of previously published evidence are an important contribution that will form the basis for building models of Early Pleistocene hominin adaptation.

      This is a good example of the advantages of the eLife reviewing process. It has become much too common, among traditional peer-reviewing journals, to reject articles when there is no coincident agreement in the reviews, regardless of the heuristics (i.e., empirically-supported weight) of the arguments on both reviewers. Reviewers 1 and 2 provide contrasting evaluations, and the eLife dialogue between authors and reviewers enable us to address their comments differentially. Reviewer 1 (R1), whose evaluation is overall positive, remarks that the methods of the zooarchaeological and taphonomic analysis are missing. We have added them now in the revised version of our manuscript. R1 also remarks that our work highlights correlation of events, but not necessarily causation. We did not establish causation because such interpretations bear a considerable amount of speculation (and they might have fostered further criticism by R2); however, in the revised version, we expanded our discussion of these issues substantially. Establishing causation among the events described is impossible, but we certainly provide arguments to link them.

      Reviewer #2 (Public review):

      The authors argue that the Emiliano Aguirre Korongo (EAK) assemblage from the base of Bed II at Olduvai Gorge shows systematic exploitation of elephants by hominins about 1.78 million years ago. They describe it as the earliest clear case of proboscidean butchery at Olduvai and link it to a larger behavioral shift from the Oldowan to the Acheulean.

      The paper includes detailed faunal and spatial data. The excavation and mapping methods appear to be careful, and the figures and tables effectively document the assemblage. The data presentation is strong, but the behavioral interpretation is not supported by the evidence.

      The claim for butchery is based mainly on the presence of green-bone fractures and the proximity of bones and stone artifacts. These observations do not prove human activity. Fractures of this kind can form naturally when bones break while still fresh, and spatial overlap can result from post-depositional processes. The studies cited to support these points, including work by Haynes and colleagues, explain that such traces alone are not diagnostic of butchery, but this paper presents them as if they were.

      The spatial analyses are technically correct, but their interpretation extends beyond what they can demonstrate. Clustering indicates proximity, not behavior. The claim that statistical results demonstrate a functional link between bones and artifacts is not justified. Other studies that use these methods combine them with direct modification evidence, which is lacking in this case.

      The discussion treats different bodies of evidence unevenly. Well-documented cut-marked specimens from Nyayanga and other sites are described as uncertain, while less direct evidence at EAK is treated as decisive. This selective approach weakens the argument and creates inconsistency in how evidence is judged.

      The broader evolutionary conclusions are not supported by the data. The paper presents EAK as marking the start of systematic megafaunal exploitation, but the evidence does not show this. The assemblage is described well, but the behavioral and evolutionary interpretations extend far beyond what can be demonstrated.

      We disagree with the arguments provided by Reviewer 2 (R2). The arguments are based on two issues: bone breakage and spatial association. We will treat both separately here.

      Bone breakage

      R2 argues that:

      “The claim for butchery is based mainly on the presence of green-bone fractures and the proximity of bones and stone artifacts. These observations do not prove human activity. Fractures of this kind can form naturally when bones break while still fresh, and spatial overlap can result from post-depositional processes. The studies cited to support these points, including work by Haynes and colleagues, explain that such traces alone are not diagnostic of butchery, but this paper presents them as if they were.”

      In our manuscript, we argued that green-breakage provides an equally good (or even  better) taphonomic evidence of butchery if documented following clear taphonomic indicators. Not all green breaks are equal and not all “cut marks” are unambiguously identifiable as such. First, “natural” elephant long limb breaks have been documented only in pre/peri-mortem stages when an elephant breaks a leg. As a matter of fact, they have only been reported in publication on femora, the thinnest long bone (Haynes et al., 2021). Unfortunately, they have been studied many months after the death of the individuals, and the published diagnosis is made under the assumption that no other process intervened in the modification of those bones during this vast time span. Most of the breaks resulting from pre-mortem fractures produce long smooth, oblique/helical outlines. Occasionally, some flake scarring may occur on the cortical surface. This has been documented as uneven, small-sized, spaced, and we are not sure if it resulted from rubbing of broken fragments while the animal was alive and attempting to walk or some may have resulted from dessication of the bone after one year. When looking at them in detail, such breaks contain sometimes step-microfractures and angular (butterfly-like) outlines. Sometimes, they may be accompanied by pseudo-notches, which are distinct and not comparable to the deep notches that hammerstone breaking generates on the same types of bones. Commonly, the edges of the breaks show some polishing, probably from separate break planes rubbing against each other. It should be emphasized that the experimental work on hammerstone breaking documented by Haynes et al. (2021) is based on bone fracture properties of bones that are no longer completely green. The cracking documented in their hammerstone experimentation, with very irregular outlines differs from the cracking that we are documented in butchery of recently dead elephants.

      All this contrasts with the overlapping notches and flake scars (mostly occurring on the medullary side of the bone), both of them bigger in size, with clear smooth, spiral and longitudinal trajectories, with a more intensive modification on the medullary surface, and with sharp break edges resulting from hammerstone breaking of the green bone. No “natural” break has been documented replicating the same morphologies displayed in the Supplementary File to our paper. We display specimens with inflection points, hackle marks on the breaks, overlapping scarring on the medullary surface, with several specimens displaying percussion marks and pitting (also most likely percussion marks). Most importantly, we document this patterned modification on elements other than femora, for which no example has been documented of purported morphological equifinality caused by pre-mortem “natural” breaking. In contrast, such morphologies are documented in hammerstone-broken completely green bones (work in progress). We cited the works of Haynes to support this, because they do not show otherwise. As a matter of fact, Haynes himself had the courtesy of making a thorough reading of our manuscript and did not encounter any contradiction with his work. 

      Spatial association

      R2 argues in this regard:

      “The spatial analyses are technically correct, but their interpretation extends beyond what they can demonstrate. Clustering indicates proximity, not behavior. The claim that statistical results demonstrate a functional link between bones and artifacts is not justified. Other studies that use these methods combine them with direct modification evidence, which is lacking in this case.”

      We should emphasize that there is some confusion in the use and interpretation of clustering by R2 when applied to EAK. R2 appears to interpret clustering as the typical naked-eye perception of the spatial association of different items. In contrast, we rely on the statistical concept of clustering, more specifically on spatial interdependence or covariance, which is different. Items may appear visually clustered but still be statistically independent. This could, for example, result from two independent depositional episodes that happen to overlap spatially. In such cases, the item-to-item relationship does not necessarily show any spatial interdependence between classes other than simple clustering (i.e., spatial coincidence in intensity).

      Spatial statistical interdependence, on the other hand, reflects a spatial relationship or co-dependence between different items. This goes beyond the mere fact that classes appear clustered: items between classes may show specific spatial relationships — they may avoid each other or occupy distinct positions in space (regular co-dependence), or they may interact within the same spatial area (clustering co-dependence). Our tests indicate the latter for EAK.

      Such patterns are difficult to explain when depositional events are unrelated, since the probability that two independent events would generate identical spatial patterns in the same loci is very low. They are also difficult to reconcile when post-depositional processes intervene and resediment part of the assemblage (Domínguez-Rodrigo et al. 2018).

      Finally, R2 concludes:

      “The discussion treats different bodies of evidence unevenly. Well-documented cut-marked specimens from Nyayanga and other sites are described as uncertain, while less direct evidence at EAK is treated as decisive. This selective approach weakens the argument and creates inconsistency in how evidence is judged.”

      The Nyayanga hippo remains bearing modifications have not been well-documented cut marks. Neither R2 nor we can differentiate those marks from those inflicted by natural abrasive processes in coarse-grained sedimentary contexts, where the carcasses are found. The fact that the observable microscopic features (through low-quality photographs as appear in the original publication) differ between the cut marks documented on smaller animals and those inferred for the hippo remains makes them even more ambiguous. Nowhere in our manuscript do we treat the EAK evidence (or any other evidence) as decisive, but as the most likely given the methods used and the results reported.

      References

      Haynes G, Krasinski K, Wojtal P. 2021. A Study of Fractured Proboscidean Bones in Recent and Fossil Assemblages. Journal of Archaeological Method and Theory 28:956–1025.

      Domínguez-Rodrigo, M., Cobo-Sánchez, L., yravedra, J., Uribelarrea, D., Arriaza, C., Organista, E., Baquedano, E. 2018. Fluvial spatial taphonomy: a new method for the study of post-depositional processes. Archaeological and Anthropological Sciences 10: 1769-1789.

      Recommendations for authors:

      Reviewer #1 (Recommendations for the authors):

      I have several recommendations that, in my opinion, could enhance the communication of this study to the readers. The first point is the only crucial one.

      (1) A detailed zooarchaeological methods section must be added, with explanations (or references to them) of precisely how the authors defined and recorded bone-surface modifications and mode of bone fragmentation.

      This appears in the revised version of the manuscript in the form of a new sub-section within the Methods section.

      (2) The title could be improved to better represent the contents of the paper. It contains two parts: the earliest evidence for elephant butchery (that's ok), and revealing the evolutionary impact of megafaunal exploitation. The latter point is not actually revealed in the manuscript, just alluded to here and there (see also below).

      We have elaborated on this in the revised version, linking megafaunal exploitation and anatomical changes (which appear discussed in much more detail in the references indicated).

      (3) The abstract does not make it clear whether the authors think that the megafaunal adaptation strongly correlates with the Acheulian technocomplex. It seems that they do, so please make this point apparent in the abstract.

      From a functional point of view, we document the correlation, but do not believe in the causation, since most butchering tools around these megafaunal carcasses are typologically non Acheulian. We have indicated so in the abstract.

      (4) Please define what you mean by "megafauna". How large should an animal be to be considered as megafauna in this particular context?

      We have added this definition: we identify as “megafauna” those animals heavier than 800 kg.

      (5) In the literature survey, consider also this Middle Pleistocene case-study of elephant butchery, including a probable bone tool: Rabinovich, R., Ackermann, O., Aladjem, E., Barkai, R., Biton, R., Milevski, I., Solodenko, N., and Marder, O., 2012. Elephants at the middle Pleistocene Acheulian open-air site of Revadim Quarry, Israel. Quaternary International, 276, pp.183-197.

      Added to the revised version

      (6) The paragraph in lines 123-160 is unclear. Do the authors argue that the lack of evidence for processing elephant carcasses for marrow and grease is universal? They bring forth a single example of a much later (MIS 5) site in Germany. Then, the authors state the huge importance of fats for foragers (when? Where? Surely not in all latitudes and ecosystems). This left me confused - what exactly are you trying to claim here?

      We have explained this a little more in the revised text. What we pointed out was that most prehistoric (and modern) elephant butchery sites leave grease-containing long bones intact. Evidence of anthropogenic breakage of these elements is rather limited. The most probably reason is the overabundance of meat and fat from the rest of the carcass and the time-consuming effort needed to access the medullary cavity of elephant long bones.

      (7) The paragraph in lines 174-187 disrupts the flow of the text, contains previously mentioned information, ends with an unclear sentence, and could be cut.

      (8) Results: please provide the MNI for the EAK site (presumably 1, but this is never mentioned).

      Done in the revised version.

      (9) Lines 292 - 295: The authors found no traces of carnivoran activity (carnivoran remains, coprolites, or gnawing marks on the elephant bones), yet they attribute the absence of some non-dense skeletal elements to carnivore ravaging. I cannot understand this rationale, given that other density-mediated processes could have deleted the missing bones and epiphysis.

      This interpretation stems from our observations of several elephant carcasses in the Okavango delta in Botswana. Those that were monitored showed deletion of remains (i.e., disappearance of certain bones, like feet) without necessarily imprinting damage on the rest of the carcass. Carnivore intervention in an elephant death site can result in deletion of a few remains without much damage (if any), or if hyena clans access the carcass, much more conspicuous damage can be documented. There is a whole range of carnivore signatures in between. We are currently working on our study of several elephant carcasses subjected to these highly variable degrees of carnivore impact.

      (10) Lines 412 - 422: "The clustering of the elephant (and hippopotamus) carcasses in the areas containing the highest densities of landscape surface artifacts is suggestive of a hominin agency in at least part of their consumption and modification." - how so? It could equally suggest that both hominins and elephants were drawn to the same lush environments.

      We agree. Both hominins and megafauna must have been drawn to the same ecological loci for interaction to emerge. However, the fact that the highest density clusters of artifacts coincide with the highest density of carcasses “showing evidence of having been broken”, is suggestive of hominin use and consumption.

      (11) Discussion: I suggest starting the Discussion with a concise appraisal of the lines of evidence detailed in the Results and their interpretation, and only then, the critical reassessment of other studies. Similarly, a new topic starts in line 508, but without any subheading or an introductory sentence that could assist the readers.

      We added the introductory lines of the former Conclusion section to the revised Discussion section, as suggested by R1.

      (12) Line 607: Neumark-Nord are Late Pleistocene sites (MIS 5), not Middle Pleistocene.

      Corrected.

      (13) Regarding the ambiguity in how megafaunal exploitation may be causally related to the other features of the early Acheulian, the authors can develop the discussion. Alternatively, they should explicitly state that correlation is not causation, and that the present study adds the megafaunal exploitation element to be considered in future discussion of the shifts in lifestyles 1.8 million years ago.

      We have done so.

      Reviewer #2 (Recommendations for the authors):

      The following detailed comments are provided to help clarify arguments, ensure accurate representation of cited literature, and strengthen the logical and methodological framing of the paper. Line numbers refer to the version provided for review.

      (1) Line 55: Such concurrency (sometimes in conjunction with other variables)

      The term "other variables" is very vague. I would suggest expanding on this or taking it out altogether.

      (2) Line 146: Megafaunal long bone green breakage (linked to continuous spiral fractures on thick cortical bone) is probably a less ambiguous trace of butchery than "cut marks", since many of the latter could be equifinal and harder to identify, especially in contexts of high abrasion and trampling (Haynes et al., 2021, 2020).

      This reasoning is not supported by the evidence or the cited sources. Green-bone spiral fractures only show that a bone broke while it was fresh and do not reveal who or what caused it. Carnivore feeding, trampling, and natural sediment pressure can all create the same patterns, so these fractures are not clearer evidence of butchery than cut marks. Cut marks, when they are preserved and morphologically clear, remain the most reliable indicator of human activity. The Haynes papers actually show the opposite of what is claimed here. They warn that spiral fractures and surface marks can form naturally and that fracture patterns alone cannot be used to infer butchery. This section should be revised to reflect what those studies actually demonstrate.

      The reasoning referred to in line 146 is further explained below in the original text as follows:

      “Despite the occurrence of green fractures on naturally-broken bones, such as those trampled by elephants (Haynes et al., 2020), those occurring through traumatic fracturing or gnawed by carnivores (Haynes and Hutson, 2020), these fail to reproduce the elongated, extensive, or helicoidal spiral fractures (uninterrupted by stepped sections), accompanied by the overlapping conchoidal scars (both cortical and medullary), the reflected scarring, the inflection points, or the impact hackled break surfaces and flakes typical of dynamic percussive breakage. Evidence of this type of green breakage had not been documented earlier for the Early Pleistocene proboscidean or hippopotamid carcasses, beyond the documentation of flaked bone with the purpose of elaboration of bone tools (Backwell and d’Errico, 2004; Pante et al., 2020; Sano et al., 2020).”

      The problem in the way that R2 uses Haynes et al.´s works is that R2 uses features separately. Natural breaks occurring while the bone is green can generate spiral smooth breaks, for example, but it is not the presence of a single feature that invalidates the diagnosis of agency or that is taphonomically relevant, but the concurrence of several of them. The best example of a naturally (pre-mortem) broken bone was published by Haynes et al.

      The natural break shows helical fractures, subjugated to linear (angular) fracture outlines. Notice how the crack displays a zig-zag. The break is smooth but most damage occurs on the cortical surface, with flaking adjacent to the break and step micro-fracturing on the edges. The cortical scarring is discontinuous (almost marginal) and very small, almost limited to the very edge of the break. No modification occurs on the medullary surface. No extensive conchoidal fractures are documented, and certainly none inside the medullary surface of the break.

      Compare with Figure S8, S10, S17 and S34 (all specimens are shown in their medullary surface):

      In these examples, we see clearly modified medullary surfaces with multiple green breaks and large-sized step fractures, accompanied in some examples by hackle marks. Some show large overlapping scars (of substantially bigger size than those documented in the natural break image). Not a single example of naturally-broken bones has been documented displaying these morphologies simultaneously. It is the comprehensive analysis of the co-occurrence of these features and not their marginal and isolated occurrence in naturally-broken bones that make a difference in the attribution of agency. Likewise, no example of naturally-broken bone has been published that could mimic any of the two green-broken bones documented at EAK. In contrast, we do have bones from our on-going experimentation with green elephant carcasses that jointly reproduce these features. See also Figure 6 of the article to find another example without any modern referent in the naturally-broken bones documented.

      We should emphasize that R2 is inaccurately portraying what Haynes et al.´s results really document. Contrary to R2´s assertion, trampling does not reproduce any of the examples shown above. Neither do carnivores. It should be stressed that Haynes & Harrod only document similar overlapping scarring on the medullary surface of bones, when using much smaller animals. In all the carnivore damage repertoire that they document for elephants, durophagous spotted hyenas can only inflict furrowing on the ends of the biggest long bones, especially if they are adults. Long bone midshafts remain inaccessible to them. The mid-shaft portions of bones that we document in our Supplementary File and at EAK cannot be the result of hyena (or carnivore damage) for this reason, and also because their intense gnawing on elephant bones leaves tooth marking on most of the elements that they modify, being absent in our sample.

      (3) Line 176: other than hominins accessed them in different taphonomically-defined stages- stages - the "Stages" is repeated twice

      Defined in the revised version

      (4) Line 174: Regardless of the type of butchery evidence - and with the taphonomic caveat that no unambiguous evidence exists to confirm that megafaunal carcasses were hunted or scavenged other than hominins accessed them in different taphonomically-defined stages- stages - the principal reasons for exploring megafaunal consumption in early human evolution is its origin, its episodic or temporally-patterned occurrence, its impact on hominin adaptation to certain landscapes, and its reflection on hominin group size and site functionality.

      This sentence is confusing and needs to be rewritten for clarity. It tries to combine too many ideas at once, and the phrasing makes it hard to tell what the main point is. The taphonomic caveat in the middle interrupts the sentence and obscures the argument. It should be broken into separate, clearer statements that distinguish what evidence exists, what remains uncertain, and what the broader goals of the discussion are.

      We believe the ideas are displayed clearly

      (5) Line 179: landscapes, and its reflection on hominin group size and site functionality. If hominins actively sought the exploitation of megafauna, especially if targeting early stages of carcass consumption, the recovery of an apparent surplus of resources reflects a substantially different behavior from the small-group/small-site pattern documented at several earlier Oldowan anthropogenic sites (Domínguez-Rodrigo et al., 2019) -or some modern foragers, like the Hadza, who only exploit megafaunal carcasses very sporadically, mostly upon opportunistic encounters (Marlowe, 2010; O'Connell et al., 1992; Wood, 2010; Wood and Marlowe, 2013).

      This sentence makes a reasonable point, but is written in a confusing way. The idea that early, deliberate access to megafauna would represent a different behavioral pattern from smaller Oldowan or modern foraging contexts is valid, but the sentence is awkward and hard to follow. It should be rephrased to make the logic clearer and more direct.

      We believe the ideas are displayed clearly

      (6) Line 186: When the process started of becoming megafaunal commensal started has major implications for human evolution.

      This sentence is awkward and needs to be rewritten for clarity. The phrasing "when the process started of becoming megafaunal commensal started" is confusing and grammatically incorrect. It could be revised to something like "Determining when hominins first began to interact regularly with megafauna has major implications for human evolution," or another version that clearly identifies the process being discussed.

      Modified in the revised version

      (7) Line189: The multiple taphonomic biases intervening in the palimpsestic nature of most of these butchery sites often prevent the detection of the causal traces linking megafaunal carcasses and hominins. Functional links have commonly been assumed through the spatial concurrence of tools and carcass remains; however, this perception may be utterly unjustified as we argued above. Functional association of both archaeological elements can more securely be detected through objective spatial statistical methods. This has been argued to be foundational for heuristic interpretations of proboscidean butchery sites (Giusti, 2021). Such an approach removes ambiguity and solidifies spatial functional association, as demonstrated at sites like Marathousa 1 (Konidaris et al., 2018) or TK Sivatherium (Panera et al., 2019). This method will play a major role in the present study.

      This section overstates what spatial analysis can demonstrate and misrepresents the cited studies. The works by Giusti (2021), Konidaris et al. (2018), and Panera et al. (2019) do use spatial statistics to examine relationships between artifacts and faunal remains, but they explicitly caution that spatial overlap alone does not prove functional or behavioral association. These studies argue that clustering can support such interpretations only when combined with detailed taphonomic and stratigraphic evidence. None of them claims that spatial analysis "removes ambiguity" or "solidifies" functional links. The text should be revised to reflect the more qualified conclusions of those papers and to avoid implying that spatial statistics can establish behavioral causation on their own.

      We disagree. Both works (Giusti and Panera) use spatial statistical tools to create an inferential basis reinforcing a functional association of lithics and bones. In both cases, the anthropogenic agency inferred is based on that. We should stress that this only provides a basis for argumentation, not a definitive causation. Again, those analyses show much more than just apparent visual clustering.

      (8) Line 200: Here, we present the discovery of a new elephant butchery site (Emiliano Aguirre Korongo, EAK), dated to 1.78 Ma, from the base of Bed II at Olduvai Gorge. It is the oldest unambiguous proboscidean butchery site at Olduvai.

      It is fine to state the main finding in the introduction, but the phrasing here is too strong. Calling EAK "the oldest unambiguous proboscidean butchery site" asserts certainty before the evidence is presented. The claim should be stated more cautiously, for example, "a new site that provides early evidence for proboscidean butchery," so that the language reflects the strength of the data rather than pre-judging it.

      We understand the caution by R2, but in this case, EAK is the oldest taphonomically-supported evidence of elephant butchery at Olduvai (see discussion about FLK North in the text). Whether this is declared at the beginning or the end of the text is irrelevant.

      (9) Line 224: The drying that characterizes Bed II had not yet taken place during this moment.

      This sentence reads like a literal translation. It should be rewritten for clarity.

      Modified in the revised version

      (10) Line 233: During the recent Holocene, the EAK site was affected by a small landslide which displaced the...

      This section contains far more geological detail than is needed for the argument. The reader only needs to know that the site block was displaced by a small Holocene landslide but retains its stratigraphic integrity. The extended discussion of regional faults, seismicity, and slope processes goes well beyond what is necessary for context and distracts from the main focus of the paper.

      We disagree. The geological information is what is most commonly missing from most archaeological reports. Here, it is relevant because of the atypical process and because it has been documented only twice with elephant butchery sites. Explaining the dynamic geological process that shaped the site helps to understand its spatial properties.

      (11) Line 264: In June 2022, a partial elephant carcass was found at EAK on a fragmented stratigraphic block...

      This section reads like field notes rather than a formal site description. Most of the details about the discovery sequence, trench setup, and excavation process are unnecessary for the main text. Only the basic contextual information about the find location, stratigraphic position, and anatomical composition is needed. The rest could be condensed or moved to the methods or supplementary material.

      We disagree. See reply above.

      (12) Line 291: hominins or other carnivores. Ongoing restoration work will provide an accurate estimate of well-preserved and modified fractions of the assemblage.

      This sentence is unclear and needs to specify what kind of restoration work is being done and what is meant by well-preserved and modified fractions. It is not clear whether modified refers to surface marks, diagenetic alteration, or something else. If the bones are still being cleaned or prepared, the analysis is incomplete, and the counts cannot be considered final. If restoration only means conservation or stabilization, that should be stated clearly so the reader understands that it does not affect the results. As written, it is not clear whether the data presented here are preliminary or complete.

      We added: For this reason, until restoration is concluded, we cannot produce any asssertion about the presence or absence of bone surface modifications.

      (13) Line 294: The tibiae were well preserved, but the epiphyseal portions of the femora were missing, probably removed by carnivores, which would also explain why a large portion of the rib cage and almost all vertebrae are missing.

      This explanation is not well supported. The missing elements could be the result of other forms of density-mediated destruction, such as sediment compaction or post-depositional fragmentation, especially since no tooth marks were found. Given the low density of ribs, vertebrae, and femoral epiphyses, these processes are more likely explanations than carnivore removal. The text should acknowledge these alternatives rather than attributing the pattern to carnivore activity without direct evidence.

      Sediment compaction and post-depositional can break bones but cannot make them disappear. Our excavation process was careful enough to detect bone if present. Their absence indicates two possibilities: erosion through the years at the front of the excavation or carnivore intervention. Carnivores can take elephant bones without impacting the remaining assemblage (see our reply above to a similar comment).

      (14) Line 304: The fact that the carcass was moved while encased in its sedimentary context, along with the close association of stone tools with the elephant bones, is in agreement with the inference that the animal was butchered by hominins. A more objective way to assess this association is through spatial statistical analysis.

      The authors state that "the carcass was moved while encased in its sedimentary context, along with the close association of stone tools with the elephant bones, is in agreement with the inference that the animal was butchered by hominins." This does not logically follow. Movement of the block explains why the bones and tools remain together, not how that association was created. The preserved association alone does not demonstrate butchery, especially in the absence of cut marks or other direct evidence of hominin activity.

      Again, we are sorry that R2 is completely overlooking the strong signal detected by the spatial statistical analysis. The way that the block moved, it preserved the original association of bones and tools. This statement is meant to clarify that despite the allochthonous nature of the block, the original autochthonous depositional process of both types of archaeological materials has been preserved. The spatial association, as statistically demonstrated, indicates that the functional link is more likely than any other alternative process. The additional fact that nowhere else in that portion of the outcrop do we identify scatters of tools (all appear clustered at a landscape scale with the elephant) adds more support to this interpretation. This would have been further supported by the presence of cut marks, no doubt, but their absence does not indicate lack of functional association, since as Haynes´ works have clearly shown, most bulk defleshing of modern elephant leaves no traces on most bones.

      (15) Line 370: This also shows that the functional connection between the elephant bones and the tools has been maintained despite the block post-sedimentary movement.

      The spatial analyses appear to have been carried out appropriately, and the interpretations of clustering and segregation are consistent with the reported results. However, the conclusion that the "functional connection" between bones and tools has been maintained goes beyond what spatial correlation alone can demonstrate. These analyses show spatial proximity and scale-dependent clustering but cannot, by themselves, confirm a behavioral or functional link.

      R2 is making this comment repeatedly and we have addressed it more than once above. We disagree and we refer to our replies above to sustain it.

      (16) Line 412: The clustering of the elephant (and hippopotamus) carcasses in the areas containing the highest densities of landscape surface artifacts is suggestive of a hominin agency in at least part of their consumption and modification. The presence of green broken elephant long bone elements in the area surveyed is only documented within such clusters, both for lower and upper Bed II. This constitutes inverse negative evidence for natural breaks occurring on those carcasses through natural (i.e., non-hominin) pre- and peri-mortem limb breaking (Haynes et al., 2021, 2020; Haynes and Hutson, 2020). In this latter case, it would be expected for green-broken bones to show a more random landscape distribution, and occur in similar frequencies in areas with intense hominin landscape use (as documented in high density artifact deposition) and those with marginal or non-hominin intervention (mostly devoid of anthropogenic lithic remains).

      The clustering of green-bone fractures with stone tools is intriguing but should be interpreted cautiously. The Haynes references are misrepresented here. Those studies address both cut marks and green-bone (spiral) fractures, emphasizing that each can arise through non-hominin processes such as trampling, carcass collapse, and sediment loading. They do not treat green fractures as clearer evidence of butchery; in fact, they caution that such breakage patterns can occur naturally and even form clustered distributions in areas of repeated animal activity. The claim that these studies support spiral fractures as unambiguous indicators of hominin activity, or that natural breaks would be randomly distributed, is not accurate.

      We would like to emphasize again that the Haynes´references are not misrepresented here. See our extensive reply above. If R2 can provide evidence of natural breakage patterns resulting from pre-mortem limb breaking or post-mortem trampling resulting in all limb bones being affected by these processes and resulting in smooth spiral breaks, accompanied with extensive and overlapping scarring on the medullary surface, in conjunction with the other features described in our replies above, then we would be willing to reconsider. With the evidence reported until now, that does not occur simultaneously on specimens resulting from studies on modern elephant bones.

      R2 seems to contradict him(her)self here by saying that Haynes studies show that cut marks are not reliable because they can also be reproduced via trampling. Until this point, R2 had been saying that only cut marks could demonstrate a functional link and support butchery. Haynes´ studies do not deal experimentally with sediment loading.

      (17) Line 424: This indicates that from lower Bed II (1.78 Ma) onwards, there is ample documented evidence of anthropogenic agency in the modification of proboscidean bones across the Olduvai paleolandscapes. The discovery of EAK constitutes, in this respect, the oldest evidence thereof at the gorge. The taphonomic evidence of dynamic proboscidean bone breaking across time and space supports, therefore, the inferences made by the spatial statistical analyses of bones and lithics at the site.

      This conclusion is overstated. The claim of "ample documented evidence of anthropogenic agency" is too strong, given that the main support comes from indirect indicators like green-bone fractures and spatial clustering rather than clear butchery marks. It would be more accurate to say that the evidence suggests or is consistent with possible hominin involvement. The final sentence also conflates association with causation; spatial and taphonomic data can indicate a relationship, but do not confirm that the carcasses were butchered by hominins.

      The evidence is based on spatially clustering (at a landscape scale) of tools and elephant (and other megafaunal taxa) bones, in conjunction with a large amount of green-broken elements. This interpretation, if we compare it against modern referents is supported even stronger. In the past few years, we have been conducting work on modern naturally dead elephant carcasses in Botswana and Zambia, and of the several carcasses that we have seen, we have not identified a single case of long bone shaft breaks like those described by Haynes as natural or like those we describe here as anthropogenic. This probably means that they are highly unlikely or marginal occurrences at a landscape scale. This seems to be supported by Haynes´ work too. Out of the hundreds of elephant carcasses that he has monitored and studied over the years for different works, we have managed to identify only two instances where he described natural pre-mortem breaks. This certainly qualifies as extremely marginal. 

      Most of the Results section is clearly descriptive, but beginning with "The clustering of the elephant (and hippopotamus) carcasses..." the text shifts from reporting observations to drawing behavioral conclusions. From this point on, it interprets the data as evidence of hominin activity rather than simply describing the patterns. This part would be more appropriate for the Discussion, or should be rewritten in a neutral, descriptive way if it is meant to stay in the Results.

      This appears extensively discussed in the Discussion section, but the data presented in the results is also interpreted in that section, following a clear argumental chain.

      (18) Line 433: A recent discovery of a couple of hippopotamus partial carcasses at the 3.0-2.6 Ma site of Nyayanga (Kenya), spatially concurrent with stone artifacts, has been argued to be causally linked by the presence of cut marks on some bones (Plummer et al., 2023). The only evidence published thereof is a series of bone surface modifications on a hippo rib and a tibial crest, which we suggest may be the result of byproduct of abiotic abrasive processes; the marks contrast noticeably with the well-defined cut marks found on smaller mammal bones (Plummer et al. ́s 2023: Figure 3C, D) associated with the hippo remains (Plummer et al., 2023).

      The authors suggest that the Nyayanga marks could result from abiotic abrasion, but this claim does not engage with the detailed evidence presented by Plummer et al. (2023). Plummer and colleagues documented well-defined, morphologically consistent cut marks and considered the sedimentary context in their interpretation. Raising abrasion as a general possibility without addressing that analysis gives the impression of selective skepticism rather than an evaluation grounded in the published data.

      We disagree again on this matter. R2 does not clarify what he/she means by well-defined or morphologically consistent. We provide an alternative interpretation of those marks that fit their morphology and features and that Plummer at al did not successfully exclude. We also emphasize that the interpretation of the Nyayanga marks was made descriptively, without any analytical approach and with a high degree of subjectivity by the researcher. All of this disqualifies the approach as well defined and keeps casting an old look at modern taphonomy. Descriptive taphonomy is a thing of the 1980´s. Today there are a plethora of analytical methods, from multivariate statistics, to geometric morphometrics to AI computer vision (so far the most reliable) which represent how taphonomy (and more specifically, analysis of bone surface modifications) should be conducted in the XXI century. This approaches would reinforce interpretations as preliminarily published by Plummer et al, provided they reject alternative explanations like those that we have provided.

      (19) Line 459: It would have been essential to document that the FLK N6 tools associated with the elephant were either on the same depositional surface as the elephant bones and/or on the same vertical position. The ambiguity about the FLK N6 elephant renders EAK the oldest secure proboscidean butchery evidence at Olduvai, and also probably one of the oldest in the early Pleistocene elsewhere in Africa.

      The concern about vertical mixing is fair, but the tone makes it sound like the association is definitely not real. It would be more accurate to say that the evidence is ambiguous, not that it should be dismissed altogether.

      We have precisely done so. We do not dismiss it, but we cannot take it for anything solid since we excavated the site and show how easily one could make functional associations if forgetting about the third dimension. It is not a secure butchery site. This is what we said and we stick to this statement.

      (20) Line 479: In all cases, these wet environments must have been preferred places for water-dependent megafauna, like elephants and hippos, and their overlapping ecological niches are reflected in the spatial co-occurrence of their carcasses. Both types of megafauna show traces of hominin use through either cutmarked or percussed bones, green-broken bones, or both (Supplementary Information).

      The environmental part is good, but the behavioral interpretation is too strong. Saying elephants and hippos "must have been" drawn to these areas is too certain, and claiming that both "show traces of hominin use" makes it sound like every carcass was modified. It should be clearer that only some have possible evidence of this.

      The sentence only refers to both types of fauna taxonomically. No inference can be drawn therefor that all carcasses are modified.

      (21) Line 496: In most green-broken limb bones, we document the presence of a medullary cavity, despite the continuous presence of trabecular bone tissue on its walls.

      This sentence is confusing and doesn't seem to add anything meaningful. All limb bones naturally have a medullary cavity lined with trabecular bone, so it's unclear why this is noted as significant. The authors should clarify what they mean here or remove it if it's simply describing normal bone structure.

      No. Modern elephant long bones do not have a hollow medullary cavity. All the medullary volume is composed of trabecular tissue. Some elephants in the past had hollow medullary cavities, which probably contained larger amounts of marrow and fat. 

      (22) Line 518: We are not confident that the artefacts reported by de la Torre et al are indeed tools.

      While I generally agree with this statement, the paragraph reads as defensive rather than comparative. It would help if they briefly summarized what de la Torre et al. actually argued before explaining why they disagree.

      We devote two full pages of the Discussion section to do so precisely.

      (23) Lines 518-574: They are similar to the green-broken specimens that we have reported here...

      This part is very detailed but inconsistent. They argue that the T69 marks could come from natural processes, but they use similar evidence (green fractures, overlapping scars) to argue for human activity at EAK. If equifinality applies to one, it applies to both.

      We are confused by this misinterpretation. Features like green fractures and overlapping scars (among others) can be used to detect anthropogenic agency in elephant bone breaking; that is, any given specimen can be determined to have been an “artifact” (in the sense of human-created item), but going from there to interpreting an artifact as a tool, there is a large distance. Whereas an artifact (something made by a human) can be created indirectly through several processes (for example, demarrowing a bone resulting in long bone fragments), a tool suggest either intentional manufacture and use or both. That is the difference between de la Torre et al.´s interpretation and ours. We believe that they are showing anthropogenically-made items, but they have provided no proof that they were tools.

      (24) Line 576: A final argument used by the authors to justify the intentional artifactual nature of their bone implements is that the bone tools were found in situ within a single stratigraphic horizon securely dated to 1.5 million years ago, indicating systematic production rather than episodic use. This is taphonomically unjustified.

      The reasoning here feels uneven in how clustering evidence is used. At EAK, clustering of bones and artifacts is taken as meaningful evidence of hominin activity, but here the same pattern at T69 is treated as a natural by-product of butchery or carnivore activity. If clustering alone cannot distinguish between intentional and incidental association, the authors should clarify why it is interpreted as diagnostic in one case but not in the other.

      Again, we are confused by this misinterpretation. It applies to two different scenarios/questions:

      a) is there a functional link between tools and bones at EAK and T69? We have statistically demonstrated that at EAK and we think de la Torre et al. is trying to do the same for T69, although using a different method. 

      b) Are the purported tools at T69 tools? Are those that we report here tools? In this regard there is no evidence for either case and given that several bones from T69 come from animals smaller than elephants, we do not discard that carnivores might have been responsible for those, whereas hominin butchery might have been responsible for the intense long limb breaking at that site. It remains to be seen how many (if any) of those specimens were tools.

      (25) Line 600: If such a bone implement was a tool, it would be the oldest bone tool documented to date (>1.7 Ma).

      The comparison to prior studies is useful, and the point about missing use-wear traces is well taken. However, the last lines feel speculative. If no clear use evidence has been found, it's premature to suggest that one specimen "would be the oldest bone tool." That claim should be either removed or clearly stated as hypothetical.

      It clearly reads as hypothetical.

      (26) Line 606: Evidence documents that the oldest systematic anthropogenic exploitation of proboscidean carcasses are documented (at several paleolandscape scales) in the Middle Pleistocene sites of Neumark-Nord (Germany)(Gaudzinski-Windheuser et al., 2023a, 2023b).

      This is the first and only mention of Neumark-Nord in the paper, and it appears without any prior discussion or connection to the rest of the study. If this site is being used for comparison or as part of a broader temporal framework, it needs to be introduced and contextualized earlier. As written, it feels out of place and disconnected from the rest of the argument.

      This is a Late Pleistocene site and we do not see the need to present it earlier, given that the scope of this work is Early Pleistocene.

      (27) Line 608: Evidence of at least episodic access to proboscidean remains goes back in time (see review in Agam and Barkai, 2018; Ben-Dor et al., 2011; Haynes, 2022).

      The distinction between "systematic" and "episodic" exploitation is useful, but the authors should clarify what criteria define each. The phrase "episodic access...goes back in time" is vague and could be replaced with a clearer statement summarizing the nature of the earlier evidence.

      It is self-explanatory

      (28) Line 610: Redundant megafaunal exploitation is well documented at some early Pleistocene sites from Olduvai Gorge (Domínguez-Rodrigo et al., 2014a, 2014b; Organista et al., 2019, 2017, 2016).

      The phrase "redundant megafaunal exploitation" needs clarification. "Redundant" is not standard terminology in this context. Does this mean repeated, consistent, or overlapping behaviors? Also, while these same Olduvai sites are mentioned earlier, this phrasing also introduces new interpretive language not used before and implies a broader behavioral generalization than what the data actually show.

      Webster: Redundant means repetitive, occurring multiple times.

      (29) Line 612: At the very same sites, the stone artifactual assemblages, as well as the site dimensions, are substantially larger than those documented in the Bed I Oldowan sites (Diez-Martín et al., 2024, 2017, 2014, 2009).

      The placement and logic of this comparison are unclear. The discussion moves from Middle Pleistocene Neumark-Nord to early Pleistocene Olduvai sites, then to Bed I Oldowan contexts without clearly signaling the temporal or geographic transitions. If the intent is to contrast Acheulean vs. Oldowan site scale or organization, that connection needs to be made explicit. As written, it reads as a disjointed shift rather than a continuation of the argument.

      We disagree. Here, we finalize by bringing in some more recent assemblages where hominin agency is not in question.

      (30) Line 616: Here, we have reported a significant change in hominin foraging behaviors during Bed I and Bed II times, roughly coinciding with the replacement of Oldowan industries by Acheulian tool kits -although during Bed II, both industries co-existed for a substantial amount of time (Domínguez-Rodrigo et al., 2023; Uribelarrea et al., 2019, 2017).

      This section should be restructured for flow. The reference to behavioral change during Bed I-II and the overlap of Oldowan and Acheulean industries is important, but feels buried after a long detour. Consider moving this earlier or rephrasing so the main conclusion (behavioral change across Beds I-II) is clearly stated first, followed by supporting examples.

      It is not within the scope of this work and is properly described in the references mentioned.

      (31) Line 620: The evidence presented here, together with that documented by de la Torre et al. (2025), represents the most geographically extensive documentation of repeated access to proboscidean and other megafaunal remains at a single fossil locality.

      The phrase "most geographically extensive documentation of repeated access" overstates what has been demonstrated. The evidence presented is site-specific and does not justify such a broad superlative. This should be toned down or supported with comparative quantitative data.

      We disagree. There is no other example where such an abundant record of green-broken elements from megafauna is documented. Neumark-Nord is more similar because it shows extensive evidence of butchery, but not so much about degreasing.

      (32) Line 623: The transition from Oldowan sites, where lithic and archaeofaunal assemblages are typically concentrated within 30-40 m2 clusters, to Acheulean sites that span hundreds or even over 1000 m2 (as in BK), with distinct internal spatial organization and redundancy in space use across multiple archaeological layers spanning meters of stratigraphic sequence (Domínguez-Rodrigo et al., 2014a, 2009b; Organista et al., 2017), reflects significant behavioral and technological shifts.

      This sentence about site size and spatial organization repeats earlier claims without adding new insight. If it's meant as a synthesis, it should explicitly say how the spatial expansion relates to changes in behavior or mobility, not just describe the difference.

      In the Conclusion section these correlations have been explained in more detail to add some causation.

      (33) Line 628: This pattern likely signifies critical innovations in human evolution, coinciding with major anatomical and physiological transformations in early hominins (Dembitzer et al., 2022; Domínguez-Rodrigo et al., 2021, 2012).

      The conclusion that this "signifies critical innovations in human evolution" is too sweeping, given the data presented. It introduces physiological and anatomical transformation without connecting it to any evidence in this paper. Either cite the relevant findings or limit the claim to behavioral implications.

      The references cited elaboration in extension this. The revised version of the Conclusion section also elaborates on this.

      Overall, the conclusions section reads as a loosely connected set of assertions rather than a focused synthesis. It introduces new interpretations and terminology not supported or developed earlier in the paper, and the argument jumps across temporal and geographic scales without clear transitions. The discussion should be restructured to summarize key results, clarify the scope of interpretation, and avoid speculative or overstated claims about evolutionary significance.

      We have done so, supported by the references used in addition to extending some of the arguments

      (34) Line 639: The systematic excavation of the stratigraphic layers involved a small crew.

      This sentence is not necessary.

      No comment

      (35) Line 643: The orientation and inclination of the artifacts were recorded using a compass and an inclinometer, respectively.

      What were these measurements used for (e.g., post-depositional movement analysis, spatial patterning)? A short note on the purpose would make this more meaningful.

      Fabric analysis has been added to the revised version.

      (36) Line 659: Restoration of the EAK elephant bones

      This section could be streamlined and clarified. It includes procedural detail that doesn't contribute to scientific replicability (e.g., the texture of gauze, number of consolidant applications), while omitting some key information (such as how restoration may have affected analytical results). It also contains interpretive comments ("most of the assemblage has been successfully studied") that don't belong in Methods.

      No comment

      (37) Line 689: In the field laboratory, cleaning of the bone remains was carried out, along with adhesion of fragments and their consolidation when necessary.

      Clarify whether cleaning or adhesion treatments might obscure or alter bone surface modifications, as this has analytical implications.

      These protocols do not impact bone like that anymore.

      (38) Line 711: (b) Percussion Tools - Includes hammerstones or cobbles exhibiting diagnostic battering, pitting, and/or impact scars consistent with percussive activities.

      Define how diagnostic features (battering, pitting) were identified - visual inspection, magnification, or quantitative criteria?

      Both macro and microscopically

      (39) Line 734: We conducted the analysis in three different ways after selecting the spatial window, i.e., the analysed excavated area (52.56 m2).

      Clarify why the 52.56 m<sup>2</sup> spatial window was chosen. Was this the total excavated area or a selected portion?

      It was what was left of the elephant accumulation after erosion.

      (40) Line 728: The spatial statistical analyses of EAK.

      Adding one or two sentences at the start explaining the analytical objective, such as testing spatial association between faunal and lithic materials, would help readers understand how each analysis relates to the broader research questions.

      This is well explained in the main text

      (41) Line 782: An intensive survey seeking stratigraphically-associated megafaunal bones was carried out in the months of June 2023 and 2024.

      It would help to specify whether the same areas were resurveyed in both field seasons or if different zones were covered each year. This information is important for understanding sampling consistency and potential spatial bias.

      Both areas were surveyed in both field seasons. We were very consistent.

      (42) Line 787: We focused on proboscidean bones and used hippopotamus bones, some of the most abundant in the megafaunal fossils, as a spatial control.

      Clarify how the hippopotamus remains functional as a "spatial control." Are they used as a proxy for water-associated taxa to test habitat patterning, or as a baseline for comparing carcass distribution? The meaning of "control" in this context is ambiguous.

      As a proxy for megafaunal distribution given their greater abundance over any other megafaunal taxa.

      (43) Line 789: Stratigraphic association was carried out by direct observation of the geological context and with the presence of a Quaternary geologist during the whole survey.

      This is good methodological practice, but it would be helpful to describe how stratigraphic boundaries were identified in the field (for example, by reference to tuffs or marker beds). That information would make the geological framework more replicable.

      This is basic geological work. Of course, both tuffs and marker beds were followed.

      (44) Line 791: When fossils found were ambiguously associated with specific strata, these were excluded from the present analysis.

      You might specify what proportion of the total finds were excluded due to uncertain stratigraphic association. Reporting this would indicate the strength of the stratigraphic control.

      This was not quantified but it was a very small amount compared to those whose stratigraphic provenience was certain.

      (45) Line 799: The goals of this survey were: a) collect a spatial sample of proboscidean and megafaunal bones enabling us to understand if carcasses on the Olduvai paleolandscapes were randomly deposited or associated to specific habitats.

      You might clarify how randomness or habitat association was tested.

      Randomness was tested spatially and comparing density according to ecotone. Same for habitat association.

      (46) The Methods section provides detailed information about excavation, restoration, and spatial analyses but omits critical details about the zooarchaeological and taphonomic procedures. There is no explanation of how faunal remains were analyzed once recovered, including how cut marks, percussion marks, or green bone fractures were identified or what magnification or diagnostic criteria were used. The authors also do not specify the analytical unit used for faunal quantification (e.g., NISP, MNI, MNE, or other), making it unclear how specimen counts were generated for spatial or taphonomic analyses. Even if these details are provided in the Supplementary Information, the main text should include at least a concise summary describing the analytical framework, the criteria for identifying surface modifications and fracture morphology, and the quantification system employed. This information is essential for transparency, replicability, and proper evaluation of the behavioral interpretations.

      See reply above. There is a new subsection on taphonomic methods now.

      Supplementary information:

      (47) The Supplementary Information includes a large number of green-broken proboscidean specimens from other Olduvai localities (BK, LAS, SC, FLK West), but it is never explained why these are shown or how they relate to the EAK study. The main analysis focuses entirely on the EAK elephant, including so much unrelated material without any stated purpose, which makes the supplement confusing. If these examples are meant only to illustrate the appearance of green fractures, that should be stated. Otherwise, the extensive inclusion of non-EAK material gives the impression that they were part of the analyzed assemblage when they were not.

      This is stated in the opening paragraph to the section.

      (48) Line 96: A small collection of green-broken elephant bones was retrieved from the lower and upper Bed II units.

      It would help to clarify whether these specimens are part of the EAK assemblage or derive from other Bed II localities. As written, it is not clear whether this description refers to material analyzed in the main text or to comparative examples shown only in the Supplementary Information.

      No, EAK only occupies the lower Bed II section. They belong in the Bed II paleolandscape units.

      (49) Line 97: One of them, a proximal femoral shaft found within the LAS unit, has all the traces of having been used as a tool (Figure 6).

      This says the bone tool in Figure 6 is from LAS, but the main text caption identifies it as from EAK. If I am not mistaken, EAK is a site at the base of Bed II, and LAS is a separate stratigraphic unit higher in the sequence, so the authors should clarify which is correct.

      Our mistake. It provenience is from LAS in the vicinity of EAK.

      (50) Line 186: Figure S20. Example of other megafaunal long bone shafts showing green breaks.

      Not cited in text or SI narrative. No indication where these bones come from or why they are relevant.

      It appears justified in the revised version.

      (51) Line 474: Figure S28-S30. Hyena-ravaged giraffe bones from Chobe (Botswana).

      These figures are not discussed in the text or SI, and their relevance to the study is unclear. The authors should explain why these modern comparative examples were included and how they inform interpretations of the Olduvai assemblages.

      It appears justified in the revised version.

      (52) Line 498: Figure S31. Bos/Bison bone from Bois Roche (France).

      This figure is not mentioned in the text or Supplementary Information. The authors should specify why this specimen is shown and how it contributes to the study's taphonomic or behavioral comparisons.

      It appears justified in the revised version.

      (53) Line 504: Figure S32. Miocene Gomphotherium femur from Spain.

      This figure is never referenced in the paper. The authors should clarify the purpose of including a Miocene specimen from outside Africa and explain what it adds to the interpretation of Bed II material.

      It appears justified in the revised version.

      (54) Line 508: Figure S33. Elephant femoral shaft from BK (Olduvai).

      This figure appears to show comparative material but is not cited or discussed in the text. The authors should explain why the BK material is presented here and how it relates to EAK or the broader analysis.

      There are two figures labeled S33.

      It appears justified in the revised version.

      (55) Line 515: Figure S33. Tibia fragment from a large medium-sized bovid displaying multiple overlapping scars on both breakage planes inflicted by carnivore damage.

      Because this figure repeats the S33 label and is not cited or explained in the text, it is unclear why this specimen is included or how it contributes to the study. The authors should correct the duplicate numbering and clarify the purpose of this figure.

      It appears justified in the revised version.

      (56) Line 522: Same specimen as shown in Figure S30, viewed on its medial side.

      This is not the same bone as S30. This figure is not discussed in the text or Supplementary Information. The authors should clarify why it is included and how it relates to the rest of the analysis.

      It appears justified in the revised version.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews: 

      Reviewer #1 (Public review): 

      Summary: 

      This paper focuses on understanding how covalent inhibitors of peroxisome proliferator-activated receptor-gamma (PPARg) show improved inverse agonist activities. This work is important because PPARg plays essential roles in metabolic regulation, insulin sensitization, and adipogenesis. Like other nuclear receptors, PPARg, is a ligand-responsive transcriptional regulator. Its important role, coupled with its ligand-sensitive transcriptional activities, makes it an attractive therapeutic target for diabetes, inflammation, fibrosis, and cancer. Traditional non-covalent ligands like thiazolininediones (TZDs) show clinical benefit in metabolic diseases, but utility is limited by off-target effects and transient receptor engagement. In previous studies, the authors characterized and developed covalent PPARg inhibitors with improved inverse agonist activities. They also showed that these molecules engage unique PPARg ligand binding domain (LBD) conformations whereby the c-terminal helix 12 penetrates into the orthosteric binding pocket to stabilize a repressive state. In the nuclear receptor superclass of proteins, helix 12 is an allosteric switch that governs pharmacologic responses, and this new conformation was highly novel. In this study, the authors did a more thorough analysis of how two covalent inhibitors, SR33065 and SR36708 influence the structural dynamics of PPARg LBD. 

      Strengths: 

      (1) The authors employed a compelling integrated biochemical and biophysical approach.  

      (2) The cobinding studies are unique for the field of nuclear receptor structural biology, and I'm not aware of any similar structural mechanism described for this class of proteins.  

      (3) Overall, the results support their conclusions.  

      (4) The results open up exciting possibilities for the development of new ligands that exploit the potential bidirectional relationship between the covalent versus non-covalent ligands studied here. 

      Weaknesses: 

      (1) The major weakness in this work is that it is hard to appreciate what these shifting allosteric ensembles actually look like on the protein structure. Additional graphical representations would really help convey the exciting results of this study. 

      We thank the review for the comments. In response to the specific recommendations below, we added two new figures—Figure 1 and Figure 8 in this resubmission—that hopefully address the weakness identified by the reviewer.

      Reviewer #2 (Public review): 

      Summary: 

      The authors use ligands (inverse agonists, partial agonists) for PPAR, and coactivators and corepressors, to investigate how ligands and cofactors interact in a complex manner to achieve functional outcomes (repressive vs. activating). 

      Strengths: 

      The data (mostly biophysical data) are compelling from well-designed experiments. Figures are clearly illustrated. The conclusions are supported by these compelling data. These results contribute to our fundamental understanding of the complex ligand-cofactor-receptor interactions. 

      Weaknesses: 

      This is not the weakness of this particular paper, but the general limitation in using simplified models to study a complex system. 

      We appreciate the reviewer’s comments. Breaking down a complex system into a simpler model system, when possible, provides a unique lens with which to probe systems with mechanistic insight. While simplified models may not always explain the complexity of systems in cells, for example, our recently published work showed that a simplified model system — biochemical assays using reconstituted PPARγ ligand-binding domain (LBD) protein and peptides derived from coregulator proteins (similar to the assays in this current work) and protein NMR structural biology studies using PPARγ LBD — can explain the activity of ligand-induced PPARγ activation and repression to a high degree (pearson/spearman correlation coefficients ~0.7-0.9):

      MacTavish BS, Zhu D, Shang J, Shao Q, He Y, Yang ZJ, Kamenecka TM, Kojetin DJ. Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states. Nat Commun. 2025 Feb 28;16(1):2065. doi: 10.1038/s41467-025-57325-4. PMID: 40021712; PMCID: PMC11871303.

      Recommendations for the authors

      Reviewer #1 (Recommendations for the authors): 

      (1) More set-up is needed in the results section. The first paragraph is unclear on what is new to this study versus what was done previously. Likewise, a brief description of the assays used and the meaning behind differences in signals would help the general reader along. 

      We modified the last paragraph of the introduction and first results section to hopefully better set the stage for what was done previously vs. what is new/recollected in this study. In our results section, we also include more description about what the assays measure.

      (2) Since this paper is building on previous work, additional figures are needed in the introduction and discussion. Graphical depictions of what was found in the first study on how these ligands uniquely influence PPARg LBD conformation. A new model/depiction in the discussion for what was learned and its context with the rest of the field. 

      Our revised manuscript includes a new Figure 1 describing the possible allosteric mechanism by which a covalent ligand inhibits binding of other non-covalent ligands that was inferred from our previous study; and a new Figure 8 with a model for what has been learned.

      (3) It is stated that the results shown are representative data for at least two biological replicates. However, I do not see the other replicates shown in the supplementary information. 

      We appreciate the Reviewer’s emphasis on data reproducibility and rigor. We confirm that the biochemical and cellular assay data presented are indeed representative of consistent findings observed across two or more biological replicates—and we show representative data in our figures but not the extensive replicate data in supplementary information consistent with standard practices.

      (4) Figure 1a could benefit from labels of antagonists, inverse agonist, etc., next to each chemical structure. Likewise, if any co-crystal or other models are available it would be helpful to include those for comparison. 

      We added the pharmacological labels to Figure 2a (old Figure 1a).

      (5) The figure legends don't seem to match up completely with the figures. For example, Figure 2b states that fitted Ki values +/- standard deviation. are stated in the legend, but it's shown as the log Ki. 

      We revised the figure legends to ensure they display the appropriate errors as reported from the data fitting.

      (6) EC50, IC50, Ki, and Kd values alongside reported errors and R2 values for the fits should be reported in a table. 

      Our revised manuscript now includes a Source Data file (Figure 5—source data 1.xlsx) of the data (n=2) plotted in Figure 5 (old Figure 4) so that readers can regenerate the plots and calculate the errors and R2 values if desired. Otherwise, fitted values and errors are reported in figures when fitting in Prism permitted and reported errors; when Prism was unable to fit data or fit the error, n.d. (not determined) is specified.

      (7) Statistical analysis is missing in some places, for example, Figure 1b. 

      We revised Figure 2b (old Figure 1b) to include statistical testing.

      Reviewer #2 (Recommendations for the authors): 

      I suggest that the authors discuss the following points to broaden the significance of the results: 

      (1) The two partial agonists MRL24 and nTZDpa) are "partial" in the coactivator and corepressor recruitment assays, but are "complete" in the TR-FRET ligand displacement assay (Figure 2). Please explain that a partial agonist is defined based on the functional outcome (cofactor recruitment in this study) but not binding affinity/efficacy. 

      We added the following sentence to describe the partial agonist activity of these compounds: “These high affinity ligands are partial agonists as defined on their functional outcome in coregulator recruitment and cellular transcription; i.e., they are less efficacious than full agonists at recruiting peptides derived from coactivator proteins in biochemical assays (Chrisman et al., 2018; Shang et al., 2019; Shang and Kojetin, 2024) and increasing PPARγ-mediated transcription (Acton et al., 2005; Berger et al., 2003).“

      (2) Will the discovery reported here be broadly applicable? 

      (a) Applicable if other partial agonists and inhibitors are used? 

      (b) Applicable if different coactivators/corepressors, or different segments of the same cofactor, are used?

      (c) Applicable to other NRs (their AF-2 are similar but with sequence variation)?

      (d) The term "allosteric" might mean different things to different people - many readers might think that it means a "distal and unrelated" binding pocket. It might be helpful to point out that in this study, the allosteric site is actually "proximal and related". 

      We expanded our introduction and/or discussion sections to expand upon these concepts; specific answers as follows:

      (a) Orthosteric partial agonists?—yes, because helix 12 would clash with an orthosteiric ligand; other covalent inhibitors?—it depends on whether the covalent inhibitor stabilizes helix 12 in the orthosteric pocket.

      (b) yes with some nuanced exceptions where certain segments of the same coregulator protein bind with high affinity and others apparently do not bind or bind with low affinity

      (c) it is not clear yet if other NRs share a similar ligand-induced conformational ensemble to PPARγ

      (d) we addressed this point in the 4th paragraph of the introduction “...the non-covalent ligand binding event we previously described at the alternate/allosteric site, which is proximal to the orthosteric ligand-binding pocket, …”

    1. Author response:

      Public Reviews: 

      Reviewer #1 (Public review): 

      Summary: 

      This study aims to explore how different forms of "fragile nucleosomes" facilitate RNA Polymerase II (Pol II) transcription along gene bodies in human cells. The authors propose that pan-acetylated, pan-phosphorylated, tailless, and combined acetylated/phosphorylated nucleosomes represent distinct fragile states that enable eFicient transcription elongation. Using CUT&Tagseq, RNA-seq, and DRB inhibition assays in HEK293T cells, they report a genome-wide correlation between histone pan-acetylation/phosphorylation and active Pol II occupancy, concluding that these modifications are essential for Pol II elongation. 

      Strengths: 

      (1) The manuscript tackles an important and long-standing question about how Pol II overcomes nucleosomal barriers during transcription. 

      (2) The use of genome-wide CUT&Tag-seq for multiple histone marks (H3K9ac, H4K12ac, H3S10ph, H4S1ph) alongside active Pol II mapping provides a valuable dataset for the community. 

      (3) The integration of inhibition (DRB) and recovery experiments oFers insight into the coupling between Pol II activity and chromatin modifications. 

      (4) The concept of "fragile nucleosomes" as a unifying framework is potentially appealing and could stimulate further mechanistic studies. 

      Really appreciate the positive or affirmative comments from the reviewer.

      Weaknesses: 

      (1)  Misrepresentation of prior literature 

      The introduction incorrectly describes findings from Bintu et al., 2012. The cited work demonstrated that pan-acetylated or tailless nucleosomes reduce the nucleosomal barrier for Pol II passage, rather than showing no improvement. This misstatement undermines the rationale for the current study and should be corrected to accurately reflect prior evidence. 

      What we said is according to the original report in the publication (Bintu et al., Cell, 2012). Here is the citation from the report:

      Page 739,(Bintu, L. et al., Cell, 2012)(PMID: 23141536)

      “Overall transcription through tailless and acetylated nucleosomes is slightly faster than through unmodified nucleosomes (Figure 1C), with crossing times that are generally under 1 min (39.5 ± 5.7 and 45.3 ± 7.6 s, respectively). Both the removal and acetylation of the tails increase eFiciency of NPS passage:71% for tailless nucleosomes and 63% for acetylated nucleosomes (Figures 1C and S1), in agreement with results obtained using bulk assays of transcription (Ujva´ ri et al., 2008).”

      We will cite this original sentence in our revision.

      (2) Incorrect statement regarding hexasome fragility

      The authors claim that hexasome nucleosomes "are not fragile," citing older in vitro work. However, recent studies clearly showed that hexasomes exist in cells (e.g., PMID 35597239) and that they markedly reduce the barrier to Pol II (e.g., PMID 40412388). These studies need to be acknowledged and discussed. 

      “hexasome” was introduced in the transcription field four decades ago. Later, several groups claimed that “hexasome” is fragile and could be generated in transcription elongation of Pol II. However, their original definition was based on the detection of ~100 bps DNA fragments (MNase resistant) in vivo by Micrococcal nuclease sequencing (MNase-seq), which is the right length to wrap up one hexasome histone subunit (two H3/4 and one H2A/2B) to form the sub-nucleosome of a hexasome. As we should all agree that acetylation or phosphorylation of the tails of histone nucleosomes will lead to the compromised interaction between DNA and histone subunits, which could lead to the intact naïve nucleosome being fragile and easy to disassemble, and easy to access by MNase. Fragile nucleosomes lead to better accessibility of MNase to DNA that wraps around the histone octamer, producing shorter DNA fragments (~100 bps instead of ~140 bps). In this regard, we believe that these ~100 bps fragments are the products of fragile nucleosomes (fragile nucleosome --> hexasome), instead of the other way around (hexasome --> fragile). 

      Actually, two early reports from Dr. David J.  Clark’s group from NIH raised questions about the existence of hexasomes in vivo (PMID: 28157509) (PMID: 25348398).

      From the report of PMID:35597239, depletion of INO80 leads to the reduction of “hexasome” for a group of genes, and the distribution of both “nucleosomes” and “hexasomes” with the gene bodies gets fuzzier (less signal to noise). In a recent theoretical model (PMID: 41425263), the corresponding PI found that chromatin remodelers could act as drivers of histone modification complexes to carry out different modifications along gene bodies. The PI found that INO80 could drive NuA3 (a H3 acetyltransferase) to carry out pan-acetylation of H3 and possibly H2B as well in the later runs of transcription of Pol II for a group of genes (SAGA-dependent). It suggests that the depletion of INO80 will affect (reduce) the pan-acetylation of nucleosomes, which leads to the drop of pan-acetylated fragile nucleosomes, subsequently the drop of “hexasomes”. This explains why depletion of INO80 leads to the fuzzier results of either nucleosomes or “hexasomes” in PMID: 35597239. The result of PMID: 35597239 could be a strong piece of evidence to support the model proposed by the corresponding PI (PMID: 41425263).

      From a recent report: PMID:40412388, the authors claimed that FACT could bind to nucleosomes to generate “hexasomes”, which are fragile for Pol II to overcome the resistance of nucleosomes. It was well established that FACT enhances the processivity of Pol II in vivo via its chaperonin property. However, the exact working mechanism of FACT still remains ambiguous. A report from Dr. Cramer’s group showed that FACT enhances the elongation of regular genes but works just opposite for pausing-regulated genes (PMID: 38810649). An excellent review by Drs. Tim Formosa and Fred Winston showed that FACT is not required for the survival of a group of differentiated cells (PMID: 33104782), suggesting that FACT is not always required for transcription. It is quite tricky to generate naïve hexasomes in vitro according to early reports from the late Dr. Widom’s group. Most importantly, the new data (the speed of Pol II, the best one on bare DNA is ~27 bps/s) from the report of PMID: 40412388, which is much slower than the speed of Pol II in vivo: ~2.5 kbs/min or ~40 bps/s. From our recovering experiments (Fig. 4C, as mentioned by reviewer #3), in 20 minutes (the period between 10 minutes and 30 minutes, due to the property of CUT-&TAG-seq, of which Pol II still active after cells are collected, there is a big delay of complete stop of Pol II during the procedure of CUT&TAG experiments, so the first period of time does not actually reflect the speed of Pol II, which is ~5 kb/min), all Pol IIs move at a uniform speed of ~2.5 kbs/min in vivo. Interestingly, a recent report from Dr. Shixin Liu’s group (PMID: 41310264) showed that adding SPT4/5 to the transcription system with bare DNA (in vitro), the speed of Pol II reaches ~2.5kbs/min, exactly the same one as we derived in vivo. Similar to the original report (PMID: 23141536), the current report of PMID:40412388 does not mimic the conditions in vivo exactly.

      There is an urgent need for a revisit of the current definition of “hexasome”, which is claimed to be fragile and could be generated during the elongation of Pol II in vivo. MNase is an enzyme that only works when the substrate is accessible. In inactive regions of the genome, due to the tight packing of chromatin, MNase is not accessible to individual nucleosomes within the bodies of a gene or upstream of promoters, which is why we only see phased/spacing or clear distribution of nucleosomes at the transcription start sites, but it becomes fuzzy downstream or upstream of promoters. On the other hand, for fragile nucleosomes, the accessibility to MNase should increase dramatically, which leads to the ~100 bps fragments. Based on the uniform rate (2.5 kbs/min) of Pol II for all genes derived from human 293T cells and the similar rate (2.5 kbs/min) of Pol II on bare DNA in vitro, it is unlikely for Pol II to pause in the middle of nucleosomes to generate “hexasomes” to continue during elongation along gene bodies. Similar to RNAPs in bacterial (no nucleosomes) and Archaea (tailless nucleosomes), there should be no resistance when Pol IIs transcribe along all fragile nucleosomes within gene bodies in all eukaryotes, as we characterized in this manuscript. 

      (3)  Inaccurate mechanistic interpretation of DRB 

      The Results section states that DRB causes a "complete shutdown of transcription initiation (Ser5-CTD phosphorylation)." DRB is primarily a CDK9 inhibitor that blocks Pol II release from promoter-proximal pausing. While recent work (PMID: 40315851) suggests that CDK9 can contribute to CTD Ser5/Ser2 di-phosphorylation, the manuscript's claim of initiation shutdown by DRB should be revised to better align with the literature. The data in Figure 4A indicate that 1 M DRB fully inhibits Pol II activity, yet much higher concentrations (10-100 ) are needed to alter H3K9ac and H4K12ac levels. The authors should address this discrepancy by discussing the differential sensitivities of CTD phosphorylation versus histone modification turnover. 

      Yes, it was reported that DRB is also an inhibitor of CDK9. However, if the reviewer agrees with us and the current view in the field, the phosphorylation of Ser5-CTD of Pol II is the initiation of transcription for all Pol II-regulated genes in eukaryotes. CDK9 is only required to work on the already phosphorylated Ser5-CTD of Pol II to release the paused Pol II, which only happens in metazoans. From a series of works by us and others: CDK9 is unique in metazoans, required only for the pausing-regulated genes but not for regular genes. We found that CDK9 works on initiated Pol II (Ser5-CTD phosphorylated Pol II) and generates a unique phosphorylation pattern on CTD of Pol II (Ser2ph-Ser2ph-Ser5ph-CTD of Pol II), which is required to recruit JMJD5 (via CID domain) to generate a tailless nucleosome at +1 from TSS to release paused Pol II (PMID: 32747552). Interestingly, the report from Dr. Jesper Svejstrup’s group (PMID: 40315851) showed that CDK9 could generate a unique phosphorylation pattern (Ser2ph-Ser5ph-CTD of Pol II), which is not responsive to the popular 3E10 antibody that recognizes the single Ser2phCTD of Pol II.  This interesting result is consistent with our early report showing the unique phosphorylation pattern (Ser2ph-Ser2ph-Ser5ph-CTD of Pol II) is specifically generated by CDK9 in animals, which is not recognized by 3E10 either (PMID: 32747552). Actually, an early report from Dr. Dick Eick’s group (PMID: 26799765) showed the difference in the phosphorylation pattern of the CTD of Pol II between animal cells and yeast cells.  We have characterized how CDK9 is released from 7SK snRNP and recruited onto paused Pol II via the coupling of JMJD6 and BRD4 (PMID: 32048991), which was published on eLIFE. It is well established that CDK9 works after CDK7 or CDK8. From our PRO-seq data (Fig. 3) and CUT&TAG-seq data of active Pol II (Fig. 4), adding DRB completely shuts down all genes via inhibiting the initiation of Pol II (generation of Ser5ph-CTD of Pol II). Due to the uniqueness of CDK9 only in metazoans, it is not required for the activation of CDK12 or CDK13 (they are orthologs of CTK1 in yeast), as we demonstrated recently (PMID: 41377501). Instead, we found that CDK11/10 acts as the ortholog of Bur1 kinase from yeast, is essential for the phosphorylation of Spt5, the link of CTD of Pol II, and CDK12 (PMID: 41377501). 

      (4) Insufficient resolution of genome-wide correlations 

      Figure 1 presents only low-resolution maps, which are Insufficient o determine whether pan-acetylation and pan-phosphorylation correlate with Pol II at promoters or gene bodies. The authors should provide normalized metagene plots (from TSS to TTS) across different subgroups to visualize modification patterns at higher resolution. In addition, the genome-wide distribution of another histone PTM with a diFerent localization pattern should be included as a negative control. 

      A popular view in the field is that the majority of genomes are inactive since they do not contain coding RNAs, which are responsible for ~20,000 protein candidates characterized in animals. However, our genomewide characterization using the four histone modification marks, active Pol II, and RNA-seq, shows a different story. Figure 1 shows that most of the human genome of HEK293T is active in producing not only protein-coding RNAs but also non-coding RNAs (the majority of them). We believe that Figure 1 could change our current view of the activity of the entire genome, and should be of great interest to general readers as well as researchers on genomics. Furthermore, it is a basis for Figure 2, which is a zoom-in of Figure 1.  

      (5) Conceptual framing 

      The manuscript frequently extrapolates correlative genome-wide data to mechanistic conclusions (e.g., that pan-acetylation/phosphorylation "generate" fragile nucleosomes). Without direct biochemical or structural evidence. Such causality statements should be toned down.  

      The reviewer is right, we should tone down the strong sentences. However, we believe that our data is strong enough to derive the general conclusion. The reviewer may agree with us that the entire field of transcription and epigenetics has been stagnant in recent decades, but there is an urgent need for fresh ideas to change the current situation. Our novel discoveries, for sure, additional supporting data are needed, should open up a brand new avenue for people to explore. We believe that a new era of transcription will emerge based on our novel discoveries. We hope that this manuscript will attract more people to these topics. As Reviewer #3 pointed out, this story establishes the connection between transcription and epigenetics in the field. 

      Reviewer #2 (Public review): 

      Summary: 

      In this manuscript, the authors use various genomics approaches to examine nucleosome acetylation, phosphorylation, and PolII-CTD phosphorylation marks. The results are synthesized into a hypothesis that 'fragile' nucleosomes are associated with active regions of PolII transcription. 

      Strengths: 

      The manuscript contains a lot of genome-wide analyses of histone acetylation, histone phosphorylation, and PolII-CTD phosphorylation. 

      Weaknesses: 

      This reviewer's main research expertise is in the in vitro study of transcription and its regulation in purified, reconstituted systems. 

      Actually, the pioneering work of the establishment of in vitro transcription assays at Dr. Robert Roeder’s group led to numerous groundbreaking discoveries in the transcription field. The contributions of in vitro work in the transcription field are the key for us to explore the complexity of transcription in eukaryotes in the early times and remain important currently.

      I am not an expert at the genomics approaches and their interpretation, and overall, I had a very hard time understanding and interpreting the data that are presented in this manuscript.  I believe this is due to a problem with the manuscript, in that the presentation of the data is not explained in a way that's understandable and interpretable to a non-expert.

      Thanks for your suggestions. You are right, we have problems expressing our ideas clearly in this manuscript, which could confuse. We will make modifications accordingly per your suggestions.

      For example: 

      (1) Figure 1 shows genome-wide distributions of H3K9ac, H4K12ac, Ser2phPolII, mRNA, H3S10ph, and H4S1ph, but does not demonstrate correlations/coupling - it is not clear from these data that pan-acetylation and pan-phosphorylation are coupled with Pol II transcription. 

      Figure 1 shows the overall distribution of the four major histone modifications, active Pol II, and mRNA genome-wide in human HEK293T cells. It tells general readers that the entire genome is quite active and far more than people predicted that most of the genome is inactive, since just a small portion of the genome expresses coding RNAs (~20,000 in animals). Figure 1 shows that the majority of the genome is active and expresses not only coded mRNA but also non-coding RNAs. After all, it is the basis of Figure 2, which is a zoom-in of Figure 1. However, it is beyond the scope of this manuscript to discuss the non-coding RNAs. 

      (2) Figure 2 - It's not clear to me what Figure 2 is supposed to be showing. 

      (A) Needs better explanation - what is the meaning of the labels at the top of the gel lanes? 

      Figure 2 is a zoom-in for the individual gene, which shows how histone modifications are coupled with Pol II activity on the individual gene. We will give a more detailed explanation of the figure per the reviewer’s suggestions.

      (B) This reviewer is not familiar with this technique, its visualization, or its interpretation - more explanation is needed. What is the meaning of the quantitation graphs shown at the top? How were these calculated (what is on the y-axis)? 

      Good suggestions, we will do some modifications.

      (3) To my knowledge, the initial observation of DRB eFects on RNA synthesis also concluded that DRB inhibited initiation of RNA chains (pmid:982026) - this needs to be acknowledged. 

      Thanks for the reference, which is the first report to show the DRB inhibits initiation of Pol II in vivo. We will cite it in the revision.  

      (4) Again, Figures 4B, 4C, 5, and 6 are very difficult to understand - what is shown in these heat maps, and what is shown in the quantitation graphs on top? 

      Thanks for the suggestions, we will give a more detailed description of the Figures.  

      Reviewer #3 (Public review): 

      Summary: 

      Li et al. investigated the prevalence of acetylated and phosphorylated histones (using H3K9ac, H4K12ac, H3S10ph & H4S1ph as representative examples) across the gene body of human HEK293T cells, as well as mapping elongating Pol II and mRNA. They found that histone acetylation and phosphorylation were dominant in gene bodies of actively transcribing genes. Genes with acetylation/phosphorylation restricted to the promoter region were also observed. Furthermore, they investigated and reported a correlation between histone modifications and Pol II activity, finding that inhibition of Pol II activity reduced acetylation/phosphorylation levels, while resuming Pol II activity restored them. The authors then proposed a model in which panacetylation or pan-phosphorylation of histones generates fragile nucleosomes; the first round of transcription is accompanied by panacetylation, while subsequent rounds are accompanied by panphosphorylation. 

      Strengths: 

      This study addresses a highly significant problem in gene regulation. The author provided riveting evidence that certain histone acetylation and/or phosphorylation within the gene body is correlated with Pol II transcription. The author furthermore made a compelling case that such transcriptionally correlated histone modification is dynamic and can be regulated by Pol II activity. This work has provided a clearer view of the connection between epigenetics and Pol II transcription. 

      Thanks for the insightful comments, which are exactly what we want to present in this manuscript. 

      Weaknesses: 

      The title of the manuscript, "Fragile nucleosomes are essential for RNA Polymerase II to transcribe in eukaryotes", suggests that fragile nucleosomes lead to transcription. While this study shows a correlation between histone modifications in gene bodies and transcription elongation, a causal relationship between the two has not been demonstrated. 

      Thanks for the suggestions. What we want to express is that the generation of fragile nucleosomes precedes transcription, or, more specifically, transcription elongation. The corresponding PI wrote a hypothetical model on how pan-acetylation is generated by the coupling of chromatin remodelers and acetyltransferase complexes along gene bodies, in which chromatin remodelers act as drivers to carry acetyltransferases along gene bodies to generate pan-acetylation of nucleosomes (PMID: 41425263). We have a series of work to show how “tailless nucleosomes” at +1 from transcription start sites are generated to release paused Pol II in metazoans (PMID: 28847961) (PMID: 29459673) (PMID: 32747552) (PMID: 32048991).   We still do not know how pan-phosphorylation along gene bodies is generated. It should be one of the focuses of our future research.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      This study by Vitar et al. probes the molecular identity and functional specialization of pH-sensing channels in cerebrospinal fluid-contacting neurons (CSFcNs). Combining patch-clamp electrophysiology, laser-based local acidification, immunohistochemistry, and confocal imaging, the authors propose that PKD2L1 channels localized to the apical protrusion (ApPr) function as the predominant dual-mode pH sensor in these cells.

      The work establishes a compelling spatial-physiological link between channel localization and chemosensory behavior. The integration of optical and electrical approaches is technically strong, and the separation of phasic and sustained response modes offers a useful conceptual advance for understanding how CSF composition is monitored.

      Several aspects of data interpretation, however, require clarification or reanalysis-most notably the single-channel analyses (event counts, Po metrics, and mixed parameters), the statistical treatment, and the interpretation of purported "OFF currents." Additional issues include PKD2L1-TRPP3 nomenclature consistency, kinetic comparison with ASICs, and the physiological relevance of the extreme acidification paradigm. Addressing these points will substantially improve reproducibility and mechanistic depth.

      Overall, this is a scientifically important and technically sophisticated study that advances our understanding of CSF sensing, provided that the analytical and interpretative weaknesses are satisfactorily corrected.

      (1) The authors should re-analyze electrophysiological data, focusing on macroscopic currents rather than statistically unreliable Po calculations. Remove or revise the Po analysis, which currently conflates current amplitude and open probability.

      We agree with the reviewer that the Po analysis has strong limitations, particularly in experiments where the recording times are short, such as when extracellular pH is changed via photolysis (Figure 4D) or puff application (Figure 3Aa). To circumvent this problem and not rely solely on Po estimations, we used alternative methods, including an analysis of the total membrane charge (extensively used throughout the manuscript, as in Figures 3A and 4D) and an analysis of event latencies (Figure 4G). Nevertheless, single channel recordings contain information that is not included in the macroscopic current analysis. In the revised version, we intend to stress that the elementary current amplitude is conserved during manipulations such as pH changes, leaving the total number of channels (N) and the channel open probability (Po) as possible culprits for the current changes. Since these changes are rapid and reversible, it is likely that N remains constant while Po changes. To address the reviewer’s concern, we propose the following changes/reanalysis: (i) report in each condition the minimum N (based on the maximum number of simultaneously open channels; for example, in Figure 3Aa, the minimum N goes from 4-5 in control conditions to 1 during the puff of the pH 6.4 solution). Although imperfect, this method provides a tentative estimate of Po; (ii) report the fraction of time that the channels remain open; (iii) revise the text and figures to use the expression “apparent Po” instead of “Po”, acknowledging the limitations of the measurement in short recordings. We also acknowledge that some traces (Figure 3Aa, top) may appear confusing, as they seem to show macroscopic currents. We will modify these figures by including the amplitude histograms (as in Figure 1Bb) to clearly demonstrate that recordings from CSFcNs primarily reflect single-channel activity when challenged with pH changes.

      (2) PKD2L1-TRPP3 nomenclature should be clarified and all figure labels, legends, and text should use consistent terminology throughout.

      We agree with the reviewer that the nomenclature for the polycystin protein family is confusing. In this manuscript, we have followed the nomenclature  proposed in a recent comprehensive review on polycystin channels by Palomero, Larmore and DeCaen (Palomero et al. 2023), which refer to the channels by their gene names. As indicated in that review, the PKD2L1 channel corresponds to TRPP2 (previously known as TRPP3, see their Table 1). However, in another recent review on TRP channels,  the PKD2L1 channel is referred to as TRPP3 (Zhang et al. 2023). To prevent any ambiguity, we will remove references to the TRPP nomenclature from the text and exclusively use the PKD2L1 acronym.

      (3) The authors should reinterpret the so-called OFF currents as pH-dependent recovery or relaxation phenomena, not as distinct current species. Remove the term "OFF response" from the manuscript.

      Although largely used in the literature, we concur with the reviewer that the term “OFF response” is not very helpful from a biophysical perspective as it may imply the existence of a distinct current. Consequently, we will remove the terms “OFF response” and “OFF current” from the revised manuscript and replace them with the term “photolysis-evoked PKD2L1 current”. Furthermore, to improve the logical flow, we will condense the two sections (“The proton-induced current is an off-current” and “The off-current is mediated by the activation of PKD2L1 channels”) into a single, new section titled “The photolysis-induced current is mediated by PKD2L1 channels”. This consolidation will prevent the artificial separation of the description of this current. Finally, we will revise the discussion to better characterize this photolysis-evoked phenomenon as a recovery current.

      (4) Evidence for physiological relevance should be provided, including data from milder acidification (pH 6.5-6.8) and, where appropriate, comparisons with ASIC-mediated currents to place PKD2L1 activity in context.

      This point is partly addressed in Figure 3. The data indicate that  PKD2L1 channels are highly sensitive to pH variations within the physiological range. To strengthen this conclusion, we will add the EC50 values derived from the curve fittings to the figure. Regarding ASIC-mediated currents, one of our main conclusions is that ASICs are not present in the apical process (ApPr), as the effects of proton photolysis in the ApPr are not blocked by ASIC antagonists. Our results suggest that PKD2L1 channels are the exclusive pH sensitive channels in the ApPr. ASIC channels likely mediate acid sensitivity in the soma, although we have not investigated the latter in detail. We intend to modify the Discussion in order to provide a physiological framework linking channel activity with physiological and pathophysiological pH changes. 

      (5) Terminology and data presentation should be unified, adopting consistent use of "predominant" (instead of "exclusive") and "sustained" (instead of "tonic"), and all statistical formats and units should be standardized.

      Folllowing the reviewer’s suggestions, an exhaustive rephrasing will be performed to unify terminology, data presentation and correct the text.

      (6) The Discussion should be expanded to address potential Ca²⁺-dependent signaling mechanisms downstream of PKD2L1 activation and their possible roles in CSF flow regulation and central chemoreception.

      This is indeed a very interesting and currently unresolved point in the physiology of CSFcNs. Published data indicate that calcium influx through PKD2L1 channels is a key regulator of apical process (ApPr) physiology. These channels are calcium permeable yet are also inhibited by intracellular calcium (DeCaen et al. 2016). Additionally, ultrastructural data show that the ApPr is rich in mitochondria and tubulo-vesicular structures resembling the Golgi apparatus (Bruni et Reddy 1987; Bjugn et al. 1988; Nakamura et al. 2023), intracellular organelles critical for calcium homeostasis. Altogether, this evidence suggests that intra-ApPr calcium concentration must be finely regulated, both in space and time, for the ApPr to fulfill its physiological roles. Based on the existing literature, we can speculate that these calcium signals are decoded by several systems: (i) calcium may act as a second messenger, linking the activation of the multimodal PKD2L1 channels to changes in CSFcN excitability, which in turn regulates spinal neuronal networks controlling locomotor activity; (ii) calcium could initiate the neurosecretion of various molecules from the ApPr into the central canal, as proposed by the Wyart group in the zebrafish in the context of bacterial infections (Prendergast et al. 2023); (iii) calcium could activate the Hedgehog signaling pathway (as has been shown by Delling et al. 2013); iv) calcium could modulate CSF flow by modulating ependymal cells ciliary activity. Resolving these downstream pathways is essential to fully define the role of CSFcNs as integrators of cerebrospinal fluid homeostasis. We will expand on this topic in the Discussion section of the revised ms.

      Reviewer #2 (Public review):

      Summary:

      Cerebrospinal fluid contacting neurons (CSF-cNs) are GABAergic cells surrounding the spinal cord central canal (CC). In mammals, their soma lies sub-ependymally, with a dendritic-like apical extension (AP) terminating as a bulb inside the CC.

      How this anatomy-soma and AP in distinct extracellular environments relate to their multimodal CSF-sensing function remains unclear.

      The authors confirm that in GATA3:GFP mice, where these cells are labeled, that CSFcNs exhibit prominent spontaneous electrical activity mediated by PKD2L1 (TRPP2) channels, non-selective cation channels with ~200 pS conductance modulated by protons and mechanical forces.

      They investigated PKD2L1 pH sensitivity and its effects on CSFcN excitability. They uncovered that PKD2L1 generates both phasic and tonic currents, bidirectionally modulated by pH with high sensitivity near physiological values.

      Combining electrophysiology (intact and isolated AP recordings) with elegant laser-photolysis, they show that functional PKD2L1 channels localize specifically to the apical extension (AP).

      This spatial segregation, coupled with PKD2L1's biophysical properties (high conductance, pH sensitivity) and the AP's unique features (very high input resistance), renders CSFcN excitability highly sensitive to PKD2L1 modulation. Their findings reveal how the AP's properties are optimised for its sensory role.

      Strengths:

      This is a very convincing demonstration using elegant and challenging approaches (uncaging, outside out patch of the AP) together to form a complete understanding of how these sensory cells can detect the changes of pH in the CSF so finely.

      Weaknesses:

      The following do not constitute weaknesses; rather, they are minor requests that this reviewer considers would complete this beautiful study.

      (1) It would be nice to quantify further the relation in spontaneous as well as in acidic or basic pH between the effects observed on channel opening and holding current: do they always vary together and in a linear way?

      Following the reviewer’s suggestion, we performed a Spearman’s rank correlation test. The analysis revealed a significant correlation between the changes in the apparent open probability and the holding current in paired experiments (control vs pH 6.4 pressure applications; p < 0.05, Spearman r = 0.72 and critical value = 0.67). The Pearson correlation coefficient calculated on the same data set was r = 0.63 (critical value = 0.632), indicating that the correlation is not linear. We thank the reviewer for raising this point and will add this analysis to the manuscript.

      (2) Since CSF-cNs also respond to changes in osmolarity (Orts Dell Immagine 2013) & mechanosensory stimulations in a PKD2L1 dependent manner (Sternberg NC 2018), it would be nice to test the same results whether the same results hold true on the role of PKD2L1 in AP for pressure application of changes in osmolarity.

      This is a very important point. As the reviewer notes, previous experimental evidence indicates that CSFcNs are also sensitive to osmolarity changes and mechanical stimulation in a PKD2L1-dependent manner. It is therefore reasonable to assume that, similar to pH sensitivity, osmotic and mechanical sensitivity depend on channels localized to the apical process (ApPr). Regarding mechanosensitivity, this spatial segregation could be tested by mechanically stimulating either the ApPr or the soma with a piezo-controlled blunt pipette (see, for example, Hao et al. 2013). Assessing sensitivity to osmotic changes, however, is more challenging, as pressure application lacks the spatial resolution to discriminate between compartments in such a compact cell. In theory, a highly localized osmotic jump could be achieved via photolysis, provided a caged compound that releases many osmotic particles simultaneously is used. In typical photolysis experiments, a localized osmotic change is produced, but its amplitude is very low (on the order of 1 to 2 mOsm).

      In mice, like in fish (Sternberg et al, NC 2018), we can observe throughout the figures that a large fraction of the channel activity occurs with partial and very fast openings of the PKD2L1 channel. I recommend the authors analyse the points below:

      (a) To what extent do these partial openings of the channel contribute to the changes in holding current and resting potential?

      As the reviewer indicates, these partial and rapid openings are characteristic of PKD2L1 single-channel activity and appear to be conserved across species. However, estimating their precise contribution to the sustained current would require a detailed channel model, which is currently lacking. Indeed, the exact mechanism underlying this prominent sustained current in CSFcNs remains unknown and should definitely be addressed in future work.

      (b) In the trace from the outside out AP, it looks like the partial transient openings are gone. Can the authors verify whether these partial openings are only present in somatic recordings?

      The outside-out recordings from the apical process also show some partial openings (see the upper trace in Figure 4Db). We will specifically mention this important point in the revised version of the ms. 

      (3) Previous studies have observed expression of metabotropic Glutamate receptors in CSF-cNs (transcriptome from Prendergast et al CB 2023). The authors only used blockers for ionotropic glutamate receptors in their recordings: could it be that these metabotropic receptors influence the response to uncaging of MNI-Glu when glutamate is co-released with a proton?

      We thank the reviewer for pointing out the presence of metabotropic glutamate receptors in CSFcNs. However, our evidence indicates that metabotropic receptors do not contribute to the response when uncaging MNI-glutamate. This conclusion is supported by two observations: (i) the response obtained when uncaging MNI-γLGG, which does not release glutamate (Figure 5Ab), and (ii) the response obtained when uncaging protons from DPNI-GABA (data not shown) (DPNI-GABA is a GABA cage with photochemistry similar to MNI cages that also releases a proton upon photolysis; Trigo et al. 2009), are the same. In both experiments (uncaging MNI-γLGG or DPNI-GABA) a clear photolysis-evoked PKD2L1 current is observed.

      (4) In the outside out patch of the AP, PKD2L1 unitary currents appear rare. Could it be that the disruption in the cilium or underlying actin/myosin cytoskeleton drastically alter the open probability of the channel?

      The reviewer is correct in noting that the opening frequency of PKD2L1 channels appears lower in outside-out patches than in whole-ApPr recordings, although we have not quantified this. We interpreted this difference as reflecting a lower channel number. However, as the reviewer suggests, a plausible alternative explanation is that the channel's biophysical properties are altered when removed from its native ionic environment or when it loses interactions with regulatory proteins. We will address this point in the Discussion.

      (5) Could the authors use drugs against ASIC to specify which ASIC channels contribute to the pH response in the soma?

      As described in the manuscript, we performed experiments with ASIC antagonists, although we did not attempt to characterize the specific ASIC subtype mediating the somatic response. Based on the published literature, we used both psalmotoxin-1, which blocks ASIC1 channels, and APETx2, which blocks ASIC3 channels. The presence of ASIC1 in mouse CSFcNs has been demonstrated previously (Orts-Del’immagine et al. 2012; Orts-Del’Immagine et al. 2016), while ASIC3 has been identified in lamprey CSFcNs (Jalalvand et al. 2016). When applying an acidic solution to the soma, we recorded an inward current that was substantially blocked by psalmotoxin-1, although a small residual component persisted, consistent with the earlier findings of Orts-Del’Immagine et al. We did not attempt to block this remaining Psalmotoxin1‑insensitive component.

      (6) This is out of the scope of this study, but we did observe in fish a very rarely-opening channel in the PKD2L1KO mutant. I wonder if the authors have similar observations in the conditions where PKD2L1 is mainly in the closed state.

      We have never seen such kind of openings in our recordings (when the channel is closed or in the presence of dibucaine).

      References

      Bjugn, R, H K Haugland, et P R Flood. 1988. “Ultrastructure of the mouse spinal cord ependyma”. Journal of Anatomy 160 (octobre): 117‑25.

      Bruni, J. E., et K. Reddy. 1987. “Ependyma of the Central Canal of the Rat Spinal Cord: A Light and Transmission Electron Microscopic Study”. Journal of Anatomy 152 (juin): 55‑70.

      Delling, Markus, Paul G. DeCaen, Julia F. Doerner, Sebastien Febvay, et David E. Clapham. 2013. ”Primary cilia are specialized calcium signaling organelles”. Nature 504 (7479): 311‑14 https://doi.org/10.1038/nature12833.

      Hao, Jizhe, Jérôme Ruel, Bertrand Coste, Yann Roudaut, Marcel Crest, et Patrick Delmas. 2013. “Piezo-Electrically Driven Mechanical Stimulation of Sensory Neurons”. In Ion Channels, édité par Nikita Gamper, vol. 998. Methods in Molecular Biology. Humana Press. https://doi.org/10.1007/978-1-62703-351-0_12.

      Jalalvand, Elham, Brita Robertson, Hervé Tostivint, Peter Wallén, et Sten Grillner. 2016. “The Spinal Cord Has an Intrinsic System for the Control of pH”. Current Biology: CB 26 (10): 1346‑51. https://doi.org/10.1016/j.cub.2016.03.048.

      Nakamura, Yuka, Miyuki Kurabe, Mami Matsumoto, et al. 2023. “Cerebrospinal Fluid-Contacting Neuron Tracing Reveals Structural and Functional Connectivity for Locomotion in the Mouse Spinal Cord”. eLife 12 (février): e83108. https://doi.org/10.7554/eLife.83108.

      Orts-Del’Immagine, Adeline, Riad Seddik, Fabien Tell, et al. 2016. “A Single Polycystic Kidney Disease 2-like 1 Channel Opening Acts as a Spike Generator in Cerebrospinal Fluid-Contacting Neurons of Adult Mouse Brainstem”. Neuropharmacology 101 (février): 549‑65. https://doi.org/10.1016/j.neuropharm.2015.07.030.

      Orts-Del’immagine, Adeline, Nicolas Wanaverbecq, Catherine Tardivel, Vanessa Tillement, Michel Dallaporta, et Jérôme Trouslard. 2012. “Properties of Subependymal Cerebrospinal Fluid Contacting Neurones in the Dorsal Vagal Complex of the Mouse Brainstem”. The Journal of Physiology 590 (16): 3719‑41. https://doi.org/10.1113/jphysiol.2012.227959.

      Prendergast, Andrew E., Kin Ki Jim, Hugo Marnas, et al. 2023. “CSF-Contacting Neurons Respond to Streptococcus Pneumoniae and Promote Host Survival during Central Nervous System Infection”. Current Biology 33 (5): 940-956.e10. https://doi.org/10.1016/j.cub.2023.01.039.

      Trigo, Federico F., George Papageorgiou, John E. T. Corrie, et David Ogden. 2009. “Laser photolysis of DPNI-GABA, a tool for investigating the properties and distribution of GABA receptors and for silencing neurons in situ”. Journal of Neuroscience Methods 181 (2): 159‑69. https://doi.org/10.1016/j.jneumeth.2009.04.022.

    1. Author response:

      Reviewer #1:

      Minor Weaknesses:

      "Transcriptomic analysis was only done for one time point. Different time points could be included to validate whether some processes occur at different time points. But this can be done in the future for more detailed studies."

      Our response regarding time points of transcriptomic analysis:

      We appreciate this constructive suggestion. We fully agree that performing RNA-seq at multiple time points would provide valuable insights into the temporal dynamics of molecular pathways during cardiac regeneration. However, given that our study represents the first comprehensive characterization of cardiac regeneration in poeciliids, we deliberately focused our resources on establishing the foundational framework, including morphological, cellular, and initial transcriptomic analyses between zebrafish and platyfish. Expanding to multiple time points would constitute a substantial additional study that, while scientifically valuable, would extend beyond the scope of this initial characterization.

      We will acknowledge this limitation in the Discussion and indicate that temporal transcriptomic profiling is an important direction for future investigation.

      Reviewer #2:

      (1) Title selection

      Our response regarding the use of the term “partially regenerate” in the title and results:

      We thank Reviewer 2 for this important point regarding the terminology used to describe the cardiac response in platyfish and swordtails. We agree that the term "partially regenerate" may overstate the regenerative capacity of these species, particularly given the persistence of a substantial collagenous scar at the injury site. The reviewer is correct that, based on established criteria in the field, including the landmark studies on cavefish (PMID: 30462998) and medaka (PMID: 24947076), the presence of such prominent fibrotic scarring would be more appropriately characterized as limited or minimal regenerative capacity rather than partial regeneration.

      While we observe a significant reduction in wound volume at 30 dpci and some degree of tissue remodeling, we acknowledge that the persistent scarring and incomplete myocardial recovery more accurately reflect a healing or repair process rather than true regeneration. We therefore agree with the reviewer's suggestion to revise our terminology throughout the manuscript.

      We will revise the title to: "The livebearers platyfish and swordtails heal their hearts with persistent scarring." We will also modify other relevant sections of the Results and Discussion to consistently describe these processes as "healing" or "repair" rather than "regeneration", while still acknowledging the biological changes that do occur (wound contraction, remodeling, limited cardiomyocyte proliferation). This revised framing better aligns our work with the established terminology in the comparative cardiac regeneration literature and more accurately represents the phenotype we observe.

      We believe this change will strengthen the manuscript by providing a more precise characterization of the cardiac response in these species and facilitating clearer comparisons with other model systems.

      (2) Cross-species comparisons

      Our response regarding the inconsistent presentation of results for different species:

      We thank the reviewer for recognizing that our conclusions regarding the regenerative capacity of livebearers are strengthened by including two poeciliid species, platyfish and swordtails. We agree that presenting results more consistently across both species will significantly improve the manuscript. We acknowledge that our current presentation creates a burden on the reader by asking them to assume similarities between species without providing supporting data. While we initially focused primarily on platyfish due to its superior genome annotation (critical for our transcriptomic analyses), we recognize that this approach left important gaps in the manuscript.

      We will address this by generating comprehensive supplementary figures that present swordtail data alongside platyfish for key findings. Specifically, we will add a complete anatomical characterization of swordtail ventricle architecture, demonstrating the structural similarities to platyfish that underpin our comparative conclusions. We will also perform quantification of wound area reduction and immune response dynamics over time in swordtails, allowing direct comparison between species.

      We clarify that we did perform detailed analyses of swordtail heart anatomy during our initial studies, which revealed remarkable similarity to platyfish. However, space constraints in Figures 1 and S1 (which already span full pages with zebrafish-platyfish comparisons) prevented us from including these data in the original submission. We now recognize that explicitly presenting these data is essential for the reader to evaluate our conclusions.

      Our response regarding quantification and comparison with zebrafish: 

      We appreciate the reviewer's suggestion to move beyond qualitative observations toward rigorous quantification of the "partial regeneration" phenotype. As suggested by the reviewer for the PCNA analysis, we will provide direct quantitative comparisons with published zebrafish regeneration studies, including data from several relevant studies and our own lab's work. This comparison will delineate the extent of differences in proliferative response between complete regenerators (zebrafish) and limitted regenerators (poeciliids).

      These additions will transform our descriptive observations into quantitative assessments that rigorously define the incomplete healing phenotype in poeciliids relative to complete regeneration in zebrafish. We believe these changes will substantially strengthen the manuscript and address the reviewer's concerns about comparative rigor.

      (3) Lack of coronary vasculature

      Our response regarding inconsistencies in vascularization data:

      We thank the reviewer for his/her comment regarding our data on the absence of coronary vasculature in the platyfish heart. The reviewer noted differences between alkaline phosphatase (AP) enzymatic staining and anti-Podocalyxin-2 immunofluorescence staining. We would like to clarify that these observed differences are not inconsistencies but rather reflect the distinct specificities of these two complementary approaches.

      Alkaline phosphatase staining is selective for arterial branches and capillaries in the heart (PMID: 13982613; PMID: 9477306; PMID: 8245430; PMID: 3562789; PMID: 29023576; PMID: 28632131) and revealed a typical vascular pattern in the bulbus arteriosus and ventricle in zebrafish but not in platyfish. Anti-Podocalyxin-2 staining displayed a vessel-like pattern in zebrafish but not in platyfish. However, in both species Podocalyxin staining also  labeled other types of non-vascular structures. This is expected given that Podocalyxin is a cell surface sialomucin with broader expression beyond blood vessels, including the endocardium (PMID: 19142011) and certain neuronal populations, in addition to other non-cardiac tissue types (PMID: 19578008; PMID: 3511072; PMID: 34201212).

      We will revise the manuscript to emphasize this distinction and clarify our rationale: we deliberately employed Podocalyxin-2 staining as a complementary, less selective approach to corroborate our alkaline phosphatase findings. In platyfish, the convergent evidence from both methods (the absence of typical vascular structures with a selective AP staining and the detection of only non-vascular patterns with the broader marker Podocalyxin-2) strengthens our conclusion that platyfish hearts lack a conventional coronary vascular network.

      Our response regarding reproducibility:

      The assays were performed independently by two researchers at different stages of the study using two different batches of adult platyfish. The results were consistent in both assays, and we are therefore confident in the reproducibility of our findings.

      Our response regarding citations of references on revascularization:

      We thank the reviewer for recommending the studies PMID: 27647901 and PMID: 31743664 that revealed the importance of rapid revascularization during heart regeneration in zebrafish. We will be pleased to integrate these works to present our data in the appropriate context of current knowledge.

      Our response regarding a link to pseudoaneurysms:

      We appreciate the reviewer's feedback regarding the link to pseudoaneurysm. We agree that the primary contributions of our work stand on their own merit, and we will revise the text to present the livebearer findings more cautiously without overstating their potential medical relevance. We will focus on the intrinsic biological significance of our findings.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Public Reviews:

      Reviewer #1 (Public review)  

      Mitochondrial staining difference is convincing, but the status of the mitochondria, fused vs fragmented, elongated vs spherical, does not seem convincing. Given the density of mito staining in CySC, it is difficult to tell whether what is an elongated or fused mito vs the overlap of several smaller mitos.

      To address this, we have now removed the statements regarding the differences in the shape of mitochondria among the stem cell population. We have limited our statements to stating that the CySCs are more mitochondria dense compared to the neighbouring GSCs.

      The quantification and conclusions about the gstD1 staining in CySC vs. GSCs is just not convincing-I cannot see how they were able to distinguish the relevant signals to quantify once cell type vs the other.

      We appreciate the reviewer’s concern. To address this, we have included new images along with z-stack reconstructions (Fig 1G-P and S1C-D’’’), which now provide clearer distinction of gstD1 staining between CySCs and GSCs and improve the accuracy of quantification. The intensity of gstD1 staining overlapping with that of Vasa+ zone has been quantified as ROS levels for GSCs. Similarly, the cytoplasmic area of gstD1 stain bounded by Dlg and Tj+ nuclei was quantified as ROS levels for CySCs.    

      Images do not appear to show reduced number of GSCs, but if they counted GSCs at the niche, then that is the correct way to do it, but its odd that they chose images that do not show the phenotype. Further, their conclusion of reduced germline overall, e.g by vasa staining, does not appear to be true in the images they present and their indication that lower vasa equals fewer GSCs is invalid since all the early germline expresses Vasa.

      We have replaced the figure with images where the GSC rosette is clearly visible, ensuring that the counted GSCs at the niche accurately reflect the phenotype (Fig. 2 C’’, D’’). We agree that Vasa is expressed in all early germline cells. The overall reduced Vasa signal intensity in our western blot analysis for Sod1RNAi reflects a general reduction in the germline population, not just the GSCs. We have modified our statements in the Results appropriately.  

      However, the effect on germline differentiation is less clear-the images shown do not really demonstrate any change in BAM expression that I can tell, which is even more confusing given the clear effect on cyst cell differentiation.

      We appreciate the reviewer’s observation. To clarify this point, we have now included z-stack projection images of Bam expression in the revised version (Fig 3E’’-F’’) .

      These images more clearly demonstrate the difference in Bam expression, thereby highlighting the effect on germline differentiation. Moreover, Bam expressing cells are present more closure to hub in Sod1RNAi condition, indicating early differentiation.

      For the last figure, any effect of SOD OE in the germline on the germline itself is apparently very subtle and is within the range observed between different "wt" genetic backgrounds.

      We acknowledge that the effect of SOD overexpression on the germline is not very significant. The germline cells already possess a modest ROS load and it is a well-established fact that they possess a robust anti-oxidant defence machinery in order to protect the genome. Therefore, elevating the levels of antioxidant enzymes such as Sod1 does not translate into a major change and the effect observed are generally subtle.     

      Reviewer #3 (Public review)  

      In Fig. 1N (tj-SODi), one can see that all of gst-GFP resides within the differentiating somatic cells and none is in the germ cells. Furthermore, the information provided in the materials and methods about quantification of gst-GFP is not sufficient. Focusing on Dlg staining is not sufficient. They need to quantify the overlap of Vasa (a cytoplasmic protein in GSCs) with GFP.

      In our analysis, we have indeed quantified the GFP intensity in area of overlap between gstD1-GFP and Vasa-positive zone in the germ cells which are in direct contact with hub, in order to accurately quantify the ROS reporter signal within the germline compartment. Further, to ensure accurate cell boundary demarcation, we used Dlg staining as an additional parameter. While Dlg staining alone was included in the figure panels for clarity of visualization, the actual quantification was performed by considering both Vasa (for germ cells cytoplasm) and Dlg (for cellular boundaries). This has been clarified in the Materials and Methods.

      Additionally, since Tj-gal4 is active in hub cells, it is not clear whether the effects of SOD depletion also arise from perturbation of niche cells.

      We acknowledge that Tj-Gal4 also shows minimal activity in hub cells. To address this, we had tested C587-Gal4 and observed similar effects on niche architecture, though weaker than with Tj-Gal4, underlying the effect of ROS originating from CySC.  

      First, the authors are studying a developmental effect, rather than an adult phenotype. Second, the characterization of the somatic lineage is incomplete. It appears that high ROS in the somatic lineage autonomously decreases MAP kinase signaling and increases Hh signaling. They assume that the MAPK signaling is due to changes in Egfr activity but there are other tyrosine kinases active in CySCs, including PVR/VEGFR (PMID: 36400422), that impinge on MAPK. In any event ,their results are puzzling because lower Egfr should reduce CySC self-renewal and CySC number (Amoyel, 2016) and the ability of cyst cells to encapsulate gonialblasts (Lenhart Dev Cell 2015). The increased Hh should increase CySC number and the ability of CySCs to outcompete GSCs. The fact that the average total number of GSCs declines in tj>SODi testes suggests that high ROS CySCs are indeed outcompeting GSCs. However, as I wrote in myfirst critique, the characterization of the high ROS soma is incomplete. And the role of high ROS in the hub cells is acknowledged but not investigated.

      We acknowledge the reviewer’s concern that our study primarily examines a developmental effect. Our rationale was that redox imbalance during early stages can set longterm trajectories for stem cell behavior and niche organization, which ultimately manifest in adult testes.

      We agree that sole evaluation of Erk levels may not reflect the actual status of EGFR signalling and there is an apparent contradictory observation of low Erk and high CySC self-renewal. We believe that this ROS mediated change in Erk status, resulting in high CySC proliferation, might be an outcome of an interplay between other RTKs beyond EGFR. While the expansion of CySCs is primarily governed by Hh, a detailed dissection of these pathways under altered redox environment will be an interesting work to develop in future. Regarding the GSC number, it cannot be definitively stated that high ROS-CySCs are indeed outcompeting the GSCs, but yes, that possibility parallely exists. However, in presence case, there is no denying that the ROS levels of GSCs are indeed high under high CySC-ROS condition. It is known that ROS imbalance in GSCs promote their differentiation which was also observed in the present study through Bam staining. Therefore, redox mediated reduction in GSC number cannot be completely ruled out.  We have already discussed these points in the revised manuscript and suggest possible non-canonical effects of ROS on signal integration within CySCs that might reconcile these findings. Further, in the present study, we have focussed on redox interplay between the two stem cell populations (GSC and CySC) of the niche. Hence, we have not covered the redox profiling of the hub in detail.   

      The paragraph in the introduction (lines 62-76) mentions autonomous ROS levels in stem cells, not the transfer of ROS from one cell to another. And this paragraph is confusing because it starts with the (inaccurate) statement all stem cells have low ROS and then they discuss ISCs, which have high ROS.

      We have revised the paragraph for clarity. It now distinguishes between stem cell types with low versus relatively high ROS requirements (e.g., ISCs, HSCs, NSCs) and includes recent evidence of non-autonomous ROS signaling, such as paracrine ROS action from pericardial cells to cardiomyocytes and gap-junction–mediated ROS waves in cardiomyocyte monolayers. This resolves the ambiguity and presents a balanced view of autonomous and nonautonomous ROS regulation.

      While there has been an improvement in the scholarship of the testis, there are still places where the correct paper is not cited and issues with the text.

      All concerns regarding missing or incorrect citations and textual issues have now been carefully addressed and corrected. Relevant references have been added in the appropriate places to ensure accuracy.

      The authors are encouraged to more completely characterize the phenotype of high ROS in hub and CySCs.

      We have now included improved images showing the respective ROS profiles GSCs, CySCs and the hub. As mentioned in the earlier response, this work focuses on the redox interplay between GSCs and CySCs hence, we have not included any analysis on hub. However, we agree with reviewer that the hub contributions should also be evaluated as a future direction.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review): 

      Summary: 

      This study presents a comprehensive single-cell atlas of mouse anterior segment development, focusing on the trabecular meshwork and Schlemm's canal. The authors profiled ~130,000 cells across seven postnatal stages, providing detailed and solid characterization of cell types, developmental trajectories, and molecular programs. 

      Strengths: 

      The manuscript is well-written, with a clear structure and thorough introduction of previous literature, providing a strong context for the study. The characterization of cell types is detailed and robust, supported by both established and novel marker genes as well as experimental validation. The developmental model proposed is intriguing and well supported by the evidence. The study will serve as a valuable reference for researchers investigating anterior segment developmental mechanisms. Additionally, the discussion effectively situates the findings within the broader field, emphasizing their significance and potential impact for developmental biologists studying the visual system. 

      Weaknesses: 

      The weaknesses of the study are minor and addressable. As the study focuses on the mouse anterior segment, a brief discussion of potential human relevance would strengthen the work by relating the findings to human anterior segment cell types, developmental mechanisms, and possible implications for human eye disease. Data availability is currently limited, which restricts immediate use by the community. Similarly, the analysis code is not yet accessible, limiting the ability to reproduce and validate the computational analyses presented in the study. 

      In the revised version we will highlight the human relevance of our work in the discussion section. Additionally, data and codes are public on single cell portal and GEO, accession numbers have been updated.

      Reviewer #2 (Public review): 

      Summary: 

      This study presents a detailed single-cell transcriptomic analysis of the postnatal development of mouse anterior chamber tissues. Analysis focused on the development of cells that comprise Schlemm's Canal (SC) and trabecular meshwork (TM). 

      Strengths: 

      This developmental atlas represents a valuable resource for the research community. The dataset is robust, consisting of ~130,000 cells collected across seven time points from early post-natal development to adulthood. Analyses reveal developmental dynamics of SC and TM populations and describe the developmental expression patterns of genes associated with glaucoma. 

      Weaknesses: 

      (1) Throughout the paper, the authors place significant weight on the spatial relationships of UMAP clusters, which can be misleading (See Chari and Patcher, Plos Comb Bio 2023). This is perhaps most evident in the assessment of vascular progenitors (VP) into BEC and SEC types (Figures 4 and 5). In the text, VPs are described as a common progenitor for these types, however, the trajectory analysis in Figure 5 denotes a path of PEC -> BEC -> VP -> SEC. These two findings are incongruous and should be reconciled. The limitations of inferring relationships based on UMAP spatial positions should be noted. 

      (2) Figure 2d does not include P60. It is also noted that technical variation resulted in fewer TM3 cells at P21; was this due to challenges in isolation? What is the expected proportion of TM3 cells at this stage? 

      (3) In Figures 3a and b it is difficult to discern the morphological changes described in the text. Could features of the image be quantified or annotated to highlight morphological features? 

      (4) Given the limited number of markers available to identify SC and TM populations during development, it would be useful to provide a table describing potential new markers identified in this study. 

      (5) The paper introduces developmental glaucoma (DG), namely Axenfeld-Rieger syndrome and Peters Anomaly, but the expression analysis (Figure S20) does not annotate which genes are associated with DG.

      (1) We agree that inferring biological relationships from the spatial arrangement of UMAP clusters has limitations and we will qualify our interpretation accordingly in the text. We will also add clarifying language to the trajectory analysis in Figure 5. The intended developmental trajectory is PEC → VP → BEC and SEC; however, the cluster labels in Figure 5 were applied incorrectly. Specifically, VP-BECs were mislabeled as BECs, which led to the confusion.

      (2) We recently published the P60 dataset separately (Tolman, Li, Balasubramanian et al., eLife 2025); these data consist of integrated single-nucleus multiome profiles that were subjected to in-depth analysis. Additionally, we found that integrating the P60 dataset with the developmental datasets obscured sub-clustering of mature cell types. In future manuscripts, we will pursue a more detailed analysis of TM development and perform time point–specific clustering, similar to the approach we used for endothelial cells (Figure 4e).

      Comparing proportions of cells at different ages and as the eyes grows needs to be done cautiously. Notwithstanding the limitations, the proportions of TM1, TM2, and TM3 clusters are expected to be similar between P14 and P21 as the proportions at P14 and P60 are similar when comparing to the separately analyzed P60 data.  Importantly, our dissection strategy changed with age: from P2 to P14, we removed approximately one-third of the cornea, whereas at P21 and P60 we removed most of the cornea to help maximize representation of limbal cells as the eyes grew. This change in dissection likely contributed to the reduced number of TM3 cells observed at P21.  TM3 cells are enriched anteriorly (at-least in adult) and so are located closer to the corneal cut during dissection of the P21 eyes (which despite being larger than younger ages are still small and more delicate to accurately dissect than at P60) and are therefore more likely to be lost. Additional details are provided in the Methods section.

      (3) For Figure 3a and b, we will work to add clarity by providing additional annotations and an additional illustration.

      (4) We will include a table listing potential new markers for developing SC and TM populations.

      (5) We will annotate the genes associated with DG in Figure S20.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This study examines a valuable question regarding the developmental trajectory of neural mechanisms supporting facial expression processing. Leveraging a rare intracranial EEG (iEEG) dataset including both children and adults, the authors reported that facial expression recognition mainly engaged the posterior superior temporal cortex (pSTC) among children, while both pSTC and the prefrontal cortex were engaged among adults. However, the sample size is relatively small, with analyses appearing incomplete to fully support the primary claims. 

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study investigates how the brain processes facial expressions across development by analyzing intracranial EEG (iEEG) data from children (ages 5-10) and post-childhood individuals (ages 13-55). The researchers used a short film containing emotional facial expressions and applied AI-based models to decode brain responses to facial emotions. They found that in children, facial emotion information is represented primarily in the posterior superior temporal cortex (pSTC) - a sensory processing area - but not in the dorsolateral prefrontal cortex (DLPFC), which is involved in higher-level social cognition. In contrast, post-childhood individuals showed emotion encoding in both regions. Importantly, the complexity of emotions encoded in the pSTC increased with age, particularly for socially nuanced emotions like embarrassment, guilt, and pride. The authors claim that these findings suggest that emotion recognition matures through increasing involvement of the prefrontal cortex, supporting a developmental trajectory where top-down modulation enhances understanding of complex emotions as children grow older.

      Strengths:

      (1) The inclusion of pediatric iEEG makes this study uniquely positioned to offer high-resolution temporal and spatial insights into neural development compared to non-invasive approaches, e.g., fMRI, scalp EEG, etc.

      (2) Using a naturalistic film paradigm enhances ecological validity compared to static image tasks often used in emotion studies.

      (3) The idea of using state-of-the-art AI models to extract facial emotion features allows for high-dimensional and dynamic emotion labeling in real time

      Weaknesses:

      (1) The study has notable limitations that constrain the generalizability and depth of its conclusions. The sample size was very small, with only nine children included and just two having sufficient electrode coverage in the posterior superior temporal cortex (pSTC), which weakens the reliability and statistical power of the findings, especially for analyses involving age

      We appreciated the reviewer’s point regarding the constrained sample size.

      As an invasive method, iEEG recordings can only be obtained from patients undergoing electrode implantation for clinical purposes. Thus, iEEG data from young children are extremely rare,  and rapidly increasing the sample size within a few years is not feasible. However, we are confident in the reliability of our main conclusions. Specifically, 8 children (53 recording contacts in total) and 13 control participants (99 recording contacts in total) with electrode coverage in the DLPFC are included in our DLPFC analysis. This sample size is comparable to other iEEG studies with similar experiment designs [1-3]. 

      For pSTC, we returned to the data set and found another two children who had pSTC coverage. After involving these children’s data, the group-level analysis using permutation test showed that children’s pSTC significantly encode facial emotion in naturalistic contexts (Figure 3B). Notably, the two new children’s (S33 and S49) responses were highly consistent with our previous observations. Moreover, the averaged prediction accuracy in children’s pSTC (r<sub>speech</sub>=0.1565) was highly comparable to that in post-childhood group (r<sub>speech</sub>=0.1515).

      (1) Zheng, J. et al. Multiplexing of Theta and Alpha Rhythms in the Amygdala-Hippocampal Circuit Supports Pafern Separation of Emotional Information. Neuron 102, 887-898.e5 (2019).

      (2) Diamond, J. M. et al. Focal seizures induce spatiotemporally organized spiking activity in the human cortex. Nat. Commun. 15, 7075 (2024).

      (3) Schrouff, J. et al. Fast temporal dynamics and causal relevance of face processing in the human temporal cortex. Nat. Commun. 11, 656 (2020).

      (2) Electrode coverage was also uneven across brain regions, with not all participants having electrodes in both the dorsolateral prefrontal cortex (DLPFC) and pSTC, and most coverage limited to the left hemisphere-hindering within-subject comparisons and limiting insights into lateralization.

      The electrode coverage in each patient is determined entirely by the clinical needs. Only a few patients have electrodes in both DLPFC and pSTC because these two regions are far apart, so it’s rare for a single patient’s suspected seizure network to span such a large territory. However, it does not affect our results, as most iEEG studies combine data from multiple patients to achieve sufficient electrode coverage in each target brain area. As our data are mainly from left hemisphere (due to the clinical needs), this study was not designed to examine whether there is a difference between hemispheres in emotion encoding. Nevertheless, lateralization remains an interesting question that should be addressed in future research, and we have noted this limitation in the Discussion (Page 8, in the last paragraph of the Discussion).

      (3) The developmental differences observed were based on cross-sectional comparisons rather than longitudinal data, reducing the ability to draw causal conclusions about developmental trajectories.  

      In the context of pediatric intracranial EEG, longitudinal data collection is not feasible due to the invasive nature of electrode implantation. We have added this point to the Discussion to acknowledge that while our results reveal robust age-related differences in the cortical encoding of facial emotions, longitudinal studies using non-invasive methods will be essential to directly track developmental trajectories (Page 8, in the last paragraph of Discussion). In addition, we revised our manuscript to avoid emphasis causal conclusions about developmental trajectories in the current study (For example, we use “imply” instead of “suggest” in the fifth paragraph of Discussion).

      (4) Moreover, the analysis focused narrowly on DLPFC, neglecting other relevant prefrontal areas such as the orbitofrontal cortex (OFC) and anterior cingulate cortex (ACC), which play key roles in emotion and social processing.

      We agree that both OFC and ACC are critically involved in emotion and social processing. However, we have no recordings from these areas because ECoG rarely covers the ACC or OFC due to technical constraints. We have noted this limitation in the Discussion(Page 8, in the last paragraph of Discussion). Future follow-up studies using sEEG or non-invasive imaging methods could be used to examine developmental patterns in these regions.

      (5) Although the use of a naturalistic film stimulus enhances ecological validity, it comes at the cost of experimental control, with no behavioral confirmation of the emotions perceived by participants and uncertain model validity for complex emotional expressions in children. A nonfacial music block that could have served as a control was available but not analyzed. 

      The facial emotion features used in our encoding models were extracted by Hume AI models, which were trained on human intensity ratings of large-scale, experimentally controlled emotional expression data[1-2]. Thus, the outputs of Hume AI model reflect what typical facial expressions convey, that is, the presented facial emotion. Our goal of the present study was to examine how facial emotions presented in the videos are encoded in the human brain at different developmental stages. We agree that children’s interpretation of complex emotions may differ from that of adults, resulting in different perceived emotion (i.e., the emotion that the observer subjectively interprets). Behavioral ratings are necessary to study the encoding of subjectively perceived emotion, which is a very interesting direction but beyond the scope of the present work. We have added a paragraph in the Discussion (see Page 8) to explicitly note that our study focused on the encoding of presented emotion.

      We appreciated the reviewer’s point regarding the value of non-facial music blocks. However,  although there are segments in music condition that have no faces presented, these cannot be used as a control condition to test whether the encoding model’s prediction accuracy in pSTC or DLPFC drops to chance when no facial emotion is present. This is because, in the absence of faces, no extracted emotion features are available to be used for the construction of encoding model (see Author response image 1 below).  Thus, we chose to use a different control analysis for the present work. For children’s pSTC, we shuffled facial emotion feature in time to generate a null distribution, which was then used to test the statistical significance of the encoding models (see Methods/Encoding model fitting for details).

      (1) Brooks, J. A. et al. Deep learning reveals what facial expressions mean to people in different cultures. iScience 27, 109175 (2024).

      (2) Brooks, J. A. et al. Deep learning reveals what vocal bursts express in different cultures. Nat. Hum. Behav. 7, 240–250 (2023).

      Author response image 1.

      Time courses of Hume AI extracted facial expression features for the first block of music condition. Only top 5 facial expressions were shown here to due to space limitation.

      (6) Generalizability is further limited by the fact that all participants were neurosurgical patients, potentially with neurological conditions such as epilepsy that may influence brain responses. 

      We appreciated the reviewer’s point. However, iEEG data can only be obtained from clinical populations (usually epilepsy patients) who have electrodes implantation.  Given current knowledge about focal epilepsy and its potential effects on brain activity, researchers believe that epilepsy-affected brains can serve as a reasonable proxy for normal human brains when confounding influences are minimized through rigorous procedures[1]. In our study, we took several steps to ensure data quality: (1) all data segments containing epileptiform discharges were identified and removed at the very beginning of preprocessing, (2) patients were asked to participate the experiment several hours outside the window of seizures. Please see Method for data quality check description (Page 9/ Experimental procedures and iEEG data processing). 

      (1) Parvizi J, Kastner S. 2018. Promises and limitations of human intracranial electroencephalography. Nat Neurosci 21:474–483. doi:10.1038/s41593-018-0108-2

      (7) Additionally, the high temporal resolution of intracranial EEG was not fully utilized, as data were down-sampled and averaged in 500-ms windows.  

      We agree that one of the major advantages of iEEG is its millisecond-level temporal resolution. In our case, the main reason for down-sampling was that the time series of facial emotion features extracted from the videos had a temporal resolution of 2 Hz, which were used for the modelling neural responses. In naturalistic contexts, facial emotion features do not change on a millisecond timescale, so a 500 ms window is sufficient to capture the relevant dynamics. Another advantage of iEEG is its tolerance to motion, which is excessive in young children (e.g., 5-year-olds). This makes our dataset uniquely valuable, suggesting robust representation in the pSTC but not in the DLPFC in young children. Moreover, since our method framework (Figure 1) does not rely on high temporal resolution method, so it can be transferred to non-invasive modalities such as fMRI, enabling future studies to test these developmental patterns in larger populations.

      (8) Finally, the absence of behavioral measures or eye-tracking data makes it difficult to directly link neural activity to emotional understanding or determine which facial features participants afended to.  

      We appreciated this point. Part of our rationale is presented in our response to (5) for the absence of behavioral measures. Following the same rationale, identifying which facial features participants attended to is not necessary for testing our main hypotheses because our analyses examined responses to the overall emotional content of the faces. However, we agree and recommend future studies use eye-tracking and corresponding behavioral measures in studies of subjective emotional understanding. 

      Reviewer #2 (Public review):

      Summary:

      In this paper, Fan et al. aim to characterize how neural representations of facial emotions evolve from childhood to adulthood. Using intracranial EEG recordings from participants aged 5 to 55, the authors assess the encoding of emotional content in high-level cortical regions. They report that while both the posterior superior temporal cortex (pSTC) and dorsolateral prefrontal cortex (DLPFC) are involved in representing facial emotions in older individuals, only the pSTC shows significant encoding in children. Moreover, the encoding of complex emotions in the pSTC appears to strengthen with age. These findings lead the authors to suggest that young children rely more on low-level sensory areas and propose a developmental shiZ from reliance on lower-level sensory areas in early childhood to increased top-down modulation by the prefrontal cortex as individuals mature.

      Strengths: 

      (1) Rare and valuable dataset: The use of intracranial EEG recordings in a developmental sample is highly unusual and provides a unique opportunity to investigate neural dynamics with both high spatial and temporal resolution. 

      (2) Developmentally relevant design: The broad age range and cross-sectional design are well-suited to explore age-related changes in neural representations. 

      (3) Ecological validity: The use of naturalistic stimuli (movie clips) increases the ecological relevance of the findings. 

      (4) Feature-based analysis: The authors employ AIbased tools to extract emotion-related features from naturalistic stimuli, which enables a data-driven approach to decoding neural representations of emotional content. This method allows for a more fine-grained analysis of emotion processing beyond traditional categorical labels. 

      Weaknesses: 

      (1) The emotional stimuli included facial expressions embedded in speech or music, making it difficult to isolate neural responses to facial emotion per se from those related to speech content or music-induced emotion. 

      We thank the reviewer for their raising this important point. We agree that in naturalistic settings, face often co-occur with speech, and that these sources of emotion can overlap. However, background music induced emotions have distinct temporal dynamics which are separable from facial emotion (See the Author response image 2 (A) and (B) below). In addition, face can convey a wide range of emotions (48 categories in Hume AI model), whereas music conveys far fewer (13 categories reported by a recent study [1]). Thus, when using facial emotion feature time series as regressors (with 48 emotion categories and rapid temporal dynamics), the model performance will reflect neural encoding of facial emotion in the music condition, rather than the slower and lower-dimensional emotion from music. 

      For the speech condition, we acknowledge that it is difficult to fully isolate neural responses to facial emotion from those to speech when the emotional content from faces and speech highly overlaps. However, in our study, (1) the time courses of emotion features from face and voice are still different (Author response image 2 (C) and (D)), (2) our main finding that DLPFC encodes facial expression information in postchildhood individuals but not in young children was found in both speech and music condition (Figure 2B and 2C). In music condition, neural responses to facial emotion are not affected by speech. Thus, we have included the DLPFC results from the music condition in the revised manuscript (Figure 2C), and we acknowledge that this issue should be carefully considered in future studies using videos with speech, as we have indicated in the future directions in the last paragraph of Discussion.

      (1) Cowen, A. S., Fang, X., Sauter, D. & Keltner, D. What music makes us feel: At least 13 dimensions organize subjective experiences associated with music across different cultures. Proc Natl Acad Sci USA 117, 1924–1934 (2020).

      Author response image 2.

      Time courses of the amusement. (A) and (B) Amusement conveyed by face or music in a 30-s music block. Facial emotion features are extracted by Hume AI. For emotion from music, we approximated the amusement time course using a weighted combination of low-level acoustic features (RMS energy, spectral centroid, MFCCs), which capture intensity, brightness, and timbre cues linked to amusement. Notice that music continues when there are no faces presented. (C) and (D) Amusement conveyed by face or voice in a 30-s speech block. From 0 to 5 seconds, a girl is introducing her friend to a stranger. The camera focuses on the friend, who appears nervous, while the girl’s voice sounds cheerful. This mismatch explains why the shapes of the two time series differ at the beginning. Such situations occur frequently in naturalistic movies

      (2) While the authors leveraged Hume AI to extract facial expression features from the video stimuli, they did not provide any validation of the tool's accuracy or reliability in the context of their dataset. It remains unclear how well the AI-derived emotion ratings align with human perception, particularly given the complexity and variability of naturalistic stimuli. Without such validation, it is difficult to assess the interpretability and robustness of the decoding results based on these features.  

      Hume AI models were trained and validated by human intensity ratings of large-scale, experimentally controlled emotional expression data [1-2]. The training process used both manual annotations from human raters and deep neural networks. Over 3000 human raters categorized facial expressions into emotion categories and rated on a 1-100 intensity scale. Thus, the outputs of Hume AI model reflect what typical facial expressions convey (based on how people actually interpret them), that is, the presented facial emotion. Our goal of the present study was to examine how facial emotions presented in the videos are encoded in the human brain at different developmental stages. We agree that the interpretation of facial emotions may be different in individual participants, resulting in different perceived emotion (i.e., the emotion that the observer subjectively interprets). Behavioral ratings are necessary to study the encoding of subjectively perceived emotion, which is a very interesting direction but beyond the scope of the present work. We have added text in the Discussion to explicitly note that our study focused on the encoding of presented emotion (second paragraph in Page 8).

      (1) Brooks, J. A. et al. Deep learning reveals what facial expressions mean to people in different cultures. iScience 27, 109175 (2024).

      (2) Brooks, J. A. et al. Deep learning reveals what vocal bursts express in different cultures. Nat. Hum. Behav. 7, 240–250 (2023).

      (3) Only two children had relevant pSTC coverage, severely limiting the reliability and generalizability of results.  

      We appreciated this point and agreed with both reviewers who raised it as a significant concern. As described in response to reviewer 1 (comment 1), we have added data from another two children who have pSTC coverage. Group-level analysis using permutation test showed that children’s pSTC significantly encode facial emotion in naturalistic contexts (Figure 3B). Because iEEG data from young children are extremely rare, rapidly increasing the sample size within a few years is not feasible. However, we are confident in the reliability of our conclusion that children’s pSTC can encode facial emotion. First,  the two new children’s responses (S33 and S49) from pSTC were highly consistent with our previous observations (see individual data in Figure 3B). Second, the averaged prediction accuracy in children’s pSTC (r<sub>speech</sub>=0.1565) was highly comparable to that in post-childhood group (r<sub>speech</sub>=0.1515).

      (4) The rationale for focusing exclusively on high-frequency activity for decoding emotion representations is not provided, nor are results from other frequency bands explored.   

      We focused on high-frequency broadband (HFB) activity because it is widely considered to reflect the responses of local neuronal populations near the recording electrode, whereas low-frequency oscillations in the theta, alpha, and beta ranges are thought to serve as carrier frequencies for long-range communication across distributed networks[1-2]. Since our study aimed to examine the representation of facial emotion in localized cortical regions (DLPFC and pSTC), HFB activity provides the most direct measure of the relevant neural responses. We have added this rationale to the manuscript (Page 3).

      (1) Parvizi, J. & Kastner, S. Promises and limitations of human intracranial electroencephalography. Nat. Neurosci. 21, 474–483 (2018).

      (2) Buzsaki, G. Rhythms of the Brain. (Oxford University Press, Oxford, 200ti).

      (5) The hypothesis of developmental emergence of top-down prefrontal modulation is not directly tested. No connectivity or co-activation analyses are reported, and the number of participants with simultaneous coverage of pSTC and DLPFC is not specified.  

      Directional connectivity analysis results were not shown because only one child has simultaneous coverage of pSTC and DLPFC. However, the  Granger Causality results from post-childhood group (N=7) clearly showed that the influence in the alpha/beta band from DLPFC to pSTC (top-down) is gradually increased above the onset of face presentation (Author response image 3, below left, plotted in red). By comparison, the influence in the alpha/beta band from pSTC to DLPFC (bottom-up) is gradually decreased after the onset of face presentation (Author response image 3, below left, blue curve). The influence in alpha/beta band from DLPFC to pSTC was significantly increased at 750 and 1250 ms after the face presentation (face vs nonface, paired t-test, Bonferroni  corrected P=0.005, 0.006), suggesting an enhanced top-down modulation in the post-childhood group during watching emotional faces. Interestingly, this top-down influence appears very different in the 8-year-old child at 1250 ms after the face presentation (Author response image 3, below left, black curve).

      As we cannot draw direct conclusions from the single-subject sample presented here, the top-down hypothesis is introduced only as a possible explanation for our current results. We have removed potentially misleading statements, and we plan to test this hypothesis directly using MEG in the future.

      Author response image 3.

      Difference of Granger causality indices (face – nonface) in alpha/beta and gamma band for both directions. We identified a series of face onset in the movie that paticipant watched. Each trial was defined as -0.1 to 1.5 s relative to the onset. For the non-face control trials, we used houses, animals and scenes. Granger causality was calculated for 0-0.5 s, 0.5-1 s and 1-1.5 s time window. For the post-childhood group, GC indices were averaged across participants. Error bar is sem.

      (6) The "post-childhood" group spans ages 13-55, conflating adolescence, young adulthood, and middle age. Developmental conclusions would benefit from finer age stratification.  

      We appreciate this insightful comment. Our current sample size does not allow such stratification. But we plan to address this important issue in future MEG studies with larger cohorts.

      (7) The so-called "complex emotions" (e.g., embarrassment, pride, guilt, interest) used in the study often require contextual information, such as speech or narrative cues, for accurate interpretation, and are not typically discernible from facial expressions alone. As such, the observed age-related increase in neural encoding of these emotions may reflect not solely the maturation of facial emotion perception, but rather the development of integrative processing that combines facial, linguistic, and contextual cues. This raises the possibility that the reported effects are driven in part by language comprehension or broader social-cognitive integration, rather than by changes in facial expression processing per se.  

      We agree with this interpretation. Indeed, our results already show that speech influences the encoding of facial emotion in the DLPFC differently in the childhood and post-childhood groups (Figure 2D), suggesting that children’s ability to integrate multiple cues is still developing. Future studies are needed to systematically examine how linguistic cues and prior experiences contribute to the understanding of complex emotions from faces, which we have added to our future directions section (last paragraph in Discussion, Page 8-9 ).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors): 

      In the introduction: "These neuroimaging data imply that social and emotional experiences shape the prefrontal cortex's involvement in processing the emotional meaning of faces throughout development, probably through top-down modulation of early sensory areas." Aren't these supposed to be iEEG data instead of neuroimaging? 

      Corrected.

      Reviewer #2 (Recommendations for the authors):

      This manuscript would benefit from several improvements to strengthen the validity and interpretability of the findings:

      (1) Increase the sample size, especially for children with pSTC coverage. 

      We added data from another two children who have pSTC coverage. Please see our response to reviewer 2’s comment 3 and reviewer 1’s comment 1.

      (2) Include directional connectivity analyses to test the proposed top-down modulation from DLPFC to pSTC. 

      Thanks for the suggestion. Please see our response to reviewer 2’s comment 5.

      (3) Use controlled stimuli in an additional experiment to separate the effects of facial expression, speech, and music. 

      This is an excellent point. However, iEEG data collection from children is an exceptionally rare opportunity and typically requires many years, so we are unable to add a controlled-stimulus experiment to the current study. We plan to consider using controlled stimuli to study the processing of complex emotion using non-invasive method in the future. In addition, please see our response to reviewer 2’s comment 1 for a description of how neural responses to facial expression and music are separated in our study.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1:

      In this well-written and timely manuscript, Rieger et al. introduce Squidly, a new deep learning framework for catalytic residue prediction. The novelty of the work lies in the aspect of integrating per-residue embeddings from large protein language models (ESM2) with a biology-informed contrastive learning scheme that leverages enzyme class information to rationally mine hard positive/negative pairs. Importantly, the method avoids reliance on the use of predicted 3D structures, enabling scalability, speed, and broad applicability. The authors show that Squidly outperforms existing ML-based tools and even BLAST in certain settings, while an ensemble with BLAST achieves state-of-the-art performance across multiple benchmarks. Additionally, the introduction of the CataloDB benchmark, designed to test generalization at low sequence and structural identity, represents another important contribution of this work.

      We thank the reviewer for their constructive and encouraging assessment of the manuscript. We appreciate the recognition of Squidly’s biology-informed contrastive learning framework with ESM2 embeddings, its scalability through the avoidance of predicted 3D structures, and the contribution of the CataloDB benchmark. We are pleased that the reviewer finds these aspects to be of value, and their comments will help us in further clarifying the strengths and scope of the work.

      The manuscript acknowledges biases in EC class representation, particularly the enrichment for hydrolases. While CataloDB addresses some of these issues, the strong imbalance across enzyme classes may still limit conclusions about generalization. Could the authors provide per-class performance metrics, especially for underrepresented EC classes?

      We thank the reviewer for raising this point. We agree that per-class performance metrics provide important insight into generalizability across underrepresented EC classes. In response, we have updated Figure 3 to include two additional panels: (i) per-EC F1, precision and recall scores, and (ii) a relative display of true positives against the total number of predictable catalytic residues. These additions allow the class imbalance to be more directly interpretable. We have also revised the text between lines 316-321 to better contextualize our generalizability claims in light of these results.

      An ablation analysis would be valuable to demonstrate how specific design choices in the algorithm contribute to capturing catalytic residue patterns in enzymes.

      We agree an ablation analysis is beneficial to show the benefits of a specific approach. We consider the main design choice in Squidly to be how we select the training pairs, hence we chose a standard design choice for the contrastive learning model. We tested the effect of different pair schemes on performance and report the results in Figure 2A and lines 244258. These results are a targeted ablation in which we evaluate Squidly against AEGAN using the AEGAN training and test datasets, while systematically varying the ESM2 model size and pair-mining scheme. As a baseline, we included the LSTM trained directly on ESM2 embeddings and random pair selection.  We showed that indeed the choice of pairs has a large impact on performance, which is significantly improved when compared to naïve pairing. This comparison suggests that performance gains are attributable to reactioninformed pair-mining strategies. We recognize that the way these results were originally presented made this ablation less clear. We have revised the wording in the Results section (lines 244-247) and updated the caption to Figure 2A to emphasize the purpose of this section of the paper.

      The statement that users can optionally use uncertainty to filter predictions is promising but underdeveloped. How should predictive entropy values be interpreted in practice? Is there an empirical threshold that separates high- from low-confidence predictions? A demonstration of how uncertainty filtering shifts the trade-off between false positives and false negatives would clarify the practical utility of this feature.

      Thank you for the suggestion. Your comment prompted us to consider what is the best way to represent the uncertainty and, additionally, what is the best metric to return to users and how to visualize the results. Based on this, we included several new figures (Figure 3H and Supplementary Figures S3-5). We used these figures to select the cutoffs (mean prediction of 0.6, and variance < 0.225) which were then set as the defaults in Squidly, and used in all subsequent analyses. The effect of these cutoffs is most evident in the tradeoff of precision and recall. Hence users may opt to select their own filters based on the mean prediction and variance across the predictions, and these cutoffs can be passed as command line parameters to Squidly. The choice to use a consistent default cutoff selected using the Uni3175 benchmark has slightly improved the reported performance for the benchmarks seen in table 1, and figure 3C. However, our interpretation remains the same.

      The excerpt highlights computational efficiency, reporting substantial runtime improvements (e.g., 108 s vs. 5757 s). However, the comparison lacks details on dataset size, hardware/software environment, and reproducibility conditions. Without these details, the speedup claim is difficult to evaluate. Furthermore, it remains unclear whether the reported efficiency gains come at the expense of predictive performance

      Thank you for pointing out this limitation in how we presented the runtime results. We have rerun the tests and updated the table. An additional comment is added underneath, which details the hardware/software environment used to run both tools, as well as that the Squidly model is the ensemble version. As per the relationship between efficiency gains and predictive performance, both 3B and 15B models are benchmarked side by side across the paper.

      Compared to the tools we were able to comprehensively benchmark, it does not come at a cost. However, we note that the increased benefits in runtime assume that a structure must be folded, which is not the case for enzymes already present in the PDB. If that is the case, then it is likely already annotated and, in those cases, we recommend using BLAST which is superior in terms of run time than either Squidly or a structure-based tool and highly accurate for homologous or annotated sequences.

      Given the well-known biases in public enzyme databases, the dataset is likely enriched for model organisms (e.g., E. coli, yeast, human enzymes) and underrepresents enzymes from archaea, extremophiles, and diverse microbial taxa. Would this limit conclusions about Squidly's generalizability to less-studied lineages?

      The enrichment for model organisms in public enzyme databases may indeed affect both ESM2 and Squidly when applied to underrepresented lineages such as archaea, extremophiles, and diverse microbial taxa. We agree that this limitation is significant and have adjusted and expanded the previous discussion of benchmarking limitations accordingly (lines 358, 369). We thank the reviewer for highlighting this issue, which has helped us to improve the transparency and balance of the manuscript.

      Reviewer #2:

      The authors aim to develop Squidly, a sequence-only catalytic residue prediction method. By combining protein language model (ESM2) embedding with a biologically inspired contrastive learning pairing strategy, they achieve efficient and scalable predictions without relying on three-dimensional structure. Overall, the authors largely achieved their stated objectives, and the results generally support their conclusions. This research has the potential to advance the fields of enzyme functional annotation and protein design, particularly in the context of screening large-scale sequence databases and unstructured data. However, the data and methods are still limited by the biases of current public databases, so the interpretation of predictions requires specific biological context and experimental validation.

      Strengths:

      The strengths of this work include the innovative methodological incorporation of EC classification information for "reaction-informed" sample pairing, thereby enhancing the discriminative power of contrastive learning. Results demonstrate that Squidly outperforms existing machine learning methods on multiple benchmarks and is significantly faster than structure prediction tools, demonstrating its practicality.

      Weaknesses:

      Disadvantages include the lack of a systematic evaluation of the impact of each strategy on model performance. Furthermore, some analyses, such as PCA visualization, exhibit low explained variance, which undermines the strength of the conclusions.

      We thank the reviewer for their comments and feedback. 

      The authors state that "Notably, the multiclass classification objective and benchmarks used to evaluate EasIFA made it infeasible to compare performance for the binary catalytic residue prediction task." However, EasIFA has also released a model specifically for binary catalytic site classification. The authors should include EasIFA in their comparisons in order to provide a more comprehensive evaluation of Squidly's performance.

      We thank the reviewer for raising this point. EasIFA’s binary classification task includes catalytic, binding, and “other” residues, which differs from Squidly’s strict catalytic residue prediction. This makes direct comparison non-trivial, which is why we originally had opted to not benchmark against EasIFA and instead highlight it in our discussion.

      Given your comment, we did our best to include a benchmark that could give an indication of a comparison between the two tools. To do this, we filtered EasIFA’s multiclass classification test dataset for a non-overlapping subset with Squidly and AEGAN training data and <40% sequence identity to all training sets. This left only 66 catalytic residue– containing sequences that we could use as a held-out test set from both tools. We note it is not directly equal as Squidly and AEGAN had lower average identity to this subset (8.2%) than EasIFA (23.8%), placing them at a relative disadvantage.

      We also identified a potential limitation in EasIFA’s original recall calculation, where sequences lacking catalytic residues were assigned a recall of 0. We adapted this to instead consider only the sequences which do have catalytic residues, which increased recall across all models. With the updated evaluation, EasIFA continues to show strong performance, consistent with it being SOTA if structural inputs are available. Squidly remains competitive given it operates solely from sequence and has a lower sequence identity to this specific test set.

      Due to the small and imbalanced benchmark size, differences in training data overlap, and differences in our analysis compared with the original EasIFA analysis, we present this comparison in a new section (A.4) of the supplementary information rather than in the main text. References to this section have been added in the manuscript at lines 265-268. Additionally, we do update the discussion and emphasize the potential benefits of using EasIFA at lines (353-356).

      The manuscript proposes three schemes for constructing positive and negative sample pairs to reduce dataset size and accelerate training, with Schemes 2 and 3 guided by reaction information (EC numbers) and residue identity. However, two issues remain:

      (a) The authors do not systematically evaluate the impact of each scheme on model performance.

      (b) In the benchmarking results, it is not explicitly stated which scheme was used for comparison with other models (e.g., Table 1, Figure 6, Figure 8). This lack of clarity makes it difficult to interpret the results and assess reproducibility.

      (c) Regarding the negative samples in Scheme 3 in Figure 1, no sampling patterns are shown for residue pairs with the same amino acid, different EC numbers, and both being catalytic residues.

      We thank the reviewer for these suggestions, which enabled us to improve the clarity and presentation of the manuscript. Please find our point by point response:

      (a) We thank the reviewer for highlighting the lack of clarity in the way we have presented our evaluation in the section describing the Uni3175 benchmark. We aimed to systematically evaluate the impact of each scheme using the Uni3175 benchmark and refer to these results at lines 244-258, Additionally, we have adjusted the presentation of this section at lines 244-247 also in line with related comments from reviewer 1 in order to make the intention of this section and benchmark results to allow a comparison of each scheme to baseline models and AEGAN. These results led us to use Scheme 3 in both models for the other benchmarks in Figures 2 and 3. Please let us know if there is anything we can do to further improve the interpretability of Squidly’s performance.

      (b) We thank the reviewer for highlighting this issue and improving the clarity of our manuscript. We agree that after the Uni3175 benchmark was used to evaluate the schemes, we did not clearly state in the other benchmarks that scheme 3 was chosen for both the 3B and 15B models. We have made changes in table 1 and the Figure legends of Figures 2 and 3 to state that scheme 3 was used. In addition, we integrated related results into panel figures (e.g. Figures 2 and 3 now show models trained and tested on consistent benchmark datasets) and standardized figure colors and legend formatting throughout. Furthermore, we suspect that the previous switch from using the individual vs ensembled Squidly models during the paper was not well indicated, and likely to confuse the reader. Therefore, we decided to consistently report the ensembled Squidly models for all benchmarks except in the ablation study (Figure 2A). In line with this, we altered the overview Figure 1A, so that it is clearer that the default and intended version of Squidly is the ensemble.

      (c) We appreciate the reviewer pointing this out. You’re correct, we explicitly did not sample the negatives described by the reviewer in scheme 3 as our focus was on the hard negatives that relate most to the binary objective.  We do think this is a great idea and would be worth exploring further in future versions of Squidly, where we will be expanding the label space used for hard-negative sampling and including binding sites in our prediction. We have updated the discussion at lines 395-396 to highlight this potential direction.

      The PCA visualization (Figure 3) explains very little variance (~5% + 1.8%), but its use to illustrate the separability of embedding and catalytic residues may overinterpret the meaning of the low-dimensional projection. We question whether this figure is appropriate for inclusion in the main text and suggest that it be moved to the Supporting Information.

      We thank the reviewer for this suggestion. We had discussed this as well, and in the end decided to include it in the main manuscript. We agree that the explained variance is low. However, when we first saw the PCA we were surprised that there was any separation at all. This then prompted us to investigate further, so we kept it in the manuscript to be true to the scientific story. However, we do agree that our interpretation could be interpreted as overly conclusive given the minimal variance explained by the top 2 PCs. Therefore, we agree with the assessment that the figure, alongside the accompanying results section, is more appropriately placed in the supplementary information. We moved this section (A.1) to the appendix to still explain the exploratory data analysis process that we used to tackle this problem, so that the general thought process behind Squidly is available for further reading.  

      Minor Comments:

      (1) Figure Quality and Legends a) In Figure 4, the legend is confusing: "Schemes 2 and 3 (S1 and S2) ..." appears inconsistent, and the reference to Scheme 3 (S3) is not clearly indicated.

      (b) In Figure 6, the legend overlaps with the y-axis labels, reducing readability. The authors should revise the figures to improve clarity and ensure consistent notation.

      The reviewer correctly notes inconsistencies in figure presentation. We have revised the legend of Figure 4 (now 2A) to ensure schemes are referred to consistently and Scheme 3 (S3) is clearly indicated. We also adjusted Figure 6 (now 2c) to remove the overlap between the legend and y-axis labels.  

      Conclusion

      We thank the reviewers and editor again for their constructive input. We believe the revisions and clarifications substantially strengthened the manuscript and the resource

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study used explicit-solvent simulations and coarse-grained models to identify the mechanistic features that allow for the unidirectional motion of SMC on DNA. Shorter explicit-solvent models describe relevant hydrogen bond energetics, which were then encoded in a coarse-grained structure-based model. In the structure-based model, the authors mimic chemical reactions as signaling changes in the energy landscape of the assembly. By cycling through the chemical cycle repeatedly, the authors show how these time-dependent energetic shifts naturally lead SMC to undergo translocation steps along DNA that are on a length scale that has been identified.

      Strengths:

      Simulating large-scale conformational changes in complex assemblies is extremely challenging. This study utilizes highly-detailed models to parameterize a coarse-grained model, thereby allowing the simulations to connect the dynamics of precise atomistic-level interactions with a large-scale conformational rearrangement. This study serves as an excellent example for this overall methodology, where future studies may further extend this approach to investigated any number of complex molecular assemblies.

      We thank the reviewer for careful reading of our manuscript and highlighting the value of our bottom-up multiscale simulation approach.

      Weaknesses:

      The only relative weakness is that the text does not always clearly communicate which aspects of the dynamics are expected to be robust. That is, which aspects of the dynamics/energetics are less precisely described by this model? Where are the limits of the models, and why should the results be considered within the range of applicability of the models?

      We appreciate this insightful comment and agree that it is important to more explicitly describe the robustness and limitations of the simulation model used in this study. In response to this comment, we have revised the Discussion section of our manuscript.

      First, to clarify the robust aspects of our model, we have added a new subsection titled “Parametric choices and robustness of simulation model” to the Discussion, which is as follows:

      “The switching Gō approach adopted in this study is a powerful tool for providing the relationship between known large-scale conformational changes and the resulting functional and mechanical dynamics of the molecular machine (Brandani and Takada, 2018b; Koga and Takada, 2006b; Nagae et al., 2025). In this study, we mimic conformational change induced by ATP binding and hydrolysis events by instantaneously switching the potential energy function from one that stabilized a given conformation to another that stabilized a different conformation. This drives the protein to undergo a conformational transition toward the minimum of the new energy landscape.

      This approach is particularly well suited to investigate whether a given conformational change in a subunit of a molecular machine can produce the overall motion observed, and whether this process is mechanically feasible. Therefore, the fundamental mechanisms identified in this study, i.e., DNA segment capture mechanism, the correlation between step size and loop length, and the unidirectional translocation mechanism originating from the asymmetric kleisin path, can be considered as robust, as they emerge directly from the structural and topological constraints of the SMC-kleisin architecture rather than from tuned parameters.”

      Additionally, to more clearly define the limits of our model, we have expanded the "Limitations in current simulations" subsection. Specifically, we have added a detailed discussion regarding the energetics and transition pathways inherent to the switching Gō approach, which is as follows:

      “First, use of switching potentials to trigger conformational changes impose a limitation on predictive power for energetics and transition pathways. The switching of potentials is akin to a “vertical excitation” from one energy landscape to another, rather than a thermally activated crossing of an energy barrier. Consequently, the model cannot provide quantitative predictions of the transition rates or the free energy barriers associated with these changes. Furthermore, while the subsequent relaxation follows the new potential landscape, it is not guaranteed to reproduce the unique, physically correct transition pathway. Nevertheless, this simplification is justified because conformational changes within the protein are expected to occur on a much faster timescale than the large-scale motion of the DNA. Thus, this simplification has a limited impact on our main conclusions regarding the functional DNA dynamics driven by these large-scale conformational changes.”

      We have not made any additions regarding the timescale and dwell times for each ATP state, as these were already discussed in the original manuscript.

      Reviewer #2 (Public review):

      Summary:

      The authors perform coarse grained and all atom simulations to provide a mechanism for loop extrusion that is involved in genome compaction.

      Strengths:

      The simulations are very thoughtful. They provide insights into the translocation process, which is only one of the mechanisms. Much of the analyses is very good. Over all the study advances the use of simulations in this complicated systems.

      We sincerely thank the reviewer for their thoughtful and encouraging comments.

      Weaknesses:

      Even the authors point out several limitations, which cannot be easily overcome in the paper because of the paucity of experimental data. Nevertheless, the authors could have done so to illustrate the main assertion that loop extrusion occurs by the motor translocating on DNA. They should mention more clearly that there are alternative theories that have accounted for a number of experimental data.

      We thank the reviewer for these constructive suggestions. As the reviewer pointed out, it is important to state more explicitly how the unidirectional DNA translocation revealed in this study relates to the widely recognized loop-extrusion hypothesis of genome organization and situate our findings with the context of major alternative theories.

      To address this, we first clarify the relationship between the translocation mechanism we observed and the phenomenon of loop extrusion. We emphasize that our simulations were designed to elucidate the core motor activity of the SMC complex, and we explicitly state our view that loop extrusion is a functional consequence of this motor activity when the complex is anchored to DNA.

      Second, as the reviewer also suggested, we addressed alternative models of loop extrusion that also have experimental support in more details. We have revised the Discussion accordingly to provide a more balanced and comprehensive context. Further details are provided in our separate response to the comment below.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, Yamauchi and colleagues combine all-atom and coarse-grained MD simulations to investigate the mechanism of DNA translocation by prokaryotic SMC complexes. Their multiscale approach is well-justified and supports a segment-capture model in which ATP-dependent conformational changes lead to the unidirectional translocation of DNA. A key insight from the study is that asymmetry in the kleisin path enforces directionality. The work introduces an innovative computational framework that captures key features of SMC motor action, including DNA binding, conformational switching, and translocation.

      This work is well executed and timely, and the methodology offers a promising route for probing other large molecular machines where ATP activity is essential.

      Strengths:

      This manuscript introduces an innovative yet simple method that merges all-atom and coarse-grained, purely equilibrium, MD simulations to investigate DNA translocation by SMC complexes, which is triggered by activated ATP processes. Investigating the impact of ATP on large molecular motors like SMC complexes is extremely challenging, as ATP catalyses a series of chemical reactions that take and keep the system out of equilibrium. The authors simulate the ATP cycle by cycling through distinct equilibrium simulations where the force field changes according to whether the system is assumed to be in the disengaged, engaged, and V-shaped states; this is very clever as it avoids attempting to model the non-equilibrium process of ATP hydrolysis explicitly. This equilibrium switching approach is shown to be an effective way to probe the mechanistic consequences of ATP binding and hydrolysis in the SMC complex system.

      The simulations reveal several important features of the translocation mechanism. These include identifying that a DNA segment of ~200 bp is captured in the engaged state and pumped forward via coordinated conformational transitions, yielding a translocation step size in good agreement with experimental estimates. Hydrogen bonding between DNA and the top of the ATPase heads is shown to be critical for segment capturtrans, as without it, translocation is shown to fail. Finally, asymmetry in the kleisin subunit path is shown to be responsible for unidirectionally.

      This work highlights how molecular simulations are an excellent complement to experiments, as they can exploit experimental findings to provide high-resolution mechanistic views currently inaccessible to experiments. The findings of these simulations are plausible and expand our understanding of how ATP hydrolysis induces directional motion of the SMC complex.

      We thank the reviewer for the thoughtful and encouraging assessment of our work. We appreciate the reviewer’s summary of our key contributions, especially our switching Gō strategy, the segment-capture mechanism of SMC translocation, and the role of kleisin-path asymmetry in ensuring unidirectionality.

      Weaknesses:

      There are aspects of the methodology and modelling assumptions that are not clear and could be better justified. The major ones are listed below:

      (1) The all-atom MD simulations involve a 47-bp DNA duplex interacting with the ATPase heads, from which key residues involved in hydrogen bonding are identified. However, DNA mechanics-including flexibility and hydrogen bond formation-are known to be sequence-dependent. The manuscript uses a single arbitrary sequence but does not discuss potential biases. Could the authors comment on how sequence variability might affect binding geometry or the number of hydrogen bonds observed?

      We thank the reviewer for this insightful comment regarding the potential effects of DNA sequence.

      The primary biological role of the SMC complex is to organize genome architecture on a global scale; as such, its fundamental interaction with DNA is considered not to be sequence-specific. Our all-atom MD simulations and analysis pipeline were designed to probe the nature of this general interaction. Our approach confirms this rationale: the analysis exclusively identified hydrogen bonds formed between amino acid residues and the phosphate groups of the DNA's sugar-phosphate backbone. As shown in Figs. 1B and 1C, the results confirm that the key stabilizing interactions occur between basic residues on the SMC head surface and the DNA backbone. Since the backbone is chemically uniform, the stable binding mode we characterized is inherently sequence-independent.

      While the final bound state is likely sequence-independent, we agree that sequence-dependent properties such as local DNA flexibility or intrinsic curvature could influence the kinetics of the binding process. For example, the rate of initial recognition or the ease of DNA bending on the head surface might vary between AT-rich and GC-rich regions. However, once the DNA is bound, we expect the stable binding geometry and the identity of the key interacting residues to be conserved across different sequences.

      Therefore, we are confident that using a single, representative DNA sequence is a valid approach for elucidating the fundamental, non-sequence-specific aspects of SMC-DNA interaction and does not alter the general validity of the translocation mechanism proposed in this work.

      (2) A key feature of the coarse-grained model is the inclusion of a specific hydrogen-bonding potential between DNA and residues on the ATPase heads. The authors select the top 15 hydrogen-bond-forming residues from the all-atom simulations (with contact probability > 0.05), but the rationale for this cutoff is not explained. Also, the strength of hydrogen bonds in coarse-grained models can be sensitive to context. How did the authors calibrate the strength of this interaction relative to electrostatics, and did they test its robustness (e.g., by varying epsilon or residue set)? Could this interaction be too strong or too weak under certain ionic conditions? What happens when salt is changed?

      Thank you for these comments. We provide our rationale for the parameter choices below.

      The contact probability cutoff of 0.05 was chosen to create a comprehensive set of residues that form physically robust interactions with DNA. To establish this robustness, we performed a parallel set of all-atom simulations using a different force field (see Fig. S2). This cross-validation revealed two key points. First, the top six residues (Arg120, Arg123, Ile63, Arg111, Arg62, and Lys56), which include experimentally confirmed DNA-binding sites, consistently exhibited the highest contact probabilities in both force fields, confirming the reliability of our identification. Second, and just as importantly, many residues with lower contact probabilities (e.g., Trp115, Tyr107, Arg105, Ser124, and Ser54) were also consistently detected across both simulations. This reproducibility suggests that these interactions are physically robust and not artifacts of a specific force field. We therefore concluded that a 0.05 cutoff is a well-balanced threshold that ensures the inclusion of not only the primary anchor residues but also the secondary, moderately interacting residues that are crucial for cooperatively stabilizing the DNA. We discussed this point in Method in the revised manuscript, which is as follows:

      “The rationale for this cutoff is the physical robustness of the identified interactions; all-atom simulations using a different force field confirmed that the same set of key interacting residues, including both strong and moderate binders, was consistently identified (Fig. S2).”

      The strength of the hydrogen bond potential was set to ϵ = 4.0 k​T (≈2.4 kcal/mol), a physically plausible value corresponding to an ideal hydrogen bond. To test the robustness of this parameterization, we performed preliminary simulations where we varied these parameters by (i) reducing the value of ϵ and (ii) restricting the interaction to only the top six anchor residues. In both test cases, while a short DNA duplex (47 bp) could still bind to the ATPase heads, simulations with a long DNA (800 bp) failed to form a stable DNA loop after initial docking. These tests demonstrated that a larger set of cooperative interactions with a physically realistic strength was necessary for the full segment capture mechanism. Our final parameter set (15 residues at ϵ = 4.0 k​T) was thus chosen as the parameter set required to capture both the initial anchoring of DNA and the subsequent cooperative stabilization of the captured loop.

      As correctly pointed out, ionic conditions are a critical factor. Our simulations revealed that the salt concentration had a more pronounced effect on the kinetics of the DNA finding its correct binding site rather than on the thermodynamic stability of the final bound state. During our parameter tuning, we found that at physiological salt conditions (150 mM), long-range electrostatic interactions become dominant. This caused the DNA to be non-specifically captured by positively charged patches on the sides of the heads, which are not the functional binding sites. This off-pathway trapping kinetically prevented the DNA from reaching its proper location within the simulation timeframe. In contrast, the high-salt conditions (300 mM) used in this study screen these long-range interactions, suppressing non-specific trapping and allowing the DNA to efficiently explore the protein surface. This enables the correct binding to be established via the specific, short-range hydrogen bonds. Therefore, the ion concentration in our model is more as a crucial kinetic control factor to reproduce correct binding pathway within a realistic simulation timeframe. This point is discussed in the new subsection entitled “Parametric choices and robustness of simulation model”.

      (3) To enhance sampling, the translocation simulations are run at 300 mM monovalent salt. While this is argued to be physiological for Pyrococcus yayanosii, such a concentration also significantly screens electrostatics, possibly altering the interaction landscape between DNA and protein or among protein domains. This may significantly impact the results of the simulations. Why did the authors not use enhanced sampling methods to sample rare events instead of relying on a high-salt regime to accelerate dynamics?

      We agree that enhanced sampling methods are powerful for exploring rare events. However, many of these techniques require the pre-definition of a suitable, low-dimensional reaction coordinate (RC) to guide the simulation. The primary goal of our study was to discover the DNA translocation mechanism as it emerges naturally from fundamental physical interactions, without imposing a priori assumptions about the specific pathway.

      The DNA segment capture process is complex, involving the coordinated motion of a long DNA polymer and multiple protein domains. Defining a simple RC in advance was not feasible and would have carried a significant risk of biasing the system toward an artificial pathway. Therefore, to avoid such bias, we chose to perform direct, unbiased molecular dynamics simulations. Using a physiologically relevant high-salt concentration (300 mM) for Pyrococcus yayanosii was a strategy to accelerate the system's natural dynamics, allowing us to observe these unbiased trajectories within a feasible computational timescale.

      Because our current work has elucidated the fundamental steps of this mechanism, we agree that this work provides a foundation for more quantitative analyses. As suggested, future studies using methods like Markov State Model analysis or enhanced sampling techniques, guided by more sophisticated RCs defined from the insights of this work, would be a valuable next step for characterizing the free-energy landscape of the process or longer time scale dynamics.

      (4) Only a small fraction of the simulated trajectories complete successful translocation (e.g., 45 of 770 in one set), and this is attributed to insufficient simulation time. While the authors are transparent about this, it raises questions about the reliability of inferred success rates and about possible artefacts (e.g., DNA trapping in coiled-coil arms). Could the authors explore or at least discuss whether alternative sampling strategies (e.g., Markov State Models, transition path sampling) might address this limitation more systematically?

      We thank the reviewer for raising this point that is crucial for considering limitations and future directions of our study.

      As we noted in a previous response, the primary reason we did not employ such enhanced sampling methods was the limited prior knowledge available to define previously uncharacterized DNA translocation process. Therefore, we first try to define the key conformational states and transitions without the potential bias of a predefined model or reaction coordinate. This approach was successful, as it allowed us to identify critical on-pathway states like “DNA segment capture” and significant off-pathway or kinetically trapped states such as 'DNA trapping' between the coiled-coil arms.

      We fully agree that the low success rate observed is a key finding that points to significant kinetic bottlenecks, and that a more systematic analysis is required. Having identified the essential states, applying techniques such as Markov State Models (MSMs) or transition path sampling represents a powerful and logical next step. These methods, using a state-space definition based on our findings, will enable a quantitative characterization of the free-energy landscape and the transition rates between states. This will provide a rigorous understanding of the kinetic factors, such as the depth of the trapped-state energy well, that underlie the low translocation efficiency.

      In the revised manuscript, we discuss the application of these advanced sampling methods as a feasible and promising future direction, which is as follows:

      “Future studies can leverage the insights from this work to overcome the current timescale limitations. Techniques such as Markov state modeling (Husic and Pande, 2018; Prinz et al., 2011) or enhanced sampling methods (Hénin et al., 2022) may be employed to quantitatively characterize the free-energy landscape and transition rates. Such an approach would provide a rigorous understanding of the kinetic barriers, such as the stability of the trapped state, that govern the efficiency of SMC translocation.”

      Reviewer #1 (Recommendations for the authors):

      As noted in the public review, there could be a more systematic description of the limits of the model. The model appears to be carefully crafted, though every model has limits. It could be helpful for the general readership to give some idea of which parametric choices are more critical, and which mechanistic features should be robust to minor changes in parameters.

      We sincerely thank the reviewer for this constructive comment. We agree that clarifying which aspects of our model is robust and sensitive to specific parameter choices is crucial for the reader's understanding.

      We have expanded the Discussion to clarify how specific simulation parameters affect the efficiency and success rate of DNA translocation in our coarse-grained simulations. In particular, we have added a description of the parametric choices for (i) selection and strength of hydrogen bonds, (ii) ionic strength, and (iii) interaction strength between the coiled-coil arms. The discussion can be found in subsection entitled “Parametric choice and robustness of simulation model” in the Discussion, which is as follows:

      “On the other hand, the efficiency and success rate of DNA translocation in our simulations are more sensitive to certain parametric choices. For instance, the selection and strength of hydrogen bond-like interactions are a key factor. Our model incorporates specific hydrogen bonds between the upper surface of the ATPase heads and DNA, based on all-atom simulations. These interactions are essential for initiating segment capture; without them, DNA fails to migrate to the correct binding surface. While the identification of these key residues is a robust finding—persisting across different all-atom force fields (Fig. S2)—their strength and number in the coarse-grained potential are critical parameters that directly influence the probability and kinetics of DNA capture. Another critical parameter is the ionic strength. We performed translocation simulations at an ionic strength of 300 mM to accelerate DNA dynamics. At lower concentrations, non-specific electrostatic interactions between DNA and positively charged patches on the sides of the ATPase heads or coiled-coil arm became dominant, hindering the efficient migration of DNA to its functional binding site. Using a higher-than-physiological ionic strength is a justified practice in coarse-grained simulations employing the Debye-Hückel approximation, as it serves as a first-order correction to mimic the strong local charge screening by condensed counterions that is not explicitly captured by the mean-field model (Brandani et al., 2021; Niina et al., 2017b). Finaly, the interaction strength between the coiled-coil arms is also important. In our model, once the arms closed during the transition from the V-shaped to the disengaged state, they remained closed on the simulated timescale, frequently trapping DNA pushed from the hinge and thereby leading to failed translocation. This behavior suggests that the arm–arm interactions may be overestimated. A parameterization that allows for more frequent, transient opening of the arms could increase the success rate of DNA pumping.”

      Reviewer #2 (Recommendations for the authors):

      This paper reports simulations (all atom and coarse grained) to provide molecular details of loop extrusion. In general, it is a well done paper. There are a few issues that the authors should address.

      (1) The study supposes that loop extrusion occurs by translocation. Although they point out alternate models like scrunching (C Dekker; the theory by Takaki is also based on the scrunching model that the authors should mention), they should discuss this further. After all, the Takaki theory does predict several experimental outcomes very accurately. The precise mechanism has not been nailed down - The paper by Terakawa in Science suggests the extrusion is by translocation, but the evidence is not clear.

      We thank the reviewer for this insightful comment. We agree that our discussion should briefly acknowledge alternative models such as scrunching. We have therefore revised the manuscript to mention the theory by Takaki et al. (Nat. Commun., 2021), which reproduces several experimental outcomes.

      Because our present work specifically addresses the translocation mechanism based on DNA segment capture, we now state that scrunching and related models represent alternative proposals for loop extrusion.

      In this revision, we have added discussion to the end of the subsection titled "DNA segment capture as the mechanism of the DNA translocation by SMC complexes." in the Discussion section, which is as follows:

      “Turning to loop extrusion mechanisms, alternative mechanisms have been proposed in addition to the DNA-segment capture model. For example, Takaki et al. developed a scrunching-based theory that quantitatively accounts for several experimental observations, including force-velocity relationships and step-size distributions. While our present study focuses on the DNA translocation mechanism via segment capture, it is important to note that scrunching and other models remain plausible alternatives for loop extrusion. The precise mechanism may depends on the specific SMC complex and their subunits and remains to be fully resolved.”

      (2) It is unclear how one can say from Figure 4I and J that translocation has taken place. These panels show that the base pair length increases. This should be explained more clearly. They should also simultaneously plot the location of the heads (2D plot).

      Thank you for this valuable suggestion. In response to the comment on how translocation is presented in Fig. 4I and J, we have revised the text to make it clear that the SMC complex moves along DNA in subsection entitled “DNA translocation via DNA-segment capture”, as follows:

      “Fig. 4I represents the one-dimensional contour coordinate of the DNA molecule, indexed by base pairs (1-800). In this plot, translocation is visualized as a discontinuous shift in the range of base-pair indices that the SMC complex contacts over one complete ATP cycle”

      “This translocation is recorded in Fig. 4I as the average coordinate of the kleisin contact region (red dots) jumps from ~400 bp before the cycle to ~600bp after, which corresponds to a translocation event of ~200 bp”

      We believe that adding this explanation makes it clearer to readers that Fig. 4I and 4J provide direct evidence for unidirectional translocation of the SMC complex.

      (3) The transitions between the states are very abrupt (see Figure 2). Please explain. Also, in which state does extrusion take place? What is the role of the V-shape - is it part of the ATPase cycle?

      We thank the reviewer for raising these questions.

      In our simulation, we implemented ATP-binding state change by instantaneously switching the structure-based (Gō-type) potential between reference conformations for the disengaged (apo), engaged (ATP-bound), and V-shaped (ADP-bound) states at predetermined times. The system rapidly relaxes along the new funnel-shaped potential energy surface toward its minimum. This rapid relaxation is why the transition appears abrupt in metrics such as the Q-score in Fig.2.

      The V-shaped state corresponds to a key ADP-bound intermediate within the ATP hydrolysis cycle. Its primary role in our model is preparatory; it establishes the necessary open geometry that allows for the subsequent "zipping" of the coiled-coil arms. Crucially, unidirectional pumping motion is generated during the transition from the V-shaped state to the disengaged state. That is, the zipping motion of the coiled-coil arm pushes the captured DNA segment forward, resulting in a net translocation along the DNA.

      (4) It appears the heads do not move between the disengaged to engaged states. Why not in their model?

      Thank you for pointing out the lack of clarity in explanation of the SMC head movement in our simulations.

      In our model, the transition from the disengaged to the engaged state involves a dynamic rearrangement of the SMC heads. Specifically, one ATPase head slides (~10 Å) and rotates (~85°) relative to the other ATPase head to re-associate at a new dimer interface. This movement drives the global conformational change of the complex from a rod-like shape to an open ring, a mechanism proposed in a previous structural study (Diebold-Durand et al., Mol. Cell, 2017).

      As reviewer 2 noted, this crucial motion, which is reflected in the changing head-head distance and hinge angle in Fig. 2A, was not sufficiently highlighted in the text. We have therefore revised the manuscript to explicitly describe this head rearrangement to improve clarity, which is as follows:

      “Upon transition to the engaged state, the two ATPase heads were quickly rearranged to form the new inter-subunit contacts. Specifically, this rearrangement involves one ATPase head sliding by approximately 10 Å and rotating by 85° relative to the other, allowing it to associate through a different interface (Diebold-Durand et al., 2017b). The fractions of formed contacts, Q-scores, that exist at the disengaged (engaged) states quickly decreased (increased) (Fig. 2A, top two plots).”

      (5) What is pumping - it has been used in Marko NAR in the DNA capture model. How is that illustrated in the simulations?

      We thank the reviewer for raising this point. In the context of the DNA segment-capture model by Marko et al. (NAR, 2019), "pumping" refers to the conceptual process where a DNA loop, captured in an upper compartment of the SMC ring, is transferred to a lower compartment, resulting in net translocation.

      Our simulations provide a direct, molecular-resolution visualization of the physical mechanism underlying this concept. We illustrate that the "pumping" action is not a passive transfer but an active, mechanical process driven by a specific conformational change. This occurs during the transition from the V-shaped (ADP-bound) to the disengaged state. As shown in our trajectories, the two coiled-coil arms close in a zipper-like manner, beginning from the hinge and progressing toward the ATPase heads. This zipping motion physically pushes the captured DNA segment from the hinge region toward the kleisin ring.

      This process is visualized in our simulations as a clear, unidirectional translocation step (see Figs. 4B–D, 4I, and S6). The result is a net forward movement of the DNA by a distance that corresponds to the length of the initially captured loop, a key prediction of the Marko’s model that we quantify in our step-size analysis (Figs. 4K–L and S8).

      To make this point clearer for the reader, we have revised the manuscript. We have explicitly defined this "zipping and pushing" action as the physical basis for the "pumping" mechanism in the subsection titled "Zipping motion of coiled-coil arms pushes the DNA from hinge domain toward kleisin ring", which is as follows:.

      “This active, mechanical pushing of the DNA loop, driven by the sequential closing of the coiled-coil arm, constitutes the physical basis of the “pumping” mechanism that drives unidirectional translocation. Our simulations thus provide a concrete, molecular-level visualization for this key step in the DNA segment-capture model.”

      (6) The length of DNA simulated is small for understandable reasons. Both experiments and theory show that loop extrusion sizes can be very large, far exceeding the sizes of the SMA complex. Could the small size of DNA be affecting the results?

      We thank the reviewer for this important comment. The relationship between our simulated system size and the large-scale phenomena observed experimentally is a key point.

      Our study was specifically designed to elucidate the fundamental mechanism of the elementary, single-cycle translocation step at near-atomic resolution. For this purpose, the 800 bp DNA length was sufficient. The observed translocation step size per cycle was 216 ± 71 bp, which is substantially smaller than the total length of the simulated DNA. This confirms that the boundaries of our system did not artificially constrain the core translocation process we aimed to investigate. Therefore, we think that the DNA length used in this study did not systematically bias our main findings regarding the motor mechanism itself.

      As the reviewer pointed out, on the other hand, our current setup cannot reproduce the formation of kilobase-scale loops. We hypothesize that these large-scale events are intrinsically linked to the stochastic nature of the ATP hydrolysis cycle, which was simplified in our simulation model. We used fixed durations for each state for computational feasibility. In a more realistic scenario, a stochastically prolonged engaged state would provide a larger duration time for a captured DNA loop to grow via thermal diffusion. This could lead to occasional, much larger translocation steps upon ATP hydrolysis, contributing to the large loop sizes seen experimentally.

      (7) Minor point: The first CG model using three sites was introduced in PNAS vol 102, 6789 2005. The authors should consider citing it.

      Thank you for this suggestion. We have now cited the paper the reviewer recommended. Please find subsection entitled Coarse-grained simulations in Materials and Methods.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      (1) As part of getting rid of cross-contamination in the bulk data, the authors model the scRNA data, extrapolate it to the bulk data and subtract out "contaminant" cell types. One wonders, however, given that low expressed genes are not represented in the scRNA data, whether the assignment of a gene to one or another cell type can really be made definitive. Indeed, it's possible that a gene is expressed at low levels in one cell, and high levels in another, and would therefore be considered a contaminant. The result would be to throw out genes that actually are expressed in a given cell type. The definitive list would therefore be a conservative estimate, and not necessarily the correct estimate.

      We agree that the various strategies we employ do not result in perfect annotation of gene expression. However, despite their limitations, they are significantly better than either the single cell or the bulk data alone. We represent these strengths and shortcomings throughout the manuscript (for example, in ROC curves).

      (2) It would be quite useful to have tested some genes with lower expression levels using in vivo gene-fusion reporters to assess whether the expression assignments hold up as predicted. i.e. provide another avenue of experimentation, non-computational, to confirm that the decontamination algorithm works.

      We agree that evaluating only highly-expressed genes might introduce bias. We used a large battery of in vivo reporters, made with best-available technology (CRISPR insertion of the fluorophore into the endogenous locus) to evaluate our approaches. These reporters were constructed without bias in terms of gene expression and therefore represent both high and low expression levels. These data are represented throughout the manuscript (for example, in ROC curves). Details about the battery of reporters may be found in Taylor et al 2021. In addition to these reporters, this manuscript also generates and analyzes two other types of gene sets: non-neuronal and ubiquitous genes. Again, these genes are selected without bias toward gene expression, and the techniques presented here are benchmarked against them as well, with positive results.

      (3) In many cases, each cell class would be composed of at least 2 if not more neurons. Is it possible that differences between members of a single class would be missed by applying the cleanup algorithms? Such transcripts would be represented only in a fraction of the cells isolated by scRNAseq, and might then be considered not real.

      For the data set presented in this manuscript, all cells of a single neuron type were labeled and isolated together by FACS, and sequencing libraries were constructed from this pool of cells. Thus, potential subtypes within a particular type (when that type includes more than one cell) cannot be resolved by this method. By contrast, such subtypes were in some cases resolved in the single cell approach. To make the two data sets compatible with each other, for the single cell data we combined any subtypes together. We state in the Methods:

      “For this work, single cell clusters of neuron subtypes were collapsed to the resolution of the bulk replicates (example: VB and VB1 clusters in the single cell data were treated as one VB cluster).”

      (4) I didn't quite catch whether the precise staging of animals was matched between the bulk and scRNAseq datasets. Importantly, there are many genes whose expression is highly stage-specific or age-specific so even slight temporal differences might yield different sets of gene expression.

      We agree that accurate staging is critically important for valid comparisons between data sets and have included an additional supplemental table with staging metadata for each sample. The staging protocol used for the bulk data set was initially employed to generate scRNA seq data and should be comparable. An additional description of our approach is now included in Methods:

      “Populations of synchronized L1s were grown at 23 C until reaching the L4 stage on 150 mM 8P plates inoculated with Na22. The time in culture to reach the L4 stage varied (40.5-49 h) and was determined for each strain. 50-100 animals were inspected with a 40X DIC objective to determine developmental stage as scored by vulval morphology (Mok et al., 2025). Cultures were predominantly composed of L4 larvae but also typically included varying fractions of L3 larvae and adults.”

      We have also updated supplementary table 1 to include additional information about each sort including the observed developmental stages and their proportions when available, the temperature the worms were grown at, the genotype of each experiment, and the number of cells collected in FACS.

      (5) To what extent does FACS sorting affect gene expression? Can the authors provide some controls?

      We appreciate this suggestion. We agree that FACS sorting (and also dissociation of the animals prior to sorting) might affect gene expression, particularly of stress-related transcripts. We note that dissociation and FACS sorting was also used to collect cells for our single cell data set (Taylor et al 2021). We would note that clean controls for this approach can be prohibitively difficult to collect, as the process of dissociation and FACS will inevitably change the proportion of cell types present in the sample, and for bulk sequencing efforts it is difficult even with deconvolution approaches to accurately account for changes in gene expression that result from dissociation and FACS, versus changes in gene expression that result from differences in cell type composition. We regrettably omitted a discussion of these issues in the manuscript. We now write in the Results:

      “The dissociation and FACS steps used to isolate neuron types induce cellular stress responsive pathways (van den Brink et al., 2017; Kaletsky et al., 2016, Taylor 2021). Genes associated with this stress response (Taylor 2021) were not removed from downstream analyses, but should be viewed with caution.”

      Reviewer #2 (Public review):

      The bulk RNA-seq data collected by the authors has high levels of contamination and, in some cases, is based on very few cells. The methodology to remove contamination partly makes up for this shortcoming, but the high background levels of contaminating RNA in the FACS-isolated neurons limit the confidence in cell-specific transcripts.

      We agree that these are the limitations of the source data. One of the manuscript’s main goals is to analyze and refine these source data, reducing these limitations and quantifying the results.

      The study does not experimentally validate any of the refined gene expression predictions, which was one of the main strengths of the initial CenGEN publication (Taylor et al, 2021). No validation experiments (e.g., fluorescence reporters or single molecule FISH) were performed for protein-coding or non-coding genes, which makes it difficult for the reader to assess how much gene predictions are improved, other than for the gold standard set, which may have specific characteristics (e.g., bias toward high expression as they were primarily identified in fluorescence reporter experiments).

      We agree that evaluating only highly-expressed genes might introduce bias. We used a large battery of in vivo reporters, made with best-available technology (CRISPR insertion of the fluorophore into the endogenous locus) to evaluate our approaches. These reporters were constructed without bias in terms of gene expression and therefore represent both high and low expression levels. These data are represented throughout the manuscript (for example, in ROC curves). Details about the battery of reporters may be found in Taylor et al 2021. In addition to these reporters, this manuscript also generates and analyzes two other types of gene sets: non-neuronal and ubiquitous genes. Again, these genes are selected without bias toward gene expression, and the techniques presented here are benchmarked against them as well, with positive results.

      The study notes that bulk RNA-seq data, in contrast to scRNA-seq data, can be used to identify which isoforms are expressed in a given cell. However, no analysis or genome browser tracks were supplied in the study to take advantage of this important information. For the community, isoform-specific expression could guide the design of cell-specific expression constructs or for predictive modeling of gene expression based on machine learning.

      We strongly agree that these datasets allow for new discoveries in neuronal splicing patterns and regulators, which is explored further in other publications from our group and other research groups in the field. We did not sufficiently highlight these works in the body of our text, and have added a reference in the discussion. “In addition, the bulk RNA-seq dataset contains transcript information across the gene body, which parallel efforts have used to identify mRNA splicing patterns that are not found in the scRNA-seq dataset.” These works can be found in references 26 and 27.

      (1) The study relies on thresholding to determine whether a gene is expressed or not. While this is a common practice, the choice of threshold is not thoroughly justified. In particular, the choice of two uniform cutoffs across protein-encoding RNAs and of one distinct threshold for non-coding RNAs is somewhat arbitrary and has several limitations. This reviewer recommends the authors attempt to use adaptive threshold-methods that define gene expression thresholds on a per-gene basis. Some of these methods include GiniClust2, Brennecke's variance modeling, HVG in Seurat, BASiCS, and/or MAST Hurdle model for dropout correction.

      We appreciate the reviewer’s suggestion, and would note that the integrated data currently incorporates some gene-specific weighting to identify gene expression patterns, as the single-cell data are weighted by maximum expression for each gene prior to integration with the LittleBites cleaned data. This gene level normalization markedly improved gene detection accuracy, and is discussed in depth in our 2021 Paper “Molecular topography of an entire nervous system”. We previously explored several methods for setting gene specific thresholds for identifying gene expression patterns in the integrated dataset. Unfortunately we found that none of the tested methods out performed setting “static” thresholds across all genes in the integrated dataset, and tended to increase false positive rates for some low abundance genes, where gene-specific thresholding can tend towards calling a gene expressed in at least one cell type when it is actually not expressed in any cell types present. These methods are likely to provide better results for expanded datasets that cover all tissue types (where one might reasonably expect that a gene is likely to be expressed in at least one sample).

      (2) Most importantly, the study lacks independent experimental validation (e.g., qPCR, smFISH, or in situ hybridization) to confirm the expression of newly detected lowly expressed genes and non-coding RNAs. This is particularly important for validating novel neuronal non-coding RNAs, which are primarily inferred from computational approaches.

      We agree that smFISH and related in situ validation methods would be an asset in this analysis. Unfortunately because most ncRNAs are very short, they are prohibitively difficult to accurately measure with smFISH. Many ncRNAs we attempted to assay with smFISH methods can bind at most 3 fluorescent probes, which unfortunately was not reliably distinguishable from background autofluorescence in the worm. Many published methods for smFISH signal amplification have not been optimized for C. elegans, and the tough cuticle is a major barrier for those efforts.

      (3) The novel biology is somewhat limited. One potential area of exploration would be to look at cell-type specific alternative splicing events.

      We appreciate this suggestion. Indeed, as we put our source data online prior to publishing this manuscript, two published papers already use this source data set to analyze alternative splicing. Further, these works include validation of splicing patterns observed in this source data, indicating the biological relevance of these data sets.

      (4) The integration method disproportionately benefits neuron types with limited representation in scRNA-seq, meaning well-sampled neuron types may not show significant improvement. The authors should quantify the impact of this bias on the final dataset.

      We agree that cell-types that are well represented in the single-cell dataset tend to have fewer new genes identified in the Integrated dataset than “rare” cell-types in the single cell data. However we would note that cell-types that are highly abundant in the single-cell data appear to become increasingly vulnerable to non-neuronal false positives, and that integration’s primary effect in high abundance cell-types appears to be reducing the false positive rate for non-neuronal genes. Thus we suggest that integration benefits all cell-types across the spectrum of single-cell abundance. The false positives are likely caused by a side-effect of normalization steps in the single-cell dataset, which is moderated by using the LittleBites cleaned bulk samples as an orthogonal measurement. The benefit of integration for cell-types with low abundance in the single-cell dataset is now quantified, and the benefits of integration for low and high abundance cell-types from the single cell data are described in the following section (p.13):

      “To test the stability of LittleBites cleanup across different single-cell reference dataset qualities, we ran the algorithm on a set of bulk samples by first subsetting the corresponding single-cell cluster’s population to 10, 50, 100, or 500 cells. We performed this process 500 times for each subsampling rate for each sample (2000 total runs per sample). We found that testing gene AUROC values are stable across reference cluster sizes (Fig. 2D), suggesting that even if the target cell type is rarely represented in a single cell reference, accurate cleaning is still possible. However, comparing gene level stability across target cluster population levels reveals that low abundance references have higher gene level variance (Fig. 2E), lower purity estimates (Fig. S2F), higher variance in the mean expression across genes (Fig. S2G), and they tend to have lower overall expression (suggesting more aggressive subtraction) (Fig. S2H). This indicates that while binary gene calling is improved even if the reference cluster is small, users should be cautious when using fewer than 100 cells in their single cell reference cluster as the resulting cleanup is less stable.”

      (5) The authors employ a logit transformation to model single-cell proportions into count space, but they need to clarify its assumptions and potential pitfalls (e.g., how it handles rare cell types).

      We agree that the assumptions and pitfalls of the logit model are key for evaluating its usefulness, especially for cell types that are rarely captured in the single-cell dataset. The assumptions and pitfalls are described in the methods section, but we regretfully omitted any mention of those pitfalls in the results, which we have now rectified.

      The description in the methods section is: “We applied this formula to our real single cell dataset and used this equation to transform proportion measures of gene expression into a count space to generate the Prop2Count dataset for downstream analysis and integration with bulk datasets. This procedure allows for proportions data to be used in downstream analyses that work with counts datasets. However, it does limit the range of potential values that each gene can have, with the potential values set as:

      As n approaches 0, the number of potential values decreases, which can be incompatible with some downstream models. Thus, caution should be used when applying this transformation to datasets with few cells.”

      The new mention in the results is: “However, caution should be taken when using this approach in scRNAseq cases where all replicates of a cell type contain few cells. scProp2Count values are limited to the space of possible proportion values, and so replicates with low numbers of cells will have fewer potential expression “levels” which may break some model assumptions in downstream applications (see Methods).”

      (6) The LittleBites approach is highly dependent on the accuracy of existing single-cell references. If the scRNA-seq dataset is incomplete or contains classification biases, this could propagate errors into the bulk RNA-seq data. The authors may want to discuss potential limitations and sensitivity to errors in the single-cell dataset, and it is critical to define minimum quality parameters (e.g. via modeling) for the scRNAseq dataset used as reference.

      We appreciate this suggestion, and agree that manuscript would benefit from a description of where the LittleBites method can give poor results. To this end, we subset our single cell reference for individual neurons of interest to the level of 10, 50, 100, or 500 cells (500 iterations per sample rate), and then ran Littlebites, and compared metrics of gene expression stability, sample composition estimates, and AUROC performance on test genes. We found that when fewer than 100 cells for the target cell type are included in the single cell reference, gene expression stability drops (variance between subsampling iterations was much higher when fewer reference cells were used). However, we found that AUROC values were consistently high regardless of how many reference cells were included, but that this stability in AUROC values was paired with lower overall counts in samples with <100 reference cells after cleanup. This indicates that in cases where few reference cells are present, higher AUROC values might be achieved by more aggressive subtraction, which is attenuated when the reference model is more complete. This analysis is shown in figure 2 and figure S2, and described in the results section, recreated here.

      “To test the stability of Littlebites cleanup across different single-cell reference dataset qualities, we ran the algorithm on a set of bulk samples by first subsetting the corresponding single-cell cluster’s population to 10, 50, 100, or 500 cells. We performed this process 500 times for each subsampling rate for each sample (2000 total runs per sample). We found that testing gene AUROC values are stable across reference cluster sizes (Fig. 2D), suggesting that even if the target cell type is rarely represented in a single cell reference, accurate cleaning is still possible. However, comparing gene level stability across target cluster population levels reveals that low population references have higher gene level variance (Fig. 2E), lower purity estimates (Fig. S2F), higher variance in the mean expression across genes (Fig. S2G), and they tend to have lower overall expression (suggesting more aggressive subtraction) (Fig. S2H). This suggests that while binary gene calling is improved similarly even if the reference cluster is small, users should be cautious when using less than 100 cells in their single cell reference cluster as the resulting cleanup is less stable.”

      (7) Also very important, the LittleBites method could benefit from a more intuitive explanation and schematic to improve accessibility for non-computational readers. A supplementary step-by-step breakdown of the subtraction process would be useful.

      We appreciate this suggestion and implemented a step-by-steo breakdown of the subtraction process in the methods section, also copied below. We also updated the graphic representation in figure 2A.

      “LittleBites Subtraction algorithm

      LittleBites is an iterative algorithm for bulk RNA-seq datasets, that improves the accuracy of cell-type specific bulk RNA-seq sample profiles by removing counts from non-target contaminants (e.g. ambient RNA from dead cells, carry-over non-target cells from FACS enrichment due to imperfect gating). This method leverages single cell reference datasets and ground truth expression information to guide iterative and conservative subtraction to enrich for true target cell-type expression. Using this approach, LittleBites balances subtraction by optimizing using both a single-cell reference, and an orthogonal ground truth reference, moderating biases inherent to either reference.

      This algorithm first calculates gene level specificity weights in a single cell reference dataset using SPM (Specificity Preservation Method) (re-add 22, re-add 23). SPM assigns high weights (approaching 1) to genes expressed in single cell types while applying conservative weights to genes with broader expression patterns, which helps to reduce inappropriate subtraction.

      The algorithm proceeds in a loop of three steps:

      Step 1: Estimate Contamination. Each bulk sample is modeled as the sum of a linear combination of single-cell profiles (target cell type and likely contaminants) using non-negative least squares (NNLS). The resulting coefficients provide the estimate of how much of the sample’s counts come from the target cell-type, and how much comes from each contaminant cell-type.

      Step 2: Weighted Subtraction. Each bulk sample is cleaned by subtracting the weighted sum of contaminant single-cell profiles. This subtraction is attempted multiple times (separately) across a series of learning rate weights (usually ranging from 0-1) which moderate the size of the subtraction step (Equation 1). This produces a range of possible “cleaned” sample options for evaluation.

      Step 3: Performance Optimization. For each learning rate, the cleaned result is evaluated against a set of ground truth genes by calculating the area under the receiver operating characteristic curve (AUROC). The learning rate that optimizes the AUROC is then selected. When multiple learning rates yielded equivalent AUROC values, the lowest learning rate value is chosen to minimize subtraction.

      If the optimal learning rate at Step 3 is 0 (no subtraction option beats the baseline) then the loop is halted. Else, the cleaned bulk profile is returned to Step 1, and the loop continues until the AUROC cannot be improved upon using the single-cell reference modeling.“

      (8) In the same vein, the ROC curves and AUROC comparisons should have clearer annotations to make results more interpretable for readers unfamiliar with these metrics.

      We agree that the ROC and AUROC metrics need a clearer explanation to make their use and interpretations clearer. We included a description of both metrics, and a suggestion for how to interpret them in the results section, copied below.

      “To evaluate the post-subtraction datasets accuracy we used the area under the Receiver-Operator Characteristic (AUROC) score. In brief, we set a wide range of thresholds to call genes expressed or unexpressed, and then compared it to expected expression from a set of ground truth genes. This comparison produces a true positive rate (TPR, the percentage of truly expressed genes that are called expressed), and false positive rate (FPR, the percentage of truly not expressed genes that are called expressed), and a false discovery rate (FDR, the percentage of genes called expressed that are truly not expressed). The Receiver-Operator Characteristic (ROC) is the graph of the line produced by the TPR and FPR values across the range of thresholds tested, and the AUROC is calculated as the sum of the area under that line. A “random” model of gene expression is expected to have an AUROC value of 0.5, and a “perfect” model is expected to have an AUROC value of 1. Thus, AUROCs below 0.5 are worse than a random guess, and values closer to 1 indicate higher accuracy.”

      (9) Finally, after the correlation-based decontamination of the 4,440 'unexpressed' genes, how many were ultimately discarded as non-neuronal?

      a) Among these non-neuronal genes, how many were actually known neuronal genes or components of neuronal pathways (e.g., genes involved in serotonin synthesis, synaptic function, or axon guidance)?

      b) Conversely, among the "unexpressed" genes classified as neuronal, how many were likely not neuron-specific (e.g., housekeeping genes) or even clearly non-neuronal (e.g., myosin or other muscle-specific markers)?

      Combined with point 10, see below.

      (10) To increase transparency and allow readers to probe false positives and false negatives, I suggest the inclusion of:

      a) The full list of all 4,440 'unexpressed' genes and their classification at each refinement step. In that list flag the subsets of genes potentially misclassified, including:

      - Neuronal genes wrongly discarded as non-neuronal.

      - Non-neuronal genes wrongly retained as neuronal.

      b) Add a certainty or likelihood ranking that quantifies confidence in each classification decision, helping readers validate neuronal vs. non-neuronal RNA assignments.

      This addition would enhance transparency, reproducibility, and community engagement, ensuring that key neuronal genes are not erroneously discarded while minimizing false positives from contaminant-derived transcripts.

      We agree that the genes called “unexpressed” in the single-cell data need more context and clarity. First, we trimmed the list to only include 2,333 genes of highest confidence. Second, for those genes we identified any with published neuronal expression patterns. Identifying genes that were retained as neuronal but are likely non-neuronal in origin is difficult as many markers are expressed in a mixture of neuronal and non-neuronal cell-types, however we used a curated list of putative non-neuronal markers to assess the accuracy of the integrated data (see supplementary table 4), and established that most non-neuronal markers are undetected in the integrated data, with the number of detected genes decreasing as our threshold stringency increases. Of note, a few putative non-neuronal genes remain detected even at high thresholds, indicating that our dataset still retains a small percentage of neuronal false positives. This result has been collected in the new supplementary figure 4F, and addressed in the following text in the results section “Testing against a curated list of non-neuronal genes from fluorescent reporters and genomic enrichment studies, we found that of 445 non-neuronal markers, each gene was detected in an average of 12.5 cells or a median of 3 cells in the single-cell dataset, and an average of 8.7 cells or a median of 1 cell in the integrated dataset, at a 14% FDR threshold.”

      We also included a list of “unexpressed” gene identities and tissue annotations as new supplementary tables 16 and 17.

      Reviewer #2 (Recommendations for the authors):

      The utility of the bulk RNA-seq data would be significantly increased if the authors were to analyze which isoforms are expressed in individual neurons. Also, it would be very useful to know if there are instances where a gene is expressed in several neurons, but different isoforms are specific to individual neurons.

      We appreciate this suggestion. Indeed, as we put our source data online prior to publishing this manuscript, two published papers already use this source data set to analyze alternative splicing. Further, these works include validation of splicing patterns observed in this source data, indicating the biological relevance of these data sets. This is now noted in our discussion section “In addition, the bulk RNA-seq dataset contains transcript information across the gene body, which parallel efforts have used to identify mRNA splicing patterns that are not found in the scRNA-seq dataset.” These works can be found in references 26 and 27.

      Reviewer #3 (Recommendations for the authors):

      (1) Describe the number of L4 animals processed to obtain good-quality bulk RNAseq libraries from the different neuronal types. If the number of worms would be different for different neuronal types, then please make a supplementary table listing the minimum number of worms needed for each neuronal type.

      We appreciate the reviewer’s recommendation, and agree that it would be a useful resource to provide suggestions for how many worms are needed per experiment. Unfortunately We did not track the total number of animals for each sample. We aimed to start with 200-300 ul of packed worms for each strain, generally equating to >500,000 worms, but yields of FACS-isolated cells varied among cell types. Because replicates for specific neuron types were also variable in some instances (See additions to supplemental Table 1), yields likely depend on multiple factors. We have previously noted (Taylor et al., 2021), for example, that some cell types were under-represented in scRNA-seq data (e.g, pharyngeal neurons) based on in vivo abundance presumptively due to the difficulty of isolation or sub-viability in the cell dissociation-FACS protocol.

      (2) List the thresholds for the parameters used during the FASTQC quality control and the threshold number of reads that would make a sample not useful.

      We now include parameters for sample exclusion in the methods section. “Samples were excluded after sequencing if they had: fewer than 1 million read pairs, <1% of uniquely mapping reads to the C. elegans genome, > 50% duplicate reads (low umi diversity), or failed deduplication steps in the nudup package.”

      (3) In Figure 5C, include an overlapping bar that shows the total number of genes in each cell type. You may need to use a log scale to see both (new and all) numbers of genes in the same graph. Add supplementary tables with the names of all new genes assigned to each neuronal type.

      We agree that this figure panel needed additional context. On further reflection we concluded that figure 5 was not sufficiently distinct from figure 4 to warrant separation, and incorporated some key findings from figure 5 into figure S4.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Weaknesses:

      (1) Weaknesses of this study include a proposed mechanism underlying the sexual dimorphism phenotype based on experimentation in only males, and widespread reliance on over-expression when investigating protein-protein interaction and localization. Additionally, a minor weakness is that the text describing the identification of cyp17a2 as a candidate contains errors that are confusing.

      We thank the reviewer for these insightful comments, which have helped us improve the manuscript.

      (1) Experimentation in males. We focused on male zebrafish for our mechanistic studies to preclude potential confounding effects from female hormones and to directly interrogate the basis of the observed male-biased resistance. As confirmed in the manuscript (lines 151-153), both wild-type and cyp17a2⁻/⁻ males developed normal male sex organs and exhibited comparable androgen levels. This crucial control gives us confidence that the differences in antiviral immunity we observed are a direct consequence of Cyp17a2 loss-of-function, rather than secondary to developmental or hormonal abnormalities. We fully agree that elucidating the mechanism in females represents a valuable and interesting direction for future research.

      (2) Over-expression studies. We acknowledge that overexpression approaches can have inherent limitations. To mitigate this and strengthen our conclusions, we complemented these experiments with loss-of-function data from both knockout zebrafish and knockdown cells, as well as validation at the endogenous level (e.g., Fig. 4J and S4C). The consistent results obtained across these diverse experimental models collectively reinforce our conclusion that Cyp17a2 interacts with and stabilizes STING.

      (3) We thank the reviewer for pointing out the lack of clarity in the text regarding the selection process of Cyp17a2. We have thoroughly revised the manuscript to provide a precise and accurate description of our methodology. The relevant text is now as follows: “Differential expression analysis identified 1511 upregulated and 1117 downregulated genes (Fig. 2A and Table S2). We then focused on a subset of known or putative sexrelated genes. Among these eight candidates, cyp17a2 exhibited the most significant male-biased upregulation, a finding that was subsequently confirmed by qPCR (Fig. 2B and S1A)” (lines 142-144).

      (2) Lines 139-140 describe the data for Figure 2 as deriving from "healthy hermaphroditic adult zebrafish". This appears to be a language error and should be corrected to something that specifies that the comparison made is between healthy adult male and female kidneys.

      We thank the reviewer for pointing out this inaccuracy. This was a terminological error, and we have corrected the text to accurately state “transcriptome sequencing was performed on head-kidney tissues from healthy adult male and female zebrafish” (lines 139-140). We have carefully reviewed the manuscript to ensure no similar errors are present.

      (3) In Figure 2A and associated text cyp17a2 is highlighted but the volcano plot does not indicate why this was an obvious choice. For example, many other genes are also highly induced in male vs female kidneys. Figure 2B and line 143 describe a subset of "eight sex-related genes" but it is not clear how these relate to Figure 2A. The narrative could be improved to clarify how cyp17a2 was selected from Figure 2A and it seems that the authors made an attempt to do this with Figure 2B but it is not clear how these are related. This is important because the available data do not rule out the possibility that other factors also mediate the sexual dimorphism they observed either in combination, in a redundant fashion, or in a more complex genetic fashion. The narrative of the text and title suggests that they consider this to be a monogenic trait but more evidence is needed.

      We thank the reviewer for raising these important points. We have revised the manuscript to clarify the candidate gene selection process and to avoid any implication that the trait is monogenic.

      The selection of cyp17a2 was not based solely on its position in the volcano plot (Fig. 2A), but on a multi-faceted rationale. We first prioritized genes with known or putative sex-related functions from the pool of differentially expressed genes. From this subset, cyp17a2 emerged as the lead candidate due to a combination of unique attributes, it exhibited the most significant and consistent male-biased upregulation among the validated candidates (Fig. 2B and S1A); it is a teleost-specific autosomal gene, suggesting a novel mechanism for sexual dimorphism independent of canonical sex chromosomes; and it showed conserved male-biased expression across multiple tissues (Fig. 2C and 2D). Regarding its representation in the volcano plot, cyp17a2 was included in the underlying dataset but was not explicitly labeled in the revised Figure 2A to maintain visual clarity, as the plot aimed to illustrate the global transcriptomic landscape rather than highlight individual genes.

      We agree with the reviewer that other genetic factors may contribute to the observed sexual dimorphism. Accordingly, we have modified the text throughout the manuscript to remove any suggestion of a purely monogenic trait. Our functional data position cyp17a2 as a key and sufficient factor, as its knockout in males was sufficient to ablate the antiviral resistance phenotype (Fig. 2E-G), demonstrating a major, nonredundant role without precluding potential contributions from other genes.

      The following specific changes have been made to the text.

      (1) The title has been revised by replacing “governs” with “orchestrates.” (line 1)  

      (2) The abstract now states “the male-biased gene cyp17a2 as a critical mediator of this enhanced response” instead of “which are driven by the male-biased gene Cyp17a2 rather than by hormones or sex chromosomes.” (lines 33-34)

      (3) The discussion now states “Our study leverages this unique context to demonstrate that enhanced antiviral immunity in males is mediated by the male-biased expression of the autosomal gene cyp17a2,” removing the comparative phrasing regarding hormones or sex chromosomes. (lines 364-366)

    1. Author response:

      (1) About ROCF figure-copy results

      Reviewer #1 queried the necessity of including the Rey-Osterrieth Complex Figure (ROCF) results in the main text. We appreciate the reviewer’s perspective on the narrative flow and the transition between the LOCUS paradigm and the ROCF results. However, we remain keen to retain these findings in the main tex, as they provide critical ecological and clinical validation for the computational mechanisms identified in our study.

      We argue that the following points support the retention of these results:

      (1)  The ROCF we used is a standard neuropsychological tool for identifying constructional apraxia. Our results bridge the gap between basic cognitive neuroscience and clinical application by demonstrating that specific remapping parameters—rather than general memory precision—predict real-world deficits in patients.

      (2)  The finding that our winning model explains approximately 62% of the variance in ROCF copy scores across all diagnostic groups further indicates that these parameters from the LOCUS task represent core computational phenotypes that underpin complex, real-life visuospatial construction (copying drawings).

      (3)  Previous research has often observed only a weak or indirect link between drawing ability and traditional working memory measures, such as digit span  (Senese et al., 2020). This was previously attributed to “deictic” strategies—like frequent eye movements—that minimise the need to hold large amounts of information in memory (Ballard et al., 1995; Cohen, 2005; Draschkow et al., 2021). While our study was not exclusively designed to catalogue all cognitive contributions to drawing, our findings provide significant and novel evidence indicating that transsaccadic integration is a critical driver of constructional (copying drawing) ability. By demonstrating this link, we offer a new direction for future research, shifting the focus from general memory capacity toward the precision of spatial updating across eye movements.

      By including the ROCF results in the main text, we provide evidence for a functional role for spatial remapping that extends beyond perceptual stability into the domain of complex visuomotor control. We will expand on these points in the Discussion in our revised manuscript.

      (2) Model complexity and overfitting

      We would like to clarify that the Bayesian model selection (BMS) procedure utilised in this manuscript inherently balances model fit with parsimony. Unlike maximum likelihood inference, where overfitting is a primary concern often requiring cross-validation via out-of-sample prediction, our approach depends upon the comparison of marginal likelihoods. This method directly penalises model complexity — a principle often described as the “Bayesian Occam’s Razor” (Rasmussen and Ghahramani, 2000). This means that a model is only favoured if the improvement in fit justifies the additional parameter space. If a parameter were redundant, it would lower the model's evidence by “diluting” the probability mass over the parameter space. The emergence of the “Dual (Saccade) + Interference” model as the winning candidate suggests it offers the most plausible generative account of the data while maintaining necessary parsimony. We would be happy to point toward literature that discusses how these marginal likelihood approximations provide a more robust guard against overfitting than standard metrics like BIC or AIC (MacKay, 2003; Murray and Ghahramani, 2005; Penny, 2012).

      (3) On model fitting across age groups

      This approach is primarily supported by our empirical findings: there was no significant interaction between age group and saccade condition for either location or colour memory. While older adults demonstrated lower baseline precision, the specific disruptive effect of saccades (the “saccade cost”) was remarkably consistent across cohorts. This justifies the use of a common generative model to assess quantitative differences in parameter estimates.

      This approach does implicitly assume that participants perform the task in a qualitatively similar way. However, as this assumption is mitigated by the fact that our winning model nests simpler models as special cases, it supports the assessment of group differences in parameters that play consistent mechanistic roles. This flexibility allows the model to naturally accommodate groups where certain components—such as interference—may play a reduced role, while remaining sensitive to the specific mechanistic failures that differentiate healthy aging from neurodegeneration.

      (4) Conceptual terminology and patient group descriptions

      We will clarify our conceptual terminology, explicitly defining the relationships between retinotopic (eye-centred), transsaccadic (across-saccade), and spatiotopic (world-centred) representations.

      Regarding the demographics of the clinical cohorts, we apologise for any lack of clarity in our initial presentation. The patient demographics for both the Parkinson’s disease (PD) and Alzheimer’s disease (AD) groups—including age, gender, education, and ACE-III scores—are currently detailed alongside the healthy control data (two groups: Young Healthy Controls and Elderly Healthy Controls) in the table within the Participants section of the Materials and Methods. In our revision. We will ensure that this table is correctly labelled as Table 2 and will provide more comprehensive recruitment and characterisation details for both patient groups within the main text. Finally, we will include a detailed discussion in the Supplementary Materials regarding eye-tracking data quality across all cohorts, specifically comparing calibration accuracy, trace stability, and trial rejection rates to demonstrate that our findings are not confounded by differences in recording quality between healthy and clinical populations.

      References

      Ballard DH, Hayhoe MM, Pelz JB. 1995. Memory Representations in Natural Tasks. Journal of Cognitive Neuroscience 7:66–80. DOI: https://doi.org/10.1162/jocn.1995.7.1.66

      Cohen DJ. 2005. Look little, look often: The influence of gaze frequency on drawing accuracy. Perception & Psychophysics 67:997–1009. DOI: https://doi.org/10.3758/BF03193626

      Draschkow D, Kallmayer M, Nobre AC. 2021. When Natural Behavior Engages Working Memory. Current Biology 31:869-874.e5. DOI: https://doi.org/10.1016/j.cub.2020.11.013, PMID: 33278355

      MacKay DJC. 2003. Information Theory, Inference and Learning Algorithms. Cambridge University Press.

      Murray I, Ghahramani Z. 2005. A note on the evidence and Bayesian Occam’s razor (Technical report No. GCNU TR 2005-003). Gatsby Unit.

      Penny WD. 2012. Comparing Dynamic Causal Models using AIC, BIC and Free Energy. Neuroimage 59:319–330. DOI: https://doi.org/10.1016/j.neuroimage.2011.07.039, PMID: 21864690

      Rasmussen C, Ghahramani Z. 2000. Occam’ s Razor. Advances in Neural Information Processing Systems. MIT Press.

      Senese VP, Zappullo I, Baiano C, Zoccolotti P, Monaco M, Conson M. 2020. Identifying neuropsychological predictors of drawing skills in elementary school children. Child Neuropsychology 26:345–361. DOI: https://doi.org/10.1080/09297049.2019.1651834, PMID: 31390949

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript describes the use of computational tools to design a mimetic of the interleukin-7 (IL-7) cytokine with superior stability and receptor binding activity compared to the naturally occurring molecule. The authors focused their engineering efforts on the loop regions to preserve receptor interfaces while remediating structural irregularities that destabilize the protein. They demonstrated the enhanced thermostability, production yield, and bioactivity of the resulting molecule through biophysical and functional studies. Overall, the manuscript is well written, novel, and of high interest to the fields of molecular engineering, immunology, biophysics, and protein therapeutic design. The experimental methodologies used are convincing; however, the article would benefit from more quantitative comparisons of bioactivity through titrations.

      Reviewer #2 (Public review):

      Summary:

      This manuscript presents the computational design and experimental validation of Neo-7, an engineered variant of interleukin-7 (IL-7) with improved folding efficiency, expression yield, and therapeutic activity. The authors employed a rational protein design approach using Rosetta loop remodeling to reconnect IL-7's functional helices through shorter, more efficient loops, resulting in a protein with superior stability and binding affinity compared to wild-type IL-7. The work demonstrates promising translational potential for cancer immunotherapy applications.

      Strengths:

      (1) The integration of Rosetta loop remodeling with AlphaFold validation represents an established computational pipeline for rational protein design. The iterative refinement process, using both single-sequence and multimer AlphaFold predictions, is methodologically sound.

      (2) The authors provide thorough characterization across multiple platforms (yeast display, bacterial expression, mammalian cell expression) and assays (binding kinetics, thermostability, bioactivity), strengthening the robustness of their findings.

      (3) The identification of the critical helix 1 kink stabilized by disulfide bonding and its recreation through G4C/L96C mutations demonstrates deep structural understanding and successful problem-solving.

      (4) The MC38 tumor model results show clear therapeutic advantages of Neo-7 variants, with compelling immune profiling data supporting CD8+ T cell-mediated anti-tumor mechanisms.

      (5) The transcriptomic profiling provides valuable mechanistic insights into T cell activation states and suggests reduced exhaustion markers, which are clinically relevant.

      Weaknesses:

      (1) While computational predictions are extensive, the manuscript lacks experimental structural validation of the designed Neo-7 variants. The term "Structural Validation" should not be used in the header.

      We thank the reviewer for this constructive comment. To better reflect the work conducted, we have revised the section title from “Structural Validation of Neo-7 in AlphaFold single sequence mode” to “Structural Modeling of Neo-7 in AlphaFold single sequence mode.” This change clarifies that our study employed in silico modeling approaches rather than experimental structural validation.

      We thank the reviewer for this insightful comment. We speculate that the slower off-rate observed for Neo-7 variants is primarily attributable to their enhanced structural stability, which promotes the formation of a more stable cytokine–receptor complex. This is consistent with prior observations in other engineered cytokines, such as IL-2 mimetics (Neo-2/15).

      In terms of biological consequences, we believe the slower off-rate is unlikely to result in signaling bias or qualitatively distinct pathways for several reasons:

      IL-7’s mechanism of action is inherently regulated to prevent over-signaling. T cells downregulate IL7R-α expression upon IL-7 stimulation, ensuring a built-in negative feedback mechanism.

      IL-7 signaling is dominated by STAT5 activation, without the signaling plasticity observed in cytokines like IL-21 or IL-22, which can bias toward STAT1/3 and drive divergent functional outcomes.

      Our RNA-seq data support this interpretation, as Neo-7–treated CD8⁺ T cells exhibited transcriptional profiles highly similar to those induced by WT-IL-7, with the difference being an enhanced magnitude of response rather than novel pathway engagement.

      Taken together, we infer that the slower off-rate of Neo-7 enhances the potency and durability of IL-7 signaling without altering its downstream specificity, thereby strengthening the magnitude of immune responses while maintaining the canonical STAT5-driven biology of IL-7.

      (3) While computational immunogenicity prediction is provided, these methods are very limited.

      We fully agree with the reviewer that current in silico immunogenicity prediction tools are limited and cannot be considered definitive. Indeed, to date, none of these algorithms has demonstrated a strong correlation with clinical immunogenicity outcomes of biologics. For example, the presence of anti-drug antibodies (ADA) in murine or non-human primate models often does not translate into ADA induction in human clinical trials. This disconnect underscores the inherent challenges of predicting immunogenicity based solely on computational or preclinical models.

      Our strategy to mitigate potential immunogenicity was therefore not to rely exclusively on prediction software, but instead to apply a conservative design principle: preserving the vast majority of the parental IL-7 sequence while introducing only the minimal number of amino acid substitutions required to achieve our engineering objectives. By maintaining sequence continuity with the native cytokine, we aim to minimize the risk of introducing novel epitopes while improving stability and developability. We acknowledge that definitive immunogenicity assessment can only be addressed in future clinical studies.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Specific Points:

      (1) The authors should describe the molecular composition of CYT-107.

      We thank the reviewer for this suggestion and have added clarification regarding the molecular composition of CYT-107. CYT-107 is a recombinant form of wild-type human interleukin-7 (IL-7) expressed in eukaryotic cells, which introduces N-linked glycosylation modifications to the protein. As a glycosylated recombinant IL-7, CYT-107 more closely mimics the natural human cytokine compared to bacterial expression systems that produce non-glycosylated IL-7. This feature contributes to its stability and bioavailability in clinical applications.

      (Reference: U.S. National Center for Advancing Translational Sciences, GSRS record for IL-7, https://gsrs.ncats.nih.gov/ginas/app/ui/substances/46bd8013-1e2d-4b6e-afcf-340f447e8710

      (2) The authors should indicate the receptor layout for IL-7 in the introduction and indicate available structural data. Also, in line 93, the authors should indicate that IL-7Ra is one subunit of the heterodimeric receptor complex.

      We thank the reviewer for this insightful suggestion. However, due to page limitations, we have chosen to orient the introduction around the design rationale, computational workflow, and biological functionality of IL-7. To address the reviewer’s point while maintaining brevity, we have now included a concise description of the IL-7 receptor layout and its available structural data in the main text. Specifically, in line 93 we revised the sentence to read:“We began by examining the crystal structure of IL-7 bound to its receptor, IL7R-α (interleukin-7 receptor alpha; PDB ID: 3DI2), which recruits IL-2Rγ to form a heterodimeric receptor complex essential for downstream signaling.”

      (3) The abbreviation IL-7Ra should be defined at first use.

      We thank the reviewer for the comment. The abbreviation has now been defined at its first appearance in the manuscript. Specifically, at Line 93 we revised the sentence as follows:

      “We began by examining the crystal structure of IL-7 bound to its receptor, IL7R-α (interleukin-7 receptor alpha; PDB ID: 3DI2), which recruits IL-2Rγ to form a heterodimeric receptor complex essential for downstream signaling..”

      (4) The authors need to clarify whether the human or murine IL-7Ra is being used in each experiment mentioned in the results text.

      We thank the reviewer for this important point. We have now specified in the main text and corresponding subsection titles whether human or murine IL-7Rα was used in each experiment.

      (5) The authors sometimes use a dash in IL7Ra and IL2Rg and sometimes do not. This should be standardized.

      We appreciate the reviewer’s observation. We have standardized the terminology throughout the manuscript to “IL7Rα” and “IL2Rγ” to maintain consistency.

      (6) In Figure 3E, the authors left out the v in "Neo7-LDv1".

      We have corrected the omission of “v” and updated the label to read Neo7-LDv1.

      (7) In Figure 3E, the authors must indicate in the bottom row that they are visualizing sequential binding to IL-2Rg following incubation with IL-7Ra. This should be stated in the results text and the figure caption as well.

      We have revised the results text and figure caption to clearly state that the bottom row illustrates sequential binding to IL-2Rγ following incubation with IL-7Rα.

      “for detection of IL-2Rγ binding, yeast cells were first incubated with recombinant IL-7Rα, washed, and subsequently incubated with IL-2Rγ”

      (8) In Figure 3E, "IL-7Rg" should be corrected to "IL-2Rg".

      We have corrected “IL-7Rγ” to “IL-2Rγ” in Figure 3E for accuracy and consistency.

      (9) In line 140, the authors claim that Neo7-LDv1 is partially folded based on the binding to the heterodimeric receptor complex. However, the data are insufficient to support this conclusion.

      We understand the concern of the reviewer and we decided to rephrase the sentence for better understanding: “A degree of binding to IL2Rγ was detected, possibly reflecting partial folding of the displayed protein in the yeast display platform.” While we do not claim the protein to be fully or uniformly folded, this deduction is supported by the yeast display data and further corroborated by AlphaFold structural predictions.

      (10) In lines 185-186, the authors claim that the binding affinity for IL-2Rg is improved, but this is not shown in Figure 3, which looks only at a single concentration and shows comparable binding between WT-IL7 and Neo7-LDv2.

      We thank the reviewer for this valuable observation. Our original wording was ambiguous and may have implied a direct comparison with WT-IL7, which was not intended. The sentence was meant to highlight that within the Neo-7 variant series, Neo7-LDv2 displayed stronger binding to both IL-7Rα and IL-2Rγ compared to other Neo-7 variants. To avoid misinterpretation, we have revised the text as follows:

      “Importantly, the enhanced binding affinity towards IL7Rα also led to improved binding towards the common IL2Rγ., relative to other variants in the Neo-7 series.”

      (11) Lines 202-203 appear to be an error.

      We thank the reviewer for pointing this out. The lines in question were indeed an error and have now been removed from the manuscript.

      (12) In yeast display validation, negative controls showing binding to the fluorescent antibody only and an irrelevant control protein should be shown for all constructs in order to evaluate nonspecific interactions.

      We agree with the reviewer that appropriate negative controls are important to validate specificity. To address this, we will include yeast display data with negative controls—native yeast (EBY100) stained with the corresponding fluorescent antibody in the Supplementary Information. This addition will provide clearer validation of binding specificity and reduce concerns regarding nonspecific interactions.

      (13) For yeast display studies, titrations rather than single concentrations should be used to compare constructs (Figures 3 and 4). The claim that any of the constructs has a higher affinity than any other construct must be supported by performing titrations.

      We thank the reviewer for this comment. We respectfully note that yeast display titrations provide relative rather than absolute estimates of binding affinity. In our study, constructs were compared under identical antigen concentrations, where the observed fluorescence intensity reflected their relative binding strength. These yeast display results served as an initial screening strategy, which we subsequently validated using surface plasmon resonance (SPR). SPR provided quantitative binding parameters and confirmed the binding differences observed in yeast display. Thus, while yeast titrations were not performed, the combination of side-by-side yeast display comparisons and orthogonal validation by SPR supports our affinity claims with both qualitative and quantitative evidence.

      (14) The acronym SPR needs to be defined, and the authors should mention that this technique was used for quantitative binding studies in line 259.

      We thank the reviewer for this suggestion. The acronym has now been defined in the main text at its first use, and we have clarified its role in the study. The revised text reads:

      “We then characterized the binding affinities of Neo-7 variants to mouse IL-7 receptor alpha (mIL-7Rα) in a quantitative manner using surface plasmon resonance (SPR).”

      (15) A titration of 2E8 cell proliferation versus concentration should be presented for IL-7 versus Neo-7 variants to directly compare EC50 values and make claims regarding potency in Figure 5H. Also, the authors should clarify whether a proliferation or viability assay was performed.

      We thank the reviewer for the helpful comment regarding the use of EC₅₀ values when discussing potency. In response, we have revised the manuscript to avoid overinterpreting the data. Specifically, we replaced the term potency with ability to stimulate, as the 2E8 cell assay was designed to validate whether receptor binding by IL-7 and Neo-7 variants translates into biological function—namely, supporting immune cell viability and proliferation under limiting cytokine conditions. The assay was not optimized to determine formal EC₅₀ values, but rather to demonstrate functional activity consistent with IL-7 receptor engagement.

      We have also clarified in the text that the experiment was a proliferation assay, with cell viability assessed as part of the readout. This revision better reflects the scope of the assay while aligning our claims with the data presented.

      (16) Isotype control is not an appropriate name for the Fc-Only construct. This should be denoted as Fc Only.

      We thank the reviewer for this comment. We have revised the terminology throughout the manuscript, changing isotype control to Fc control.

      (17) A titration of mouse splenocyte proliferation versus concentration should be presented for IL-7 versus Neo-7 variants to directly compare EC50 values and make claims regarding potency in Figure 6.

      We thank the reviewer for this insightful suggestion regarding EC₅₀ analysis. In this study, the splenocyte proliferation assay was designed as a preliminary in vitro screen to confirm the biological activity of Neo-7 variants relative to wild-type IL-7 prior to in vivo testing. The assay was not optimized for quantitative potency determination, but rather to provide an initial functional validation of the constructs. We have therefore revised the manuscript wording to avoid overinterpreting the data and refrained from making claims regarding EC₅₀-based potency. Instead, we emphasize that the in vivo tumor model provides a more physiologically relevant and rigorous platform for assessing cytokine functionality, including proliferation and immunomodulation.

      (18) The legends in Figure 6 should indicate the colors used for each construct.

      We thank the reviewer for pointing this out. We have revised the legend for Figure 6 to include the color codes corresponding to each construct.

      (19) Metabolism should be singular in lines 433 and 435.

      We have corrected the wording so that “metabolism” is consistently used in the singular form.

      (20) In Figure 8D, "cycling" should be changed to "cycle".

      The word “cycling” has been corrected to “cycle” in Figure 8D.

      (21) The treatments need to be indicated in Figure 8D. Also, a color scale is needed.

      We agree with the reviewer, and a color scale description has now been included in the Figure legend to aid interpretation. “The gene expression heatmap is derived from Z-scores calculated from the RNA sequencing data, with expression levels color-coded from high (red) to low (blue). ”

      (22) More comparisons between RNASeq data for Fc-WTIL7 versus Fc-Neo7 (Figure 8) should be presented in the results section.

      We thank the reviewer for this suggestion. Due to space limitations in the main manuscript, we are unable to include an expanded description of all RNA-Seq comparisons. However, we will provide a more detailed analysis of Fc-WT-IL7 versus Fc-Neo7 in the supplementary section, including expanded differential gene expression comparisons and pathway enrichment analyses. This will allow readers to fully appreciate the differences while maintaining focus in the main text.

      (23) The strikethrough in line 464 needs to be corrected.

      We have corrected the strikethrough error in line 464.

      (24) It is unclear how stabilizing IL-7 improves its toxicity or half-life. The authors should indicate more clearly which limitations of IL-7 were addressed by their molecule in the abstract, introduction, and discussion.

      Native IL-7 demonstrates an excellent safety profile but faces two major challenges in clinical application: (1) short plasma half-life and (2) suboptimal developability due to poor stability. The short half-life is typically addressed through Fc-fusion strategies, which extend systemic exposure via FcRn recycling. However, wild-type IL-7 exhibits a strong aggregation tendency when fused to Fc, rendering the fusion protein poorly developable. By redesigning IL-7 into the more stable Neo-7 format, we substantially improved the folding efficiency and purity of the Fc-fusion protein after affinity purification, thereby enabling its advancement as a recombinant biologic candidate.

      We do not intend to claim that increased stability directly reduces in vivo toxicity. The favorable safety profile of IL-7 arises primarily from its intrinsic biology (mechanism of action and downstream signaling), rather than from its structural stability. That said, improved stability and reduced aggregation propensity could potentially lower the immunogenicity risk of protein biologics. Nevertheless, there are currently no validated in vitro or in vivo assays that reliably correlate protein stability or aggregation with clinical immunogenicity outcomes.

      (25) The acronym MSA needs to be defined.

      We have defined the acronym MSA (Multiple Sequence Alignment) on page 7, line 142.

      (26) The acronym CPD needs to be defined.

      We have defined the acronym CPD (Computational Protein Design) on page 23, line 468.

      Reviewer #2 (Recommendations for the authors):

      Any experimental structural data would be good to have.

      We plan to pursue X-ray crystallography of Neo-7 in future studies to obtain high-resolution structural confirmation. However, we emphasize that such experiments require significant time and resources, and the results would not alter the biological claims made in this study. Our focus here is to demonstrate that with recent advances in in silico protein structure prediction algorithms, such as AlphaFold2, it is now feasible to redesign therapeutic proteins with sufficient accuracy to achieve improved developability and biological performance. This study highlights how computational approaches can streamline protein drug engineering, reducing reliance on labor-intensive structural studies during the early stages of therapeutic development.

      Please add details of how the changed kinetics might affect downstream pathways.

      We appreciate the reviewer’s suggestion to elaborate on the biological implications of the altered binding kinetics.

      Our data show that Neo-7 variants display a slower off-rate relative to WT-IL-7, which likely reflects enhanced stabilization of the cytokine–receptor complex. In principle, this could prolong receptor occupancy and modestly extend downstream signaling duration. However, several biological features of IL-7 constrain the risk of excessive or aberrant signaling:

      Receptor Regulation: IL-7 signaling induces rapid downregulation of IL7Rα on T cells, serving as a feedback mechanism to prevent sustained or uncontrolled activation. This "hardwired" receptor regulation reduces the likelihood that a slower off-rate translates into pathological over-signaling.

      Pathway Specificity: IL-7 primarily signals through the JAK/STAT5 axis, with little evidence of signaling bias. Unlike other cytokines (e.g., IL-21, IL-22) that can activate STAT1 or STAT3 and drive distinct functional outcomes, IL-7’s pathway specificity minimizes concerns about altered signaling directionality.

      Transcriptional Evidence: Our RNA-seq analysis further supports this, showing that Neo-7 and WT-IL-7 activate similar transcriptional programs. The differences we observed were in the magnitude of response, not in the qualitative nature of the pathways engaged. This suggests that Neo-7 variants enhance the intensity of canonical IL-7 signaling rather than redirecting it toward alternative or unintended pathways.

      Together, these findings support the interpretation that the slower off-rate of Neo-7 variants likely contributes to stronger or more sustained activation of IL-7’s canonical STAT5 pathway, while intrinsic regulatory mechanisms and pathway fidelity safeguard against inappropriate signaling outcomes.

      Minor:

      (1) The Figure 3 text is hard to read.

      We acknowledge the reviewer’s concern regarding the readability of Figure 3. In the revised manuscript, we will provide a higher-resolution version of the figure to ensure that all labels and text are clearly visible upon magnification.

      (2) The manuscript switches between "Neo-7" and "Neo7" .

      We agree with the reviewer’s observation. To maintain consistency throughout the manuscript, all references have been standardized to Neo-7.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public reviews:

      Reviewer #1 (Public review):

      Summary:

      Wu and colleagues aimed to explain previous findings that adolescents, compared to adults, show reduced cooperation following cooperative behaviour from a partner in several social scenarios. The authors analysed behavioural data from adolescents and adults performing a zero-sum Prisoner's Dilemma task and compared a range of social and non-social reinforcement learning models to identify potential algorithmic differences. Their findings suggest that adolescents' lower cooperation is best explained by a reduced learning rate for cooperative outcomes, rather than differences in prior expectations about the cooperativeness of a partner. The authors situate their results within the broader literature, proposing that adolescents' behaviour reflects a stronger preference for self-interest rather than a deficit in mentalising.

      Strengths:

      The work as a whole suggests that, in line with past work, adolescents prioritise value accumulation, and this can be, in part, explained by algorithmic differences in weighted value learning. The authors situate their work very clearly in past literature, and make it obvious the gap they are testing and trying to explain. The work also includes social contexts that move the field beyond non-social value accumulation in adolescents. The authors compare a series of formal approaches that might explain the results and establish generative and modelcomparison procedures to demonstrate the validity of their winning model and individual parameters. The writing was clear, and the presentation of the results was logical and well-structured.

      We thank the reviewer for recognizing the strengths of our work.

      Weaknesses:

      (1) I also have some concerns about the methods used to fit and approximate parameters of interest. Namely, the use of maximum likelihood versus hierarchical methods to fit models on an individual level, which may reduce some of the outliers noted in the supplement, and also may improve model identifiability.

      We thank the reviewer for this suggestion. Following the comment, we added a hierarchical Bayesian estimation. We built a hierarchical model with both group-level (adolescent group and adult group) and individual-level structures for the best-fitting model. Four Markov chains with 4,000 samples each were run, and the model converged well (see Figure supplement 7).

      We then analyzed the posterior parameters for adolescents and adults separately. The results were consistent with those from the MLE analysis. These additional results have been included in the Appendix Analysis section (also see Figure supplement 5 and 7). In addition, we have updated the code and provided the link for reference. We appreciate the reviewer’s suggestion, which improved our analysis.

      (2) There was also little discussion given the structure of the Prisoner's Dilemma, and the strategy of the game (that defection is always dominant), meaning that the preferences of the adolescents cannot necessarily be distinguished from the incentives of the game, i.e. they may seem less cooperative simply because they want to play the dominant strategy, rather than a lower preferences for cooperation if all else was the same.

      We thank the reviewer for this comment and agree that adolescents’ lower cooperation may partly reflect a rational response to the incentive structure of the Prisoner’s Dilemma. 

      However, our computational modeling explicitly addressed this possibility. Model 4 (inequality aversion) captures decisions that are driven purely by self-interest or aversion to unequal outcomes, including a parameter reflecting disutility from advantageous inequality, which represents self-oriented motives. If participants’ behavior were solely guided by the payoff-dominant strategy, this model should have provided the best fit. However, our model comparison showed that Model 5 (social reward) performed better in both adolescents and adults, suggesting that cooperative behavior is better explained by valuing social outcomes beyond payoff structures.

      Besides, if adolescents’ lower cooperation is that they strategically respond to the payoff structure by adopting defection as the more rewarding option. Then, adolescents should show reduced cooperation across all rounds. Instead, adolescents and adults behaved similarly when partners defected, but adolescents cooperated less when partners cooperated and showed little increase in cooperation even after consecutive cooperative responses. This pattern suggests that adolescents’ lower cooperation cannot be explained solely by strategic responses to payoff structures but rather reflects a reduced sensitivity to others’ cooperative behavior or weaker social reciprocity motives. We have expanded our Discussion to acknowledge this important point and to clarify how the behavioral and modeling results address the reviewer’s concern.

      “Overall, these findings indicate that adolescents’ lower cooperation is unlikely to be driven solely by strategic considerations, but may instead reflect differences in the valuation of others’ cooperation or reduced motivation to reciprocate. Although defection is the payoff-dominant strategy in the Prisoner’s Dilemma, the selective pattern of adolescents’ cooperation and the model comparison results indicate that their reduced cooperation cannot be fully explained by strategic incentives, but rather reflects weaker valuation of social reciprocity.”

      Appraisal & Discussion:

      (3) The authors have partially achieved their aims, but I believe the manuscript would benefit from additional methodological clarification, specifically regarding the use of hierarchical model fitting and the inclusion of Bayes Factors, to more robustly support their conclusions. It would also be important to investigate the source of the model confusion observed in two of their models.

      We thank the reviewer for this comment. In the revised manuscript, we have clarified the hierarchical Bayesian modeling procedure for the best-fitting model, including the group- and individual-level structure and convergence diagnostics. The hierarchical approach produced results that fully replicated those obtained from the original maximumlikelihood estimation, confirming the robustness of our findings. Please also see the response to (1).

      Regarding the model confusion between the inequality aversion (Model 4) and social reward (Model 5) models in the model recovery analysis, both models’ simulated behaviors were best captured by the baseline model. This pattern arises because neither model includes learning or updating processes. Given that our task involves dynamic, multi-round interactions, models lacking a learning mechanism cannot adequately capture participants’ trial-by-trial adjustments, resulting in similar behavioral patterns that are better explained by the baseline model during model recovery. We have added a clarification of this point to the Results:

      “The overlap between Models 4 and 5 likely arises because neither model incorporates a learning mechanism, making them less able to account for trial-by-trial adjustments in this dynamic task.”

      (4) I am unconvinced by the claim that failures in mentalising have been empirically ruled out, even though I am theoretically inclined to believe that adolescents can mentalise using the same procedures as adults. While reinforcement learning models are useful for identifying biases in learning weights, they do not directly capture formal representations of others' mental states. Greater clarity on this point is needed in the discussion, or a toning down of this language.

      We sincerely thank the reviewer for this professional comment. We agree that our prior wording regarding adolescents’ capacity to mentalise was somewhat overgeneralized. Accordingly, we have toned down the language in both the Abstract and the Discussion to better align our statements with what the present study directly tests. Specifically, our revisions focus on adolescents’ and adults’ ability to predict others’ cooperation in social learning. This is consistent with the evidence from our analyses examining adolescents’ and adults’ model-based expectations and self-reported scores on partner cooperativeness (see Figure 4). In the revised Discussion, we state:

      “Our results suggest that the lower levels of cooperation observed in adolescents stem from a stronger motive to prioritize self-interest rather than a deficiency in predicting others’ cooperation in social learning”.

      (5) Additionally, a more detailed discussion of the incentives embedded in the Prisoner's Dilemma task would be valuable. In particular, the authors' interpretation of reduced adolescent cooperativeness might be reconsidered in light of the zero-sum nature of the game, which differs from broader conceptualisations of cooperation in contexts where defection is not structurally incentivised.

      We thank the reviewer for this comment and agree that adolescents’ lower cooperation may partly reflect a rational response to the incentive structure of the Prisoner’s Dilemma. However, our behavioral and computational evidence suggests that this pattern cannot be explained solely by strategic responses to payoff structures, but rather reflects a reduced sensitivity to others’ cooperative behavior or weaker social reciprocity motives. We have expanded the Discussion to acknowledge this point and to clarify how both behavioral and modeling results address the reviewer’s concern (see also our response to 2).

      (6) Overall, I believe this work has the potential to make a meaningful contribution to the field. Its impact would be strengthened by more rigorous modelling checks and fitting procedures, as well as by framing the findings in terms of the specific game-theoretic context, rather than general cooperation.

      We thank the reviewer for the professional comments, which have helped us improve our work.

      Reviewer #2 (Public review):

      Summary:

      This manuscript investigates age-related differences in cooperative behavior by comparing adolescents and adults in a repeated Prisoner's Dilemma Game (rPDG). The authors find that adolescents exhibit lower levels of cooperation than adults. Specifically, adolescents reciprocate partners' cooperation to a lesser degree than adults do. Through computational modeling, they show that this relatively low cooperation rate is not due to impaired expectations or mentalizing deficits, but rather a diminished intrinsic reward for reciprocity. A social reinforcement learning model with asymmetric learning rate best captured these dynamics, revealing age-related differences in how positive and negative outcomes drive behavioral updates. These findings contribute to understanding the developmental trajectory of cooperation and highlight adolescence as a period marked by heightened sensitivity to immediate rewards at the expense of long-term prosocial gains.

      Strengths:

      (1) Rigid model comparison and parameter recovery procedure.

      (2) Conceptually comprehensive model space.

      (3) Well-powered samples.

      We thank the reviewer for highlighting the strengths of our work.

      Weaknesses:

      A key conceptual distinction between learning from non-human agents (e.g., bandit machines) and human partners is that the latter are typically assumed to possess stable behavioral dispositions or moral traits. When a non-human source abruptly shifts behavior (e.g., from 80% to 20% reward), learners may simply update their expectations. In contrast, a sudden behavioral shift by a previously cooperative human partner can prompt higher-order inferences about the partner's trustworthiness or the integrity of the experimental setup (e.g., whether the partner is truly interactive or human). The authors may consider whether their modeling framework captures such higher-order social inferences. Specifically, trait-based models-such as those explored in Hackel et al. (2015, Nature Neuroscience)-suggest that learners form enduring beliefs about others' moral dispositions, which then modulate trial-bytrial learning. A learner who believes their partner is inherently cooperative may update less in response to a surprising defection, effectively showing a trait-based dampening of learning rate.

      We thank the reviewer for this thoughtful comment. We agree that social learning from human partners may involve higher-order inferences beyond simple reinforcement learning from non-human sources. To address this, we had previously included such mechanisms in our behavioral modeling. In Model 7 (Social Reward Model with Influence), we tested a higher-order belief-updating process in which participants’ expectations about their partner’s cooperation were shaped not only by the partner’s previous choices but also by the inferred influence of their own past actions on the partner’s subsequent behavior. In other words, participants could adjust their belief about the partner’s cooperation by considering how their partner’s belief about them might change. Model comparison showed that Model 7 did not outperform the best-fitting model, suggesting that incorporating higher-order influence updates added limited explanatory value in this context. As suggested by the reviewer, we have further clarified this point in the revised manuscript.

      Regarding trait-based frameworks, we appreciate the reviewer’s reference to Hackel et al. (2015). That study elegantly demonstrated that learners form relatively stable beliefs about others’ social dispositions, such as generosity, especially when the task structure provides explicit cues for trait inference (e.g., resource allocations and giving proportions). By contrast, our study was not designed to isolate trait learning, but rather to capture how participants update their expectations about a partner’s cooperation over repeated interactions. In this sense, cooperativeness in our framework can be viewed as a trait-like latent belief that evolves as evidence accumulates. Thus, while our model does not include a dedicated trait module that directly modulates learning rates, the belief-updating component of our best-fitting model effectively tracks a dynamic, partner-specific cooperativeness, potentially reflecting a prosocial tendency.

      This asymmetry in belief updating has been observed in prior work (e.g., Siegel et al., 2018, Nature Human Behaviour) and could be captured using a dynamic or belief-weighted learning rate. Models incorporating such mechanisms (e.g., dynamic learning rate models as in Jian Li et al., 2011, Nature Neuroscience) could better account for flexible adjustments in response to surprising behavior, particularly in the social domain.

      We thank the reviewer for the suggestion. Following the comment, we implemented an additional model incorporating a dynamic learning rate based on the magnitude of prediction errors. Specifically, we developed Model 9:  Social reward model with Pearce–Hall learning algorithm (dynamic learning rate), in which participants’ beliefs about their partner’s cooperation probability are updated using a Rescorla–Wagner rule with a learning rate dynamically modulated by the Pearce–Hall (PH) Error Learning mechanism. In this framework, the learning rate increases following surprising outcomes (larger prediction errors) and decreases as expectations become more stable (see Appendix Analysis section for details).

      The results showed that this dynamic learning rate model did not outperform our bestfitting model in either adolescents or adults (see Figure supplement 6). We greatly appreciate the reviewer’s suggestion, which has strengthened the scope of our analysis. We now have added these analyses to the Appendix Analysis section (see Figure Supplement 6) and expanded the Discussion to acknowledge this modeling extension and further discuss its implications.

      Second, the developmental interpretation of the observed effects would be strengthened by considering possible non-linear relationships between age and model parameters. For instance, certain cognitive or affective traits relevant to social learning-such as sensitivity to reciprocity or reward updating-may follow non-monotonic trajectories, peaking in late adolescence or early adulthood. Fitting age as a continuous variable, possibly with quadratic or spline terms, may yield more nuanced developmental insights.

      We thank the reviewer for this professional comment. In addition to the linear analyses, we further conducted exploratory analyses to examine potential non-linear relationships between age and the model parameters. Specifically, we fit LMMs for each of the four parameters as outcomes (α+, α-, β, and ω). The fixed effects included age, a quadratic age term, and gender, and the random effects included subject-specific random intercepts and random slopes for age and gender. Model comparison using BIC did not indicate improvement for the quadratic models over the linear models for α<sup>+</sup> (ΔBIC<sub>quadratic-linear</sub> = 5.09), α− (ΔBICquadratic-linear = 3.04), β (ΔBICquadratic-linear = 3.9), or ω (ΔBICquadratic-linear = 0). Moreover, the quadratic age term was not significant for α<sup>+</sup>, α<sup>−</sup>, or β (all ps > 0.10). For ω, we observed a significant linear age effect (b = 1.41, t = 2.65, p = 0.009) and a significant quadratic age effect (b = −0.03, t = −2.39, p = 0.018; see Author response image 1). This pattern is broadly consistent with the group effect reported in the main text. The shaded area in the figure represents the 95% confidence interval. As shown, the interval widens at older ages (≥ 26 years) due to fewer participants in that range, which limits the robustness of the inferred quadratic effect. In consideration of the limited precision at older ages and the lack of BIC improvement, we did not emphasize the quadratic effect in the revised manuscript and present these results here as exploratory.

      Author response image 1.

      Linear and quadratic model fits showing the relationship between age and the ω parameter, with 95% confidence intervals.<br />

      Finally, the two age groups compared - adolescents (high school students) and adults (university students) - differ not only in age but also in sociocultural and economic backgrounds. High school students are likely more homogenous in regional background (e.g., Beijing locals), while university students may be drawn from a broader geographic and socioeconomic pool. Additionally, differences in financial independence, family structure (e.g., single-child status), and social network complexity may systematically affect cooperative behavior and valuation of rewards. Although these factors are difficult to control fully, the authors should more explicitly address the extent to which their findings reflect biological development versus social and contextual influences.

      We appreciate this comment. Indeed, adolescents (high school students) and adults (university students) differ not only in age but also in sociocultural and socioeconomic backgrounds. In our study, all participants were recruited from Beijing and surrounding regions, which helps minimize large regional and cultural variability. Moreover, we accounted for individual-level random effects and included participants’ social value orientation (SVO) as an individual difference measure. 

      Nonetheless, we acknowledge that other contextual factors, such as differences in financial independence, socioeconomic status, and social experience—may also contribute to group differences in cooperative behavior and reward valuation. Although our results are broadly consistent with developmental theories of reward sensitivity and social decisionmaking, sociocultural influences cannot be entirely ruled out. Future work with more demographically matched samples or with socioeconomic and regional variables explicitly controlled will help clarify the relative contributions of biological and contextual factors. Accordingly, we have revised the Discussion to include the following statement:  “Third, although both age groups were recruited from Beijing and nearby regions, minimizing major regional and cultural variation, adolescents and adults may still differ in socioeconomic status, financial independence, and social experience. Such contextual differences could interact with developmental processes in shaping cooperative behavior and reward valuation. Future research with demographically matched samples or explicit measures of socioeconomic background will help disentangle biological from sociocultural influences.”

      Reviewer #3 (Public review):

      Summary:

      Wu and colleagues find that in a repeated Prisoner's Dilemma, adolescents, compared to adults, are less likely to increase their cooperation behavior in response to repeated cooperation from a simulated partner. In contrast, after repeated defection by the partner, both age groups show comparable behavior.

      To uncover the mechanisms underlying these patterns, the authors compare eight different models. They report that a social reward learning model, which includes separate learning rates for positive and negative prediction errors, best fits the behavior of both groups. Key parameters in this winning model vary with age: notably, the intrinsic value of cooperating is lower in adolescents. Adults and adolescents also differ in learning rates for positive and negative prediction errors, as well as in the inverse temperature parameter.

      Strengths: 

      The modeling results are compelling in their ability to distinguish between learned expectations and the intrinsic value of cooperation. The authors skillfully compare relevant models to demonstrate which mechanisms drive cooperation behavior in the two age groups.

      We thank the reviewer’s recognition of our work’s strengths.

      Weaknesses:

      Some of the claims made are not fully supported by the data:

      The central parameter reflecting preference for cooperation is positive in both groups. Thus, framing the results as self-interest versus other-interest may be misleading.

      We thank the reviewer for this insightful comment. In the social reward model, the cooperation preference parameter is positive by definition, as defection in the repeated rPDG always yields a +2 monetary advantage regardless of the partner’s action. This positive value represents the additional subjective reward assigned to mutual cooperation (e.g., reciprocity value) that counterbalances the monetary gain from defection. Although the estimated social reward parameter ω was positive, the effective advantage of cooperation is Δ=p×ω−2. Given participants’ inferred beliefs p, Δ was negative for most trials (p×ω<2), indicating that the social reward was insufficient to offset the +2 advantage of defection. Thus, both adolescents and adults valued cooperation positively, but adolescents’ smaller ω and weaker responsiveness to sustained partner cooperation suggest a stronger weighting on immediate monetary payoffs. 

      In this light, our framing of adolescents as more self-interested derives from their behavioral pattern: even when they recognized sustained partner cooperation and held high expectations of partner cooperation, adolescents showed lower cooperative behavior and reciprocity rewards compared with adults. Whereas adults increased cooperation after two or three consecutive partner cooperations, this pattern was absent among adolescents. We therefore interpret their behavior as relatively more self-interested, reflecting reduced sensitivity to the social reward from mutual cooperation rather than a categorical shift from self-interest to other-interest, as elaborated in the Discussion.

      It is unclear why the authors assume adolescents and adults have the same expectations about the partner's cooperation, yet simultaneously demonstrate age-related differences in learning about the partner. To support their claim mechanistically, simulations showing that differences in cooperation preference (i.e., the w parameter), rather than differences in learning, drive behavioral differences would be helpful.

      We thank the reviewer for raising this important point. In our model, both adolescents and adults updated their beliefs about partner cooperation using an asymmetric reinforcement learning (RL) rule. Although adolescents exhibited a higher positive and a lower negative learning rate than adults, the two groups did not differ significantly in their overall updating of partner cooperation probability (Fig. 4a-b). We then examined the social reward parameter ω, which was significantly smaller in adolescents and determined the intrinsic value of mutual cooperation (i.e., p×ω). This variable differed significantly between groups and closely matched the behavioral pattern.

      Following the reviewer’s suggestion, we conducted additional simulations varying one model parameter at a time while holding the others constant. The difference in mean cooperation probability between adults and adolescents served as the index (positive = higher cooperation in adults). As shown in the Author response image 2, decreases in ω most effectively reproduced the observed group difference (shaded area), indicating that age-related differences in cooperation are primarily driven by variation in the social reward parameter ω rather than by others.

      Author response image 2.

      Simulation results showing how variations in each model parameter affect the group difference in mean cooperation probability (Adults – Adolescents). Based on the best-fitting Model 8 and parameters estimated from all participants, each line represents one parameter (i.e., α+, α-, ω, β) systematically varied within the tested range (α±:0.1–0.9; ω, β:1–9) while other parameters were held constant. Positive values indicate higher cooperation in adults. Smaller ω values most strongly reproduced the observed group difference, suggesting that reduced social reward weighting primarily drives adolescents’ lower cooperation.

      Two different schedules of 120 trials were used: one with stable partner behavior and one with behavior changing after 20 trials. While results for order effects are reported, the results for the stable vs. changing phases within each schedule are not. Since learning is influenced by reward structure, it is important to test whether key findings hold across both phases.

      We thank the reviewer for this thoughtful and professional comment. In our GLMM and LMM analyses, we focused on trial order rather than explicitly including the stable vs. changing phase factor, due to concerns about multicollinearity. In our design, phases occur in specific temporal segments, which introduces strong collinearity with trial order. In multi-round interactions, order effects also capture variance related to phase transitions. 

      Nonetheless, to directly address this concern, we conducted additional robustness analyses by adding a phase variable (stable vs. changing) to GLMM1, LMM1, and LMM3 alongside the original covariates. Across these specifications, the key findings were replicated (see GLMM<sub>sup</sub>2 and LMM<sub>sup</sub>4–5; Tables 9-11), and the direction and significance of main effects remained unchanged, indicating that our conclusions are robust to phase differences.

      The division of participants at the legal threshold of 18 years should be more explicitly justified. The age distribution appears continuous rather than clearly split. Providing rationale and including continuous analyses would clarify how groupings were determined.

      We thank the reviewer for this thoughtful comment. We divided participants at the legal threshold of 18 years for both conceptual and practical reasons grounded in prior literature and policy. In many countries and regions, 18 marks the age of legal majority and is widely used as the boundary between adolescence and adulthood in behavioral and clinical research. Empirically, prior studies indicate that psychosocial maturity and executive functions approach adult levels around this age, with key cognitive capacities stabilizing in late adolescence (Icenogle et al., 2019; Tervo-Clemmens et al., 2023). We have clarified this rationale in the Introduction section of the revised manuscript.

      “Based on legal criteria for majority and prior empirical work, we adopt 18 years as the boundary between adolescence and adulthood (Icenogle et al., 2019; Tervo-Clemmens et al., 2023).”

      We fully agree that the underlying age distribution is continuous rather than sharply divided. To address this, we conducted additional analyses treating age as a continuous predictor (see GLMM<sub>sup</sub>1 and LMM<sub>sup</sub>1–3; Tables S1-S4), which generally replicated the patterns observed with the categorical grouping. Nevertheless, given the limited age range of our sample, the generalizability of these findings to fine-grained developmental differences remains constrained. Therefore, our primary analyses continue to focus on the contrast between adolescents and adults, rather than attempting to model a full developmental trajectory.

      Claims of null effects (e.g., in the abstract: "adults increased their intrinsic reward for reciprocating... a pattern absent in adolescents") should be supported with appropriate statistics, such as Bayesian regression.

      We thank the reviewer for highlighting the importance of rigor when interpreting potential null effects. To address this concern, we conducted Bayes factor analyses of the intrinsic reward for reciprocity and reported the corresponding BF10 for all relevant post hoc comparisons. This approach quantifies the relative evidence for the alternative versus the null hypothesis, thereby providing a more direct assessment of null effects. The analysis procedure is now described in the Methods and Materials section: 

      “Post hoc comparisons were conducted using Bayes factor analyses with MATLAB’s bayesFactor Toolbox (version v3.0, Krekelberg, 2024), with a Cauchy prior scale σ = 0.707.”

      Once claims are more closely aligned with the data, the study will offer a valuable contribution to the field, given its use of relevant models and a well-established paradigm.

      We are grateful for the reviewer’s generous appraisal and insightful comments.

      Recommendations for the authors

      Reviewer #1 (Recommendations for the authors):

      I commend the authors on a well-structured, clear, and interesting piece of work. I have several questions and recommendations that, if addressed, I believe will strengthen the manuscript.

      We thank the reviewer for commending the organization of our paper.

      Introduction: - Why use a zero-sum (Prisoner's Dilemma; PD) versus a mixed-motive game (e.g. Trust Task) to study cooperation? In a finite set of rounds, the dominant strategy can be to defect in a PD.

      We thank the reviewer for this helpful comment. We agree that both the rationale for using the repeated Prisoner’s Dilemma (rPDG) and the limitations of this framework should be clarified. We chose the rPDG to isolate the core motivational conflict between selfinterest and joint welfare, as its symmetric and simultaneous structure avoids the sequential trust and reputation dependencies/accumulation inherent to asymmetric tasks such as the Trust Game (King-Casas et al., 2005; Rilling et al., 2002).

      Although a finitely repeated rPDG theoretically favors defection, extensive prior research shows that cooperation can still emerge in long repeated interactions when players rely on learning and reciprocity rather than backward induction (Rilling et al., 2002; Fareri et al., 2015). Our design employed 120 consecutive rounds, allowing participants to update expectations about partner behavior and to establish stable reciprocity patterns over time. We have added the following clarification to the Introduction:

      “The rPDG provides a symmetric and simultaneous framework that isolates the motivational conflict between self-interest and joint welfare, avoiding the sequential trust and reputation dynamics characteristic of asymmetric tasks such as the Trust Game (Rilling et al., 2002; King-Casas et al., 2005)”

      Methods:

      Did the participants know how long the PD would go on for?

      Were the participants informed that the partner was real/simulated?

      Were the participants informed that the partner was going to be the same for all rounds?

      We thank the reviewer for the meticulous review work, which helped us present the experimental design and reporting details more clearly. the following clarifications: I. Participants were not informed of the total number of rounds in the rPDG. This prevented endgame expectations and avoided distraction from counting rounds, which could introduce additional effects. II. Participants were told that their partner was another human participant in the laboratory. However, the partner’s behavior was predetermined by a computer program. This design enabled tighter experimental control and ensured consistent conditions across age groups, supporting valid comparisons. III. Participants were informed that they would interact with the same partner across all rounds, aligning with the essence of a multiround interaction paradigm and stabilizing partner-related expectations. For transparency, we have clarified these points in the Methods and Materials section:

      “Participants were told that their partner was another human participant in the laboratory and that they would interact with the same partner across all rounds. However, in reality, the actions of the partner were predetermined by a computer program. This setup allowed for a clear comparison of the behavioral responses between adolescents and adults. Participants were not informed of the total number of rounds in the rPDG.”

      The authors mention that an SVO was also recorded to indicate participant prosociality. Where are the results of this? Did this track game play at all? Could cooperativeness be explained broadly as an SVO preference that penetrated into game-play behaviour?

      We thank the reviewer for pointing this out. We agree that individual differences in prosociality may shape cooperative behavior, so we conducted additional analyses incorporating SVO. Specifically, we extended GLMM1 and LMM3 by adding the measured SVO as a fixed effect with random slopes, yielding GLMM<sub>sup</sub>3 and LMM<sub>sup</sub>6 (Tables 12–13). The results showed that higher SVO was associated with greater cooperation, whereas its effect on the reward for reciprocity was not significant. Importantly, the primary findings remained unchanged after controlling for SVO. These results indicate that cooperativeness in our task cannot be explained solely by a broad SVO preference, although a more prosocial orientation was associated with greater cooperation. We have reported these analyses and results in the Appendix Analysis section.

      Why was AIC chosen rather an BIC to compare model dominance?

      Sorry for the lack of clarification. Both the Akaike Information Criterion (AIC, Akaike, 1974) and Bayesian Information Criterion (BIC, Schwarz, 1978) are informationtheoretic criterions for model comparison, neither of which depends on whether the models to be compared are nested to each other or not (Burnham et al., 2002). We have added the following clarification into the Methods.

      “We chose to use the AICc as the metric of goodness-of-fit for model comparison for the following statistical reasons. First, BIC is derived based on the assumption that the “true model” must be one of the models in the limited model set one compares (Burnham et al., 2002; Gelman & Shalizi, 2013), which is unrealistic in our case. In contrast, AIC does not rely on this unrealistic “true model” assumption and instead selects out the model that has the highest predictive power in the model set (Gelman et al., 2014). Second, AIC is also more robust than BIC for finite sample size (Vrieze, 2012).”

      I believe the model fitting procedure might benefit from hierarchical estimation, rather than maximum likelihood methods. Adolescents in particular seem to show multiple outliers in a^+ and w^+ at the lower end of the distributions in Figure S2. There are several packages to allow hierarchical estimation and model comparison in MATLAB (which I believe is the language used for this analysis; see https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007043).

      We thank the reviewer for this helpful comment and for referring us to relevant methodological work (Piray et al., 2019). We have addressed this point by incorporating hierarchical Bayesian estimation, which effectively mitigates outlier effects and improves model identifiability. The results replicated those obtained with MLE fitting and further revealed group-level differences in key parameters. Please see our detailed response to Reviewer#1 Q1 for the full description of this analysis and results.

      Results: Model confusion seems to show that the inequality aversion and social reward models were consistently confused with the baseline model. Is this explained or investigated? I could not find an explanation for this.

      The apparent overlap between the inequality aversion (Model 4) and social reward (Model 5) models in the recovery analysis likely arises because neither model includes a learning mechanism, making them unable to capture trial-by-trial adjustments in this dynamic task. Consequently, both were best fit by the baseline model. Please see Response to Reviewer #1 Q3 for related discussion.

      Figures 3e and 3f show the correlation between asymmetric learning rates and age. It seems that both a^+ and a^- are around 0.35-0.40 for young adolescents, and this becomes more polarised with age. Could it be that with age comes an increasing discernment of positive and negative outcomes on beliefs, and younger ages compress both positive and negative values together? Given the higher stochasticity in younger ages (\beta), it may also be that these values simply represent higher uncertainty over how to act in any given situation within a social context (assuming the differences in groups are true).

      We appreciate this insightful interpretation. Indeed, both α+ and α- cluster around 0.35–0.40 in younger adolescents and become increasingly polarized with age, suggesting that sensitivity to positive versus negative feedback is less differentiated early in development and becomes more distinct over time. This interpretation remains tentative and warrants further validation. Based on this comment, we have revised the Discussion to include this developmental interpretation.

      We also clarify that in our model β denotes the inverse temperature parameter; higher β reflects greater choice precision and value sensitivity, not higher stochasticity. Accordingly, adolescents showed higher β values, indicating more value-based and less exploratory choices, whereas adults displayed relatively greater exploratory cooperation. These group differences were also replicated using hierarchical Bayesian estimation (see Response to Reviewer #1 Q1). In response to this comment, we have added a statement in the Discussion highlighting this developmental interpretation.

      “Together, these findings suggest that the differentiation between positive and negative learning rates changes with age, reflecting more selective feedback sensitivity in development, while higher β values in adolescents indicate greater value sensitivity. This interpretation remains tentative and requires further validation in future research.”

      A parameter partial correlation matrix (off-diagonal) would be helpful to understand the relationship between parameters in both adolescents and adults separately. This may provide a good overview of how the model properties may change with age (e.g. a^+'s relation to \beta).

      We thank the reviewer for this helpful comment. We fully agree that a parameter partial correlation matrix can further elucidate the relationships among parameters. Accordingly, we conducted a partial correlation analysis and added the visually presented results to the revised manuscript as Figure 2-figure supplement 4.

      It would be helpful to have Bayes Factors reported with each statistical tests given that several p-values fall within the 0.01 and 0.10.

      We thank the reviewer for this important recommendation. We have conducted Bayes factor analyses and reported BF10 for all relevant post hoc comparisons. We also clarified our analysis in the Methods and Materials section: 

      “Post hoc comparisons were conducted using Bayes factor analyses with MATLAB’s bayesFactor Toolbox (version v3.0, Krekelberg, 2024), with a Cauchy prior scale σ = 0.707.”

      Discussion: I believe the language around ruling out failures in mentalising needs to be toned down. RL models do not enable formal representational differences required to assess mentalising, but they can distinguish biases in value learning, which in itself is interesting. If the authors were to show that more complex 'ToM-like' Bayesian models were beaten by RL models across the board, and this did not differ across adults and adolescents, there would be a stronger case to make this claim. I think the authors either need to include Bayesian models in their comparison, or tone down their language on this point, and/or suggest ways in which this point might be more thoroughly investigated (e.g., using structured models on the same task and running comparisons: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087619).

      We thank the reviewer for the comments. Please see our response to Reviewer 1 (Appraisal & Discussion section) for details.

      Reviewer #2 (Recommendations for the authors):

      The authors may want to show the winning model earlier (perhaps near the beginning of the Results section, when model parameters are first mentioned).

      We thank the reviewer for this suggestion. We agree that highlighting the winning model early improves clarity. Currently, we have mentioned the winning model before the beginning of the Results section. Specifically, in the penultimate paragraph of the Introduction we state:

      “We identified the asymmetric RL learning model as the winning model that best explained the cooperative decisions of both adolescents and adults.”

      Reviewer #3 (Recommendations for the authors):

      In addition to the points mentioned above, I suggest the following:

      (1) Clarify plots by clearly explaining each variable. In particular, the indices 1 vs. 1,2 vs. 1,2,3 were not immediately understandable.

      We thank the reviewer for this suggestion. We agree that the indices were not immediately clear. We have revised the figure captions (Figure 1 and 4) to explicitly define these terms more clearly: 

      “The x-axis represents the consistency of the partner’s actions in previous trials (t<sub>−1</sub>: last trial; t<sub>−1,2</sub>: last two trials; t<sub>−1,2,3</sub>: last three trials).”

      It's unclear why the index stops at 3. If this isn't the maximum possible number of consecutive cooperation trials, please consider including all relevant data, as adolescents might show a trend similar to adults over more trials.

      We thank the reviewer for raising this point. In our exploratory analyses, we also examined longer streaks of consecutive partner cooperation or defection (up to four or five trials). Two empirical considerations led us to set the cutoff at three in the final analyses. First, the influence of partner behavior diminished sharply with temporal distance. In both GLMMs and LMMs, coefficients for earlier partner choices were small and unstable, and their inclusion substantially increased model complexity and multicollinearity. This recency pattern is consistent with learning and decision models emphasizing stronger weighting of recent evidence (Fudenberg & Levine, 2014; Fudenberg & Peysakhovich, 2016). Second, streaks longer than three were rare, especially among some participants, leading to data sparsity and inflated uncertainty. Including these sparse conditions risked biasing group estimates rather than clarifying them. Balancing informativeness and stability, we therefore restricted the index to three consecutive partner choices in the main analyses, which we believe sufficiently capture individuals’ general tendencies in reciprocal cooperation.

      The term "reciprocity" may not be necessary. Since it appears to reflect a general preference for cooperation, it may be clearer to refer to the specific behavior or parameter being measured. This would also avoid confusion, especially since adolescents do show negative reciprocity in response to repeated defection.

      We thank you for this comment. In our work, we compute the intrinsic reward for reciprocity as p × ω, where p is the partner cooperation expectation and ω is the cooperation preference. In the rPDG, this value framework manifests as a reciprocity-derived reward: sustained mutual cooperation maximizes joint benefits, and the resulting choice pattern reflects a value for reciprocity, contingent on the expected cooperation of the partner. This quantity enters the trade-off between U<sub>cooperation</sub> and U<sub>defection</sub>and captures the participant’s intrinsic reward for reciprocity versus the additional monetary reward payoff of defection. Therefore, we consider the term “reciprocity” an acceptable statement for this construct.

      Interpretation of parameters should closely reflect what they specifically measure.

      We thank the reviewer for pointing this out. We have refined the relevant interpretations of parameters in the current Results and Discussion sections.

      Prior research has shown links between Theory of Mind (ToM) and cooperation (e.g., Martínez-Velázquez et al., 2024). It would be valuable to test whether this also holds in your dataset.

      We thank the reviewer for this thoughtful comment. Although we did not directly measure participants’ ToM, our design allowed us to estimate participants’ trial-by-trial inferences (i.e., expectations) about their partner’s cooperation probability. We therefore treat these cooperation expectations as an indirect representation for belief inference, which is related to ToM processes. To test whether this belief-inference component relates to cooperation in our dataset, we further conducted an exploratory analysis (GLMM<sub>sup</sub>4) in which participants’ choices were regressed on their cooperation expectations, group, and the group × cooperation-expectation interaction, controlling for trial number and gender, with random effects. Consistent with the ToM–cooperation link in prior research (MartínezVelázquez et al., 2024), participants’ expectations about their partner’s cooperation significantly predicted their cooperative behavior (Table 14), suggesting that decisions were shaped by social learning about others’ inferred actions. Moreover, the interaction between group and cooperation expectation was not significant, indicating that this inference-driven social learning process likely operates similarly in adolescents and adults. This aligns with our primary modeling results showing that both age groups update beliefs via an asymmetric learning process. We have reported these analyses in the Appendix Analysis section.

      More informative table captions would help the reader. Please clarify how variables are coded (e.g., is female = 0 or 1? Is adolescent = 0 or 1?), to avoid the need to search across the manuscript for this information.

      We thank the reviewer for raising this point. We have added clear and standardized variable coding in the table notes of all tables to make them more informative and avoid the need to search the paper. We have ensured consistent wording and formatting across all tables.

      I hope these comments are helpful and support the authors in further strengthening their manuscript.

      We thank the three reviewers for their comments, which have been helpful in strengthening this work.

      Reference

      (1) Fudenberg, D., & Levine, D. K. (2014). Recency, consistent learning, and Nash equilibrium. Proceedings of the National Academy of Sciences of the United States of America, 111(Suppl. 3), 10826–10829. https://doi.org/10.1073/pnas.1400987111

      (2) Fudenberg, D., & Peysakhovich, A. (2016). Recency, records, and recaps: Learning and nonequilibrium behavior in a simple decision problem. ACM Transactions on Economics and Computation, 4(4), Article 23, 1–18. https://doi.org/10.1145/2956581

      (3) Hackel, L., Doll, B., & Amodio, D. (2015). Instrumental learning of traits versus rewards: Dissociable neural correlates and effects on choice. Nature Neuroscience, 18, 1233– 1235. https://doi.org/10.1038/nn.4080

      (4) Icenogle, G., Steinberg, L., Duell, N., Chein, J., Chang, L., Chaudhary, N., Di Giunta, L.,Dodge, K. A., Fanti, K. A., Lansford, J. E., Oburu, P., Pastorelli, C., Skinner, A. T.,Sorbring, E., Tapanya, S., Uribe Tirado, L. M., Alampay, L. P., Al-Hassan, S. M.,Takash, H. M. S., & Bacchini, D. (2019). Adolescents’ cognitive capacity reaches adult levels prior to their psychosocial maturity: Evidence for a “maturity gap” in a multinational, cross-sectional sample. Law and Human Behavior, 43(1), 69–85. https://doi.org/10.1037/lhb0000315

      (5) Krekelberg, B. (2024). Matlab Toolbox for Bayes Factor Analysis (v3.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.13744717

      (6) Martínez-Velázquez, E. S., Ponce-Juárez, S. P., Díaz Furlong, A., & Sequeira, H. (2024). Cooperative behavior in adolescents: A contribution of empathy and emotional regulation? Frontiers in Psychology, 15, 1342458. https://doi.org/10.3389/fpsyg.2024.1342458

      (7) Tervo-Clemmens, B., Calabro, F. J., Parr, A. C., et al. (2023). A canonical trajectory of executive function maturation from adolescence to adulthood. NatureCommunications, 14, 6922. https://doi.org/10.1038/s41467-023-42540-8

      (8) King-Casas, B., Tomlin, D., Anen, C., Camerer, C. F., Quartz, S. R., & Montague, P. R. (2005). Getting to know you: reputation and trust in a two-person economic exchange. Science, 308(5718), 78-83. https://doi.org/10.1126/science.1108062

      (9) Rilling, J. K., Gutman, D. A., Zeh, T. R., Pagnoni, G., Berns, G. S., & Kilts, C. D. (2002). A neural basis for social cooperation. Neuron, 35(2), 395-405. https://doi.org/10.1016/s0896-6273(02)00755-9

      (10) Fareri, D. S., Chang, L. J., & Delgado, M. R. (2015). Computational substrates of social value in interpersonal collaboration. Journal of Neuroscience, 35(21), 8170-8180. https://doi.org/10.1523/JNEUROSCI.4775-14.2015

      (11) Akaike, H. (2003). A new look at the statistical model identification. IEEE transactions on automatic control, 19(6), 716-723. https://doi.org/10.1109/TAC.1974.1100705

      (12) Schwarz, G. (1978). Estimating the dimension of a model. The annals of statistics, 461464. https://doi.org/10.1214/aos/1176344136

      (13) Burnham, K. P., & Anderson, D. R. (2002). Model selection and multimodel inference: A practical information-theoretic approach (2nd ed.). Springer.https://doi.org/10.1007/b97636

      (14) Gelman, A., & Shalizi, C. R. (2013). Philosophy and the practice of Bayesian statistics. British Journal of Mathematical and Statistical Psychology, 66(1), 8–38. https://doi.org/10.1111/j.2044-8317.2011.02037.x

      (15) Gelman, A., Carlin, J. B., Stern, H. S., Dunson, D. B., Vehtari, A., & Rubin, D. B. (2014). Bayesian data analysis (3rd ed.). Chapman and Hall/CRC. https://doi.org/10.1201/b16018

      (16) Vrieze, S. I. (2012). Model selection and psychological theory: A discussion of the differences between the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC). Psychological Methods, 17(2), 228–243. https://doi.org/10.1037/a0027127.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary: 

      Zhang and colleagues examine neural representations underlying abstract navigation in the entorhinal cortex (EC) and hippocampus (HC) using fMRI. This paper replicates a previously identified hexagonal modulation of abstract navigation vectors in abstract space in EC in a novel task involving navigating in a conceptual Greeble space. In HC, the authors claim to identify a three-fold signal of the navigation angle. They also use a novel analysis technique (spectral analysis) to look at spatial patterns in these two areas and identify phase coupling between HC and EC. Finally, the authors propose an EC-HPC PhaseSync Model to understand how the EC and HC construct cognitive maps. While the wide array of techniques used is impressive and their creativity in analysis is admirable, overall, I found the paper a bit confusing and unconvincing. I recommend a significant rewrite of their paper to motivate their methods and clarify what they actually did and why. The claim of three-fold modulation in HC, while potentially highly interesting to the community, needs more background to motivate why they did the analysis in the first place, more interpretation as to why this would emerge in biology, and more care taken to consider alternative hypotheses seeped in existing models of HC function. I think this paper does have potential to be interesting and impactful, but I would like to see these issues improved first.

      General comments:

      (1) Some of the terminology used does not match the terminology used in previous relevant literature (e.g., sinusoidal analysis, 1D directional domain).

      We thank the reviewer for this valuable suggestion, which helps to improve the consistency of our terminology with previous literature and to reduce potential ambiguity. Accordingly, we have replaced “sinusoidal analysis” with “sinusoidal modulation” (Doeller et al., 2010; Bao et al., 2019; Raithel et al., 2023) and “1D directional domain” with “angular domain of path directions” throughout the manuscript.

      (2) Throughout the paper, novel methods and ideas are introduced without adequate explanation (e.g., the spectral analysis and three-fold periodicity of HC).

      We thank the reviewer for raising this important point. In the revised manuscript, we have substantially extended the Introduction (paragraphs 2–4) to clarify our hypothesis, explicitly explaining why the three primary axes of the hexagonal grid cell code may manifest as vector fields. We have also revised the first paragraph of the “3-fold periodicity in the HPC” section in the Results to clarify the rationale for using spectral analysis. Please refer to our responses to comment 2 and 3 below for details.

      Reviewer #2 (Public review):

      The authors report results from behavioral data, fMRI recordings, and computer simulations during a conceptual navigation task. They report 3-fold symmetry in behavioral and simulated model performance, 3-fold symmetry in hippocampal activity, and 6-fold symmetry in entorhinal activity (all as a function of movement directions in conceptual space). The analyses are thoroughly done, and the results and simulations are very interesting.

      We sincerely thank the reviewer for the positive and encouraging comments on our study.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) This paper has quite a few spelling and grammatical mistakes, making it difficult to understand at times.

      We apologize for the wordings and grammatical errors. We have thoroughly re-read and carefully edited the entire manuscript to correct typographical and grammatical errors, ensuring improved clarity and readability.

      (2) Introduction - It's not clear why the three primary axes of hexagonal grid cell code would manifest as vector fields.

      We thank the reviewer for raising this important point. In the revised Introduction (paragraphs 2, 3, and 4), we now explicitly explain the rationale behind our hypothesis that the three primary axes of the hexagonal grid cell code manifest as vector fields.

      In paragraph 2, we present empirical evidence from rodent, bat, and human studies demonstrating that mental simulation of prospective paths relies on vectorial representations in the hippocampus (Sarel et al., 2017; Ormond and O’Keefe, 2022; Muhle-Karbe et al., 2023).

      In paragraphs 3 and 4, we introduce our central hypothesis: vectorial representations may originate from population-level projections of entorhinal grid cell activity, based on three key considerations:

      (1) The EC serves as the major source of hippocampal input (Witter and Amaral, 1991; van Groen et al., 2003; Garcia and Buffalo, 2020).

      (2) Grid codes exhibit nearly invariant spatial orientations (Hafting et al., 2005; Gardner et al., 2022), which makes it plausible that their spatially periodic activity can be detected using fMRI.

      (3) A model-based inference: for example, in the simplest case, when one mentally simulates a straight pathway aligned with the grid orientation, a subpopulation of grid cells would be activated. The resulting population activity would form a near-perfect vectorial representation, with constant activation strength along the path. In contrast, if the simulated path is misaligned with the grid orientation, the population response becomes a distorted vectorial code. Consequently, simulating all possible straight paths spanning 0°–360° results in 3-fold periodicity in the activity patterns—due to the 180° rotational symmetry of the hexagonal grid, orientations separated by 180° are indistinguishable.

      We therefore speculate that vectorial representations embedded in grid cell activity exhibit 3-fold periodicity across spatial orientations and serve as a periodic structure to represent spatial direction. Supporting this view, reorientation paradigms in both rodents and young children have shown that subjects search equally in two opposite directions, reflecting successful orientation encoding but a failure to integrate absolute spatial direction (Hermer and Spelke, 1994; Julian et al., 2015; Gallistel, 2017; Julian et al., 2018).

      (3) It took me a few reads to understand what the spectral analysis was. After understanding, I do think this is quite clever. However, this paper needs more motivation to understand why you are performing this analysis. E.g., why not just take the average regressor at the 10º, 70º, etc. bins and compare it to the average regressor at 40º, 100º bins? What does the Fourier transform buy you?

      We are sorry for the confusion. we outline the rationale for employing Fast Fourier Transform (FFT) analysis to identify neural periodicity. In the revised manuscript, we have added these clarifications into the first paragraph of the “3-fold periodicity in the HPC” subsection in the Results.

      First, FFT serves as an independent approach to cross-validate the sinusoidal modulation results, providing complementary evidence for the 6-fold periodicity in EC and the 3-fold periodicity in HPC.

      Second, FFT enables unbiased detection of multiple candidate periodicities (e.g., 3–7-fold) simultaneously without requiring prior assumptions about spatial phase (orientation). By contrast, directly comparing “aligned” versus “misaligned” angular bins (e.g., 10°/70° vs. 40°/100°) would implicitly assume knowledge of the phase offset, which was not known a priori.

      Finally, FFT uniquely allows periodicity analysis of behavioral performance, which is not feasible with standard sinusoidal GLM approaches. This methodological consistency makes it possible to directly compare periodicities across neural and behavioral domains.

      (4) A more minor point: at one point, you say it’s a spectral analysis of the BOLD signals, but the methods description makes it sound like you estimated regressors at each of the bins before performing FFT. Please clarify. 

      We apologize for the confusion. In our manuscript, we use the term spectral analysis to distinguish this approach from sinusoidal modulation analysis. Conceptually, our spectral analysis involves a three-level procedure:

      (1) First level: We estimated direction-dependent activity maps using a general linear model (GLM), which included 36 regressors corresponding to path directions, down-sampled in 10° increments.

      (2) Second level: We applied a Fast Fourier Transform (FFT) to the direction-dependent activity maps derived from the GLM to examine the spectral magnitude of potential spatial periodicities.

      (3) Third level: We conducted group-level statistical analyses across participants to assess the consistency of the observed periodicities.

      We have revised the “Spectral analysis of MRI BOLD signals” subsection in the Methods to clarify this multi-level procedure.

      (5) Figure 4a:

      Why do the phases go all the way to 2*pi if periodicity is either three-fold or six-fold? 

      When performing correlation between phases, you should perform a circular-circular correlation instead of a Pearson's correlation.

      We thank the reviewer for raising this important point. In the original Figure 4a, both EC and HPC phases spanned 0–2π because their sinusoidal phase estimates were projected into a common angular space by scaling them according to their symmetry factors (i.e., multiplying the 3-fold phase by 3 and the 6-fold phase by 6), followed by taking the modulo 2π. However, this projection forced signals with distinct intrinsic periodicities (120° vs. 60° cycles) into a shared 360° space, thereby distorting their relative angular distances and disrupting the one-to-one correspondence between physical directions and phase values. Consequently, this transformation could bias the estimation of their phase relationship.

      In the revised analysis and Figure 4a, we retained the original phase estimates derived from the sinusoidal modulation within their native periodic ranges (0–120° for 3-fold and 0–60° for 6-fold) by applying modulo operations directly. Following your suggestion, the relationship between EC and HPC phases was then quantified using circular–circular correlation (Jammalamadaka & Sengupta, 2001), as implemented in the CircStat MATLAB toolbox. This updated analysis avoids the rescaling artifact and provides a statistically stronger and conceptually clearer characterization of the phase correspondence between EC and HPC.

      (6) Figure 4d needs additional clarification:

      Phase-locking is typically used to describe data with a high temporal precision. I understand you adopted an EEG analysis technique to this reconstructed fMRI time-series data, but it should be described differently to avoid confusion. This needs additional control analyses (especially given that 3 is a multiple of 6) to confirm that this result is specific to the periodicities found in the paper.

      We thank the reviewer for this insightful comment. We have extensively revised the description of the Figure 4 to avoid confusion with EEG-based phase-locking techniques. The revised text now explicitly clarifies that our approach quantifies spatial-domain periodic coupling across path directions, rather than temporal synchronization of neural signals.

      To further address the reviewer’s concern about potential effects of the integer multiple relationship between the 3-fold HPC and 6-fold EC periodicities, we additionally performed two control analyses using the 9-fold and 12-fold EC components, both of which are also integer multiples of the 3-fold HPC periodicity. Neither control analysis showed significant coupling (p > 0.05), confirming that the observed 3-fold–6-fold coupling was specific and not driven by their harmonic relationship.

      The description of the revised Figure 4 has been updated in the “Phase Synchronization Between HPC and EC Activity” subsection of the Results.

      (7) Figure 5a is misleading. In the text, you say you test for propagation to egocentric cortical areas, but I don’t see any analyses done that test this. This feels more like a possible extension/future direction of your work that may be better placed in the discussion.

      We are sorry for the confusion. Figure 5a was intended as a hypothesis-driven illustration to motivate our analysis of behavioral periodicity based on participants’ task performance. However, we agree with the reviewer that, on its own, Figure 5a could be misleading, as it does not directly present supporting analyses.

      To provide empirical support for the interpretation depicted in Figure 5a, we conducted a whole-brain analysis (Figure S8), which revealed significant 3-fold periodic signals in egocentric cortical regions, including the parietal cortex (PC), precuneus (PCU), and motor regions.

      To avoid potential misinterpretation, we have revised the main text to include these results and explicitly referenced Figure S8 in connection with Figure 5a.

      The updated description in the “3-fold periodicity in human behavior” subsection in the Results is as follows:

      “Considering the reciprocal connectivity between the medial temporal lobe (MTL), where the EC and HPC reside, and the parietal cortex implicated in visuospatial perception and action, together with the observed 3-fold periodicity within the DMN (including the PC and PCu; Fig. S8), we hypothesized that the 3-fold periodic representations of path directions extend beyond the MTL to the egocentric cortical areas, such as the PC, thereby influencing participants' visuospatial task performance (Fig. 5a)”.

      Additionally, Figure 5a has been modified to more clearly highlight the hypothesized link between activity periodicity and behavioral periodicity, rather than suggesting a direct anatomical pathway.

      (8) PhaseSync model: I am not an expert in this type of modeling, so please put a lower weight on this comment (especially compared to some of the other reviewers). While the PhaseSync model seems interesting, it’s not clear from the discussion how this compares to current models. E.g., Does it support them by adding the three-fold HC periodicity? Does it demonstrate that some of them can't be correct because they don't include this three-fold periodicity?

      We thank the reviewer for the insightful comment regarding the PhaseSync model. We agree that further clarifying its relationship to existing computational frameworks is important.

      The EC–HPC PhaseSync model is not intended to replace or contradict existing grid–place cell models of navigation (e.g., Bicanski and Burgess, 2019; Whittington et al., 2020; Edvardsen et al., 2020). Instead, it offers a hierarchical extension by proposing that vectorial representations in the hippocampus emerge from the projections of periodic grid codes in the entorhinal cortex. Specifically, the model suggests that grid cell populations encode integrated path information, forming a vectorial gradient toward goal locations.

      To simplify the theoretical account, our model was implemented in an idealized square layout. In more complex real-world environments, hippocampal 3-fold periodicity may interact with additional spatial variables, such as distance, movement speed, and environmental boundaries.

      We have revised the final two paragraphs of the Discussion to clarify this conceptual framework and emphasize the importance of future studies in exploring how periodic activity in the EC–HPC circuit interacts with environmental features to support navigation.

      Reviewer #2 (Recommendations for the authors):

      (1) Please show a histogram of movement direction sampling for each participant.

      We thank the reviewer for this helpful suggestion. We have added a new supplementary figure (Figure S2) showing histograms of path direction sampling for each participant (36 bins of 10°). The figure is also included. Rayleigh tests for circular uniformity revealed no significant deviations from uniformity (all ps > 0.05, Bonferroni-corrected across participants), confirming that path directions were sampled evenly across 0°–360°.

      (2) Why didn’t you use participants’ original trajectories (instead of the trajectories inferred from the movement start and end points) for the hexadirectional analyses? 

      In our paradigm, participants used two MRI-compatible 2-button response boxes (one for each hand) to adjust the two features of the greebles. As a result, the raw adjustment path contained only four cardinal directions (up, down, left, right). If we were to use the raw stepwise trajectories, the analysis would be restricted to these four directions, which would severely limit the angular resolution. By instead defining direction as the vector from the start to the end position in feature space, we can expand the effective range of directions to the full 0–360°. This approach follows previous literature on abstract grid-like coding in humans (e.g., Constantinescu et al., 2016), where direction was similarly defined by the relative change between two feature dimensions rather than the literal stepwise path. We have added this clarification in the “Sinusoidal modulation” subsection of the revised method.

      (3) Legend of Figure 2: the statement "localizing grid cell activity" seems too strong because it is still not clear whether hexadirectional signals indeed result from grid-cell activity (e.g., Bin Khalid et al., eLife, 2024). I would suggest rephrasing this statement (here and elsewhere). 

      Thank you for this helpful suggestion. We have removed the statement “localizing grid cell activity” to avoid ambiguity and revised the legend of Figure 2a to more explicitly highlight its main purpose—defining how path directions and the aligned/misaligned conditions were constructed in the 6-fold modulation. We have also modified similar expressions throughout the manuscript to ensure consistency and clarity.

      (4) Legend of Figure 2: “cluster-based SVC correction for multiple comparisons” - what is the small volume you are using for the correction? Bilateral EC?

      For both Figure 2 and Figure 3, the anatomical mask of the bilateral medial temporal lobe (MTL), as defined by the AAL atlas, was used as the small volume for correction. This has been clarified in the revised Statistical Analysis section of the Methods as “… with small-volume correction (SVC) applied within the bilateral MTL”.

      (5) Legend of Figure 2: "ROI-based analysis" - what kind of ROI are you using? "corrected for multiple comparisons" - which comparisons are you referring to? Different symmetries and also the right/left hemisphere?

      In Figure 2b, the ROI was defined as a functional mask derived from the significant activation cluster in the right entorhinal cortex (EC). Since no robust clusters were observed in the left EC, the functional ROI was restricted to the right hemisphere. We indeed included Figure 2c to illustrate this point; however, we recognize that our description in the text was not sufficiently clear.

      Regarding the correction for multiple comparisons, this refers specifically to the comparisons across different rotational symmetries (3-, 4-, 5-, 6-, and 7-fold). Only the 6-fold symmetry survived correction, whereas no significant effects were detected for the other symmetries.

      We have clarified these points in the “6-fold periodicity in the EC” subsection of the result as “… The ROI was defined as a functional mask of the right EC identified in the voxel-based analysis and further restricted within the anatomical EC. These analyses revealed significant periodic modulation only at 6-fold (Figure  2c; t(32) = 3.56, p = 0.006, two-tailed, corrected for multiple comparisons across rotational symmetries; Cohen’s d = 0.62) …”.

      We have also revised the “3-fold periodicity in the HPC” subsection of the result as “… ROI analysis, using a functional mask of the HPC identified in the spectral analysis and further restricted within the anatomical HPC, indicated that HPC activity selectively fluctuated at 3-fold periodicity (Figure 3e; t(32) = 3.94, p = 0.002, corrected for multiple comparisons across rotational symmetries; Cohen’s d = 0.70) …”.

      (6) Figure 2d: Did you rotationally align 0{degree sign} across participants? Please state explicitly whether (or not) 0{degree sign} aligns with the x-axis in Greeble space.

      We thank the reviewer for this helpful question. Yes, before reconstructing the directional tuning curve in Figure 2d, path directions were rotationally aligned for each participant by subtracting the participant-specific grid orientation (ϕ) estimated from the independent dataset (odd sessions). We have now made this description explicit in the revised manuscript in the “6-fold periodicity in the EC” subsection of the Results, stating “… To account for individual difference in spatial phase, path directions were calibrated by subtracting the participant-specific grid orientation estimated from the odd sessions ...”.

      (7) Clustering of grid orientations in 30 participants: What does “Bonferroni corrected” refer to? Also, the Rayleigh test is sensitive to the number of voxels - do you obtain the same results when using pair-wise phase consistency? 

      “Bonferroni corrected” here refers to correction across participants. We have clarified this in the first paragraph of the “6-fold periodicity in the EC” subsection of the Result and in the legend of Supplementary Figure S5 as “Bonferroni-corrected across participants.”

      To examine whether our findings were sensitive to the number of voxels, we followed the reviewer’s guidance to compute pairwise phase consistency (PPC; Vinck et al., 2010) for each participant. The PPC results replicated those obtained with the Rayleigh test. We have updated the new results into the Supplementary Figure S5. We also updated the “Statistical Analysis” subsection of the Methods to describe PPC as “For the PPC (Vinck et al., 2010), significance was tested using 5,000 permutations of uniformly distributed random phases (0–2π) to generate a null distribution for comparison with the observed PPC”.

      (8) 6-fold periodicity in the EC: Do you compute an average grid orientation across all EC voxels, or do you compute voxel-specific grid orientations?

      Following the protocol originally described by Doeller et al. (2010), we estimated voxel-wise grid orientations within the EC and then obtained a participant-specific orientation by averaging across voxels within a hand-drawn bilateral EC mask. The procedure is described in detail in the “Sinusoidal modulation” subsection of the Methods.

      (9) Hand-drawn bilateral EC mask: What was your procedure for drawing this mask? What results do you get with a standard mask, for example, from Freesurfer or SPM? Why do you perform this analysis bilaterally, given that the earlier analysis identified 6-fold symmetry only in the right EC? What do you mean by "permutation corrected for multiple comparisons"?

      We thank the reviewer for raising these important methodological points. To our knowledge, no standard volumetric atlas provides an anatomically defined entorhinal cortex (EC) mask. For example, the built-in Harvard–Oxford cortical structural atlas in FSL contains only a parahippocampal region that encompasses, but does not isolate, the EC. The AAL atlas likewise does not contain an EC region. In FreeSurfer, an EC label is available, but only in the fsaverage surface space, which is not directly compatible with MNI-based volumetric group-level analyses.

      Therefore, we constructed a bilateral EC mask by manually delineating the EC according to the detailed anatomical landmarks described by Insausti et al. (1998). Masks were created using ITK-SNAP (Version 3.8, www.itksnap.org). For transparency and reproducibility, the mask has been made publicly available at the Science Data Bank (link: https://www.scidb.cn/s/NBriAn), as indicated in the revised Data and Code availability section.

      Regarding the use of a bilateral EC mask despite voxel-wise effects being strongest in the right EC. First, we did not have any a priori hypothesis regarding laterality of EC involvement before performing analyses. Second, previous studies estimated grid orientation using a bilateral EC mask in their sinusoidal analyses (Doeller et al., 2010; Constantinescu et al., 2016; Bao et al., 2019; Wagner et al., 2023; Raithel et al., 2023). We therefore followed this established approach to estimate grid orientation.

      By “permutation corrected for multiple comparisons” we refer to the family-wise error correction applied to the reconstructed directional tuning curves (Figure 2d for the EC, Figure 3f for the HPC). Specifically, directional labels were randomly shuffled 5,000 times, and an FFT was applied to each shuffled dataset to compute spectral power at each fold. This procedure generated null distributions of spectral power for each symmetry. For each fold, the 95th percentile of the maximal power across permutations was used as the uncorrected threshold. To correct across folds, the 95th percentile of the maximal suprathreshold power across all symmetries was taken as the family-wise error–corrected threshold. We have clarified this procedure in the revised “Statistical Analysis” subsection of the Methods.

      (10) Figures 3b and 3d: Why do different hippocampal voxels show significance for the sinusoidal versus spectral analysis? Shouldn’t the analyses be redundant and, thus, identify the same significant voxels? 

      We thank the reviewer for this insightful question. Although both sinusoidal modulation and spectral analysis aim to detect periodic neural activity, the two approaches are methodologically distinct and are therefore not expected to identify exactly the same significant voxels.

      Sinusoidal modulation relies on a GLM with sine and cosine regressors to test for phase-aligned periodicity (e.g., 3-fold or 6-fold), calibrated according to the estimated grid orientation. This approach is highly specific but critically depends on accurate orientation estimation. In contrast, spectral analysis applies Fourier decomposition to the directional tuning profile, enabling the detection of periodic components without requiring orientation calibration.

      Accordingly, the two analyses are not redundant but complementary. The FFT approach allows for an unbiased exploration of multiple candidate periodicities (e.g., 3–7-fold) without predefined assumptions, thereby providing a critical cross-validation of the sinusoidal GLM results. This strengthens the evidence for 6-fold periodicity in EC and 3-fold periodicity in HPC. Furthermore, FFT uniquely facilitates the analysis of periodicities in behavioral performance data, which is not feasible with standard sinusoidal GLM approaches. This methodological consistency enables direct comparison of periodicities across neural and behavioral domains.

      Additionally, the anatomical distributions of the HPC clusters appear more similar between Figure 3b and Figure 3d after re-plotting Figure 3d using the peak voxel coordinates (x = –24, y = –18), which are closer to those used for Figure 3b (x = –24, y = –20), as shown in the revised Figure 3.

      Taken together, the two analyses serve distinct but complementary purposes.

      (11) 3-fold sinusoidal analysis in hippocampus: What kind of small volume are you using to correct for multiple comparisons?

      We thank the reviewer for this comment. The same small volume correction procedure was applied as described in R4. Specifically, the anatomical mask of the bilateral medial temporal lobe (MTL), as defined by the AAL atlas, was used as the small volume for correction. This procedure has been clarified in the revised Statistical Analysis section of the Methods as following: “… with small-volume correction (SVC) applied within the bilateral MTL.”

      (12) Figure S5: “right HPC” – isn’t the cluster in the left hippocampus? 

      We are sorry for the confusion. The brain image was present in radiological orientation (i.e., the left and right orientations are flipped). We also checked the figure and confirmed that the cluster shown in the original Figure S5 (i.e., Figure S6 in the revised manuscript) is correctly labeled as the right hippocampus, as indicated by the MNI coordinate (x = 22), where positive x values denote the right hemisphere. To avoid potential confusion, we have explicitly added the statement “Volumetric results are displayed in radiological orientation” to the figure legends of all volume-based results.

      (13) Figure S5: Why are the significant voxels different from the 3-fold symmetry analysis using 10{degree sign} bins?

      As shown in R10, the apparent differences largely reflect variation in MNI coordinates. After adjusting for display coordinates, the anatomical locations of the significant clusters are in fact highly similar between the 10°-binned (Figure 3d, shown above) and the 20°-binned results (Figure S6).

      Although both analyses rely on sinusoidal modulation, they differ in the resolution of the input angular bins (10° vs. 20°). Combined with the inherent noise in fMRI data, this makes it unlikely that the two approaches would yield exactly the same set of significant voxels. Importantly, both analyses consistently reveal robust 3-fold periodicity in the hippocampus, indicating that the observed effect is not dependent on angular bin size.

      (14) Figure 4a and corresponding text: What is the unit? Phase at which frequency? Are you using a circular-circular correlation to test for the relationship?

      We thank the reviewer for raising this important point. In the revised manuscript, we have clarified that the unit of the phase values is radians, corresponding to the 6-fold periodic component in the EC and the 3-fold periodic component in the HPC. In the original Figure 4a, both EC and HPC phases—estimated from sinusoidal modulation—were analyzed using Pearson correlation. We have since realized issues with this approach, as also noted R5 to Reviewer #1.

      In the revised analysis and Figure 4a (as shown above), we re-evaluated the relationship between EC and HPC phases using a circular–circular correlation (Jammalamadaka & Sengupta, 2001), implemented in the CircStat MATLAB toolbox. The “Phase synchronization between the HPC and EC activity” subsection of the Result has been accordingly updated as following:

      “To examine whether the spatial phase structure in one region could predict that in another, we tested whether the orientations of the 6-fold EC and 3-fold HPC periodic activities, estimated from odd-numbered sessions using sinusoidal modulation with rotationally symmetric parameters (in radians), were correlated across participants. A cross-participant circular–circular correlation was conducted between the spatial phases of the two areas to quantify the spatial correspondence of their activity patterns (EC: purple dots; HPC: green dots) (Jammalamadaka & Sengupta, 2001). The analysis revealed a significant circular correlation (Figure 4a; r = 0.42, p < 0.001) …”.

      In the “Statistical analysis” subsection of the method:

      “… The relationship between EC and HPC phases was evaluated using the circular–circular correlation (Jammalamadaka & Sengupta, 2001) implemented in the CircStat MATLAB toolbox …”.

      (15) Paragraph following “We further examined amplitude-phase coupling...” - please clarify what data goes into this analysis.

      We thank the reviewer for this helpful comment. In this analysis, the input data consisted of hippocampal (HPC) phase and entorhinal (EC) amplitude, both extracted using the Hilbert transform from the reconstructed BOLD signals of the EC and HPC derived through sinusoidal modulation. We have substantially revised the description of the amplitude–phase coupling analysis in the third paragraph of the “Phase Synchronization Between HPC and EC Activity” subsection of the Results to clarify this procedure.

      (16) Alignment between EC 6-fold phases and HC 3-fold phases: Why don't you simply test whether the preferred 6-fold orientations in EC are similar to the preferred 3-fold phases in HC? The phase-amplitude coupling analyses seem sophisticated but are complex, so it is somewhat difficult to judge to what extent they are correct. 

      We thank the reviewer for this thoughtful comment. We employed two complementary analyses to examine the relationship between EC and HPC activity. In the revised Figure 4 (as shown in Figure 4 for Reviewer #1), Figure 4a provides a direct and intuitive measure of the phase relationship between the two regions using circular–circular correlation. Figure 4b–c examines whether the activity peaks of the two regions are aligned across path directions using cross-frequency amplitude–phase coupling, given our hypothesis that the spatial phase of the HPC depends on EC projections. These two analyses are complementary: a phase correlation does not necessarily imply peak-to-peak alignment, and conversely, peak alignment does not always yield a statistically significant phase correlation. We therefore combined multiple analytical approaches as a cross-validation across methods, providing convergent evidence for robust EC–HPC coupling.

      (17) Figure 5: Do these results hold when you estimate performance just based on “deviation from the goal to ending locations” (without taking path length into account)? 

      We thank the reviewer for this thoughtful suggestion. Following the reviewer’s advice, we re-estimated behavioral performance using the deviation between the goal and ending locations (i.e., error size) and path length independently. As shown in the new Figure S9, no significant periodicity was observed in error size (p > 0.05), whereas a robust 3-fold periodicity was found for path length (p < 0.05, corrected for multiple comparisons).

      We employed two behavioral metrics,(1) path length and (2) error size, for complementary reasons. In our task, participants navigated using four discrete keys corresponding to the cardinal directions (north, south, east, and west). This design inherently induces a 4-fold bias in path directions, as described in the “Behavioral performance” subsection of the Methods. To minimize this artifact, we computed the objectively optimal path length and used it to calibrate participants’ path lengths. However, error size could not be corrected in the same manner and retained a residual 4-fold tendency (see Figure S9d).

      Given that both path length and error size are behaviorally relevant and capture distinct aspects of task performance, we decided to retain both measures when quantifying behavioral periodicity. This clarification has been incorporated into the “Behavioral performance” subsection of the Methods, and the 2<sup>nd</sup> paragraph of the “3-fold periodicity in human behavior” subsection of the Results.

      (18) Phase locking between behavioral performance and hippocampal activity: What is your way of creating surrogates here?

      We thank the reviewer for this helpful question. Surrogate datasets were generated by circularly shifting the signal series along the direction axis across all possible offsets (following Canolty et al., 2006). This procedure preserves the internal phase structure within each domain while disrupting consistent phase alignment, thereby removing any systematic coupling between the two signals. Each surrogate dataset underwent identical filtering and coherence computation to generate a null distribution, and the observed coherence strength was compared with this distribution using paired t-tests across participants. The statistical analysis section has been systematically revised to incorporate these methodological details.

      (19) I could not follow why the authors equate 3-fold symmetry with vectorial representations. This includes statements such as “these empirical findings provide a potential explanation for the formation of vectorial representation observed in the HPC.” Please clarify.

      We thank the reviewer for raising this point. Please refer to our response to R2 for Reviewer #1 and the revised Introduction (paragraphs 2–4), where we explicitly explain why the three primary axes of the hexagonal grid cell code can manifest as vector fields.

      (20) It was unclear whether the sentence “The EC provides a foundation for the formation of periodic representations in the HPC” is based on the authors’ observations or on other findings. If based on the authors’ findings, this statement seems too strong, given that no other studies have reported periodic representations in the hippocampus to date (to the best of my knowledge).

      We thank the reviewer for this comment. We agree that the original wording lacked sufficient rigor. We have extensively revised the 3rd paragraph of the Discussion section with more cautious language by reducing overinterpretation and emphasizing the consistency of our findings with prior empirical evidence, as follows: “The EC–HPC PhaseSync model demonstrates how a vectorial representation may emerge in the HPC from the projections of populations of periodic grid codes in the EC. The model was motivated by two observations. First, the EC intrinsically serves as the major source of hippocampal input (Witter and Amaral, 1991; van Groen et al., 2003; Garcia and Buffalo, 2020), and grid codes exhibit nearly invariant spatial orientations (Hafting et al., 2005; Gardner et al., 2022). Second, mental planning, characterized by “forward replay” (Dragoi and Tonegawa, 2011; Pfeiffer, 2020), has the capacity to activate populations of grid cells that represent sequential experiences in the absence of actual physical movement (Nyberg et al., 2022). We hypothesize that an integrated path code of sequential experiences may eventually be generated in the HPC, providing a vectorial gradient toward the goal location. The path code exhibits regular, vector-like representations when the path direction aligns with the orientations of grid axes, and becomes irregular when they misalign. This explanation is consistent with the band-like representations observed in the dorsomedial EC (Krupic et al., 2012) and the irregular activity fields of trace cells in the HPC (Poulter et al., 2021). ”

    1. Author response:

      The following is the authors’ response to the original reviews

      A point by point response included below. Before we turn to that we want to note one change that we decided to introduce, related to generalization on unseen tissues/cell types (Figure 3a in the original submission and related question by Reviewer #2 below). This analysis was based on adding a latent “RBP state” representation during learning of condition/tissue specific splicing. The “RBP state” per condition is captured by a dedicated encoder. Our original plan was to have a paper describing a new RBP-AE model we developed in parallel, which also served as the base to capture this “RBP State”. However, we got delayed in getting this second paper finalized (it was led by other lab members, some of whom have already left the lab). This delay affected the TrASPr manuscript as TrASPr’s code should be available and analysis reproducible upon publication. After much deliberation, we decided that in order to comply with reproducibility standards while not self scooping the RBP-AE paper, we eventually decided to take out the RBP-AE and replace it with a vanilla PCA based embedding for the “RBP-State”. The PCA approach is simpler and reproducible, based on linear transformation of the RBPs expression vector into a lower dimension. The qualitative results included in Figure 3a still hold, and we also produced the new results suggested by Reviewer #2 in other GTEX tissues with this PCA based embedding (below). 

      We don’t believe the switch to PCA based embedding should have any bearing on the current manuscript evaluation but wanted to take this opportunity to explain the reasoning behind this additional change.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors propose a transformer-based model for the prediction of condition - or tissue-specific alternative splicing and demonstrate its utility in the design of RNAs with desired splicing outcomes, which is a novel application. The model is compared to relevant existing approaches (Pangolin and SpliceAI) and the authors clearly demonstrate its advantage. Overall, a compelling method that is well thought out and evaluated.

      Strengths:

      (1) The model is well thought out: rather than modeling a cassette exon using a single generic deep learning model as has been done e.g. in SpliceAI and related work, the authors propose a modular architecture that focuses on different regions around a potential exon skipping event, which enables the model to learn representations that are specific to those regions. Because each component in the model focuses on a fixed length short sequence segment, the model can learn position-specific features. Another difference compared to Pangolin and SpliceAI which are focused on modeling individual splice junctions is the focus on modeling a complete alternative splicing event.

      (2) The model is evaluated in a rigorous way - it is compared to the most relevant state-of-the-art models, uses machine learning best practices, and an ablation study demonstrates the contribution of each component of the architecture.

      (3) Experimental work supports the computational predictions.     

      (4) The authors use their model for sequence design to optimize splicing outcomes, which is a novel application.

      We wholeheartedly thank Reviewer #1 for these positive comments regarding the modeling approach we took to this task and the evaluations we performed. We have put a lot of work and thought into this and it is gratifying to see the results of that work acknowledged like this.

      Weaknesses:

      No weaknesses were identified by this reviewer, but I have the following comments:

      (1) I would be curious to see evidence that the model is learning position-specific representations.

      This is an excellent suggestion to further assess what the model is learning. To get a better sense of the position-specific representation we performed the following analyses:

      (1) Switching the transformers relative order: All transformers are pretrained on 3’ and 5’ splice site regions before fine-tunning for the PSI and dPSI prediction task. We hypothesized that if relative position is important, switching the order of the transformers would make a large difference on prediction accuracy. Indeed if we switch the 3’ and 5’ we see as expected a severe drop in performance, with Pearson correlation on test data dropping from 0.82 to 0.11. Next, we switched the two 5’ and 3’ transformers, observing a drop to 0.65 and 0.78 respectively. When focusing only on changing events the drop was from 0.66 to 0.54 (for 3’ SS transformers), 0.48 (for 5’ SS transformers), and 0.13 (when the 3’ and 5’ transformers flanking the alternative exon were switched). 

      (2) Position specific effect of RBPs: We wanted to test whether the model is able to learn position specific effects for RBPs. For this we focused on two RBPs, FOX (a family of three highly related RBPs), and QKI, both have a relatively well defined motif, known condition and position specific effect identified via RBP KD experiments combined with CLIP experiments (e.g. PMID: 23525800, PMID: 24637117, PMID: 32728246). For each, we randomly selected 40 highly and 40 lowly included cassette exons sequences. We then ran in-silico mutagenesis experiments where we replaced small windows of sequences with the RBP motifs (80 for RBFOX and 80 for QKI), then compared TrASPR’s predictions for the average predictions for 5 random sequences inserted in the same location. The results of this are now shown in Figure 4 Supp 3, where the y-axis represents the dPSI effect per position (x-axis), and the color represents the percentile of observed effects over inserting motifs in that position across all 80 sequences tested. We see that both RBPs have strong positional preferences for exerting a strong effect on the alternative exon. We also see differences between binding upstream and downstream of the alternative exon. These results, learned by the model from natural tissue-specific variations, recapitulate nicely the results derived from high-throughput experimental assays. However, we also note that effects were highly sequence specific. For example, RBFOX is generally expected to increase inclusion when binding downstream of the alternative exon and decrease inclusion when binding upstream. While we do observe such a trend we also see cases where the opposite effects are observed. These sequence specific effects have been reported in the literature but may also represent cases where the model errs in the effect’s direction. We discuss these new results in the revised text.

      (3) Assessing BOS sequence edits to achieve tissue-specific splicing: Here we decided to test whether BOS edits in intronic regions (at least 8b away from the nearest splice site) are important for the tissue-specific effect. The results are now included in Figure 6 Supp 1, clearly demonstrating that most of the neuronal specific changes achieved by BOS were based on changing the introns, with a strong effect observed for both up and downstream intron edits.

      (2) The transformer encoders in TrASPr model sequences with a rather limited sequence size of 200 bp; therefore, for long introns, the model will not have good coverage of the intronic sequence. This is not expected to be an issue for exons.

      The reviewer is raising a good question here. On one hand, one may hypothesize that, as the reviewer seems to suggest, TrASPr may not do well on long introns as it lacks the full intronic sequence.

      Conversely, one may also hypothesize that for long introns, where the flanking exons are outside the window of SpliceAI/Pangolin, TrASPr may have an advantage.

      Given this good question and a related one by Reviewer #2, we divided prediction accuracy by intron length and the alternative exon length.

      For short exons  (<100bp) we find TrASPr and Pangolin perform similarly, but for longer exons, especially those > 200, TrASPr results are better. When dividing samples by the total length of the upstream and downstream intron, we find TrASPr outperform all other models for introns of combined length up to 6K, but Pangolin gets better results when the combined intron length is over 10K. This latter result is interesting as it means that contrary to the second hypothesis laid out above, Pangolin’s performance did not degrade for events where the flanking exons were outside its field of view. We note that all of the above holds whether we assess all events or just cases of tissue specific changes. It is interesting to think about the mechanistic causes for this. For example, it is possible that cassette exons involving very long introns evoke a different splicing mechanism where the flanking exons are not as critical and/or there is more signal in the introns which is missed by TrASPr. We include these new results now as Figure 2 - Supp 1,2 and discuss these in the main text.

      (3) In the context of sequence design, creating a desired tissue- or condition-specific effect would likely require disrupting or creating motifs for splicing regulatory proteins. In your experiments for neuronal-specific Daam1 exon 16, have you seen evidence for that? Most of the edits are close to splice junctions, but a few are further away.

      That is another good question. Regarding Daam1 exon 16, in the original paper describing the mutation locations some motif similarities were noted to PTB (CU) and CUG/Mbnl-like elements (Barash et al Nature 2010). In order to explore this question beyond this specific case we assessed the importance of intronic edits by BOS to achieve a tissue specific splicing profile - see above.

      (4) For sequence design, of tissue- or condition-specific effect in neuronal-specific Daam1 exon 16 the upstream exonic splice junction had the most sequence edits. Is that a general observation? How about the relative importance of the four transformer regions in TrASPr prediction performance?

      This is another excellent question. Please see new experiments described above for RBP positional effect and BOS edits in intronic regions which attempt to give at least partial answers to these questions. We believe a much more systematic analysis can be done to explore these questions but such evaluation is beyond the scope of this work.

      (5) The idea of lightweight transformer models is compelling, and is widely applicable. It has been used elsewhere. One paper that came to mind in the protein realm:

      Singh, Rohit, et al. "Learning the language of antibody hypervariability." Proceedings of the National Academy of Sciences 122.1 (2025): e2418918121.

      We definitely do not make any claim this approach of using lighter, dedicated models instead of a large ‘foundation’ model has not been taken before. We believe Rohit et al mentioned above represents a somewhat different approach, where their model (AbMAP) fine-tunes large general protein foundational models (PLM) for antibody-sequence inputs by supervising on antibody structure and binding specificity examples. We added a description of this modeling approach citing the above work and another one which specifically handles RNA splicing (intron retention, PMID: 39792954).

      Reviewer #2 (Public review):

      Summary:

      The authors present a transformer-based model, TrASPr, for the task of tissue-specific splicing prediction (with experiments primarily focused on the case of cassette exon inclusion) as well as an optimization framework (BOS) for the task of designing RNA sequences for desired splicing outcomes.

      For the first task, the main methodological contribution is to train four transformer-based models on the 400bp regions surrounding each splice site, the rationale being that this is where most splicing regulatory information is. In contrast, previous work trained one model on a long genomic region. This new design should help the model capture more easily interactions between splice sites. It should also help in cases of very long introns, which are relatively common in the human genome.

      TrASPr's performance is evaluated in comparison to previous models (SpliceAI, Pangolin, and SpliceTransformer) on numerous tasks including splicing predictions on GTEx tissues, ENCODE cell lines, RBP KD data, and mutagenesis data. The scope of these evaluations is ambitious; however, significant details on most of the analyses are missing, making it difficult to evaluate the strength of the evidence. Additionally, state-of-the-art models (SpliceAI and Pangolin) are reported to perform extremely poorly in some tasks, which is surprising in light of previous reports of their overall good prediction accuracy; the reasoning for this lack of performance compared to TrASPr is not explored.

      In the second task, the authors combine Latent Space Bayesian Optimization (LSBO) with a Transformer-based variational autoencoder to optimize RNA sequences for a given splicing-related objective function. This method (BOS) appears to be a novel application of LSBO, with promising results on several computational evaluations and the potential to be impactful on sequence design for both splicing-related objectives and other tasks.

      We thank Reviewer #2 for this detailed summary and positive view of our work. It seems the main issue raised in this summary regards the evaluations: The reviewer finds details of the evaluations missing and the fact that SpliceAI and Pangolin perform poorly on some of the tasks to be surprising. We made a concise effort to include the required details, including code and data tables. In short, some of the concerns were addressed by adding additional evaluations, some by clarifying missing details, and some by better explaining where Pangolin and SpliceAI may excel vs. settings where these may not do as well. More details are given below. 

      Strengths:

      (1) A novel machine learning model for an important problem in RNA biology with excellent prediction accuracy.

      (2) Instead of being based on a generic design as in previous work, the proposed model incorporates biological domain knowledge (that regulatory information is concentrated around splice sites). This way of using inductive bias can be important to future work on other sequence-based prediction tasks.

      Weaknesses:

      (1) Most of the analyses presented in the manuscript are described in broad strokes and are often confusing. As a result, it is difficult to assess the significance of the contribution.

      We made an effort to make the tasks be specific and detailed,  including making the code and data of those available. We believe this helped improve clarity in the revised version.

      (2) As more and more models are being proposed for splicing prediction (SpliceAI, Pangolin, SpliceTransformer, TrASPr), there is a need for establishing standard benchmarks, similar to those in computer vision (ImageNet). Without such benchmarks, it is exceedingly difficult to compare models. For instance, Pangolin was apparently trained on a different dataset (Cardoso-Moreira et al. 2019), and using a different processing pipeline (based on SpliSER) than the ones used in this submission. As a result, the inferior performance of Pangolin reported here could potentially be due to subtle distribution shifts. The authors should add a discussion of the differences in the training set, and whether they affect your comparisons (e.g., in Figure 2). They should also consider adding a table summarizing the various datasets used in their previous work for training and testing. Publishing their training and testing datasets in an easy-to-use format would be a fantastic contribution to the community, establishing a common benchmark to be used by others.

      There are several good points to unpack here. Starting from the last one, we very much agree that a standard benchmark will be useful to include. For tissue specific splicing quantification we used the GTEx dataset from which we select six representative human tissues (heart, cerebellum, lung, liver, spleen, and EBV-transformed lymphocytes). In total, we collected 38394 cassette exon events quantified across 15 samples (here a ‘sample’ is a cassette exon quantified in two tissues) from the GTEx dataset with high-confidence quantification for their PSIs based on MAJIQ. A detailed description of how this data was derived is now included in the Methods section, and the data itself is made available via the bitbucket repository with the code.

      Next, regarding the usage of different data and distribution shifts for Pangolin: The reviewer is right to note there are many differences between how Pangolin and TrASPr were trained. This makes it hard to determine whether the improvements we saw are not just a result of different training data/labels. To address this issue, we first tried to finetune the pre-trained Pangolin with MAJIQ’s PSI dataset: we use the subset of the GTEx dataset described above, focusing on the three tissues analyzed in Pangolin’s paper—heart, cerebellum, and liver—for a fair comparison. In total, we obtained 17,218 events, and we followed the same training and test split as reported in the Pangolin paper. We got Pearson: 0.78 Spearman: 0.68 which are values similar to what we got without this extra fine tuning. Next, we retrained Pangolin from scratch, with the full tissues and training set used for TrASPr, which was derived from MAJIQ’s quantifications. Since our model only trained on human data with 6 tissues at the same time, we modified Pangolin from original 4 splice site usage outputs to 6 PSI outputs. We tried to take the sequence centered with the first or the second splice site of the mid exon. This test resulted in low performance (3’ SS: pearson 0.21 5’ SS: 0.26.). 

      The above tests are obviously not exhaustive but their results suggest that the differences we observe are unlikely to be driven by distribution shifts. Notably, the original Pangolin was trained on much more data (four species, four tissues each, and sliding windows across the entire genome). This training seems to be important for performance while the fact we switched from Pangolin’s splice site usage to MAJIQ’s PSI was not a major contributor. Other potential reasons for the improvements we observed include the architecture, target function, and side information (see below) but a complete delineation of those is beyond the scope of this work. 

      (3) Related to the previous point, as discussed in the manuscript, SpliceAI, and Pangolin are not designed to predict PSI of cassette exons. Instead, they assign a "splice site probability" to each nucleotide. Converting this to a PSI prediction is not obvious, and the method chosen by the authors (averaging the two probabilities (?)) is likely not optimal. It would be interesting to see what happens if an MLP is used on top of the four predictions (or the outputs of the top layers) from SpliceAI/Pangolin. This could also indicate where the improvement in TrASPr comes from: is it because TrASPr combines information from all four splice sites? Also, consider fine-tuning Pangolin on cassette exons only (as you do for your model).

      Please see the above response. We did not investigate more sophisticated models that adjust Pangolin’s architecture further as such modifications constitute new models which are beyond the scope of this work.

      (4) L141, "TrASPr can handle cassette exons spanning a wide range of window sizes from 181 to 329,227 bases - thanks to its multi-transformer architecture." This is reported to be one of the primary advantages compared to existing models. Additional analysis should be included on how TrASPr performs across varying exon and intron sizes, with comparison to SpliceAI, etc.

      This was a good suggestion, related to another comment made by Reviewer #1. Please see above our response to them with a breakdown by exon/intron length.

      (5) L171, "training it on cassette exons". This seems like an important point: previous models were trained mostly on constitutive exons, whereas here the model is trained specifically on cassette exons. This should be discussed in more detail.

      Previous models were not trained exclusively on constitutive exons and Pangolin specifically was trained with their version of junction usage across tissues. That said, the reviewer’s point is valid (and similar to ones made above) about a need to have a matched training/testing and potential distribution shifts. Please see response and evaluations described above. 

      (6) L214, ablations of individual features are missing.

      These were now added to the table which we moved to the main text (see table also below).

      (7) L230, "ENCODE cell lines", it is not clear why other tissues from GTEx were not included.

      Good question. The task here was to assess predictions in unseen conditions, hence we opted to test on completely different data of human cell lines rather than additional tissue samples. Following the reviewers suggestion we also evaluated predictions on two additional GTEx tissues, Cortex and Adrenal Gland. These new results, as well as the previous ones for ENCODE, were updated to use the PCA based embedding of “RBP-State” as described above. We also compared the predictions using the PCA based embedding of the “RBP-State” to training directly on data (not the test data of course) from these tissues. See updated Figure 3a,b. Figure 3 Supp 1,2.

      (8) L239, it is surprising that SpliceAI performs so badly, and might suggest a mistake in the analysis. Additional analysis and possible explanations should be provided to support these claims. Similarly, the complete failure of SpliceAI and Pangolin is shown in Figure 4d.

      Line 239 refers to predicting relative inclusion levels between competing 3’ and 5’ splice sites. We admit we too expected this to be better for SpliceAI and Pangolin but we were not able to find bugs in our analysis (which is all made available for readers and reviewers alike). Regarding this expectation to perform better, first we note that we are not aware of a similar assessment being done for either of those algorithms (i.e. relative inclusion for 3’ and 5’ alternative splice site events). Instead, our initial expectation, and likely the reviewer’s as well, was based on their detection of splice site strengthening/weakening due to mutations, including cryptic splice site activation. More generally though, it is worth noting in this context that given how SpliceAI, Pangolin and other algorithms have been presented in papers/media/scientific discussions, we believe there is a potential misperception regarding tasks that SpliceAI and Pangolin excel at vs other tasks where they should not necessarily be expected to excel. Both algorithms focus on cryptic splice site creation/disruption. This has been the focus of those papers and subsequent applications.  While Pangolin added tissue specificity to SpliceAI training, the authors themselves admit “...predicting differential splicing across tissues from sequence alone is possible but remains a considerable challenge and requires further investigation”. The actual performance on this task is not included in Pangolin’s main text, but we refer Reviewer #2 to supplementary figure S4 in the Pangolin manuscript to get a sense of Pangolin’s reported performance on this task. Similar to that, Figure 4d in our manuscript is for predicting ‘tissue specific’ regulators. We do not think it is surprising that SpliceAI (tissue agnostic) and Pangolin (slight improvement compared to SpliceAI in tissue specific predictions) do not perform well on this task. Similarly, we do not find the results in Figure 4C surprising either. These are for mutations that slightly alter inclusion level of an exon, not something SpliceAI was trained on - SpiceAI was trained on genomic splice sites with yes/no labels across the genome. As noted elsewhere in our response, re-training Pangolin on this mutagenesis dataset results in performance much closer to that of TrASPr. That is to be expected as well - Pangolin is constructed to capture changes in PSI (or splice site usage as defined by the authors), those changes are not even tissue specific for the CD19 data and the model has no problem/lack of capacity to generalize from the training set just like TrASPr does. In fact, if you only use combinations of known mutations seen during training a simple regression model gives correlation of ~92-95% (Cortés-López et al 2022). In summary, we believe that better understanding of what one can realistically expect from models such as SpliceAI, Pangolin, and TrASPr will go a long way to have them better understood and used effectively. We have tried to make this more clear in the revision.

      (9) BOS seems like a separate contribution that belongs in a separate publication. Instead, consider providing more details on TrASPr.

      We thank the reviewer for the suggestion. We agree those are two distinct contributions/algorithms and we indeed considered having them as two separate papers. However, there is strong coupling between the design algorithm (BOS) and the predictor that enables it (TrASPr). This coupling is both conceptual (TrASPr as a “teacher”) and practical in terms of evaluations. While we use experimental data (experiments done involving Daam1 exon 16, CD19 exon 2) we still rely heavily on evaluations by TrASPr itself. A completely independent evaluation would have required a high-throughput experimental system to assess designs, which is beyond the scope of the current paper. For those reasons we eventually decided to make it into what we hope is a more compelling combined story about generative models for prediction and design of RNA splicing.

      (10) The authors should consider evaluating BOS using Pangolin or SpliceTransformer as the oracle, in order to measure the contribution to the sequence generation task provided by BOS vs TrASPr.

      We can definitely see the logic behind trying BOS with different predictors. That said, as we note above most of BOS evaluations are based on the “teacher”. As such, it is unclear what value replacing the teacher would bring. We also note that given this limitation we focus mostly on evaluations in comparison to existing approaches (genetic algorithm or random mutations as a strawman). 

      Recommendations for the authors: 

      Reviewer #1 (Recommendations for the authors):

      Additional comments:

      (1) Is your model picking up transcription factor binding sites in addition to RBPs? TFs have been recently shown to have a role in splicing regulation:

      Daoud, Ahmed, and Asa Ben-Hur. "The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models." PLOS Computational Biology 21.1 (2025): e1012755.

      We agree this is an interesting point to explore, especially given the series of works from the Ben-Hur’s group. We note though that these works focus on intron retention (IR) which we haven’t focused on here, and we only cover short intronic regions flanking the exons. We leave this as a future direction as we believe the scope of this paper is already quite extensive.

      (2) SpliceNouveau is a recently published algorithm for the splicing design problem:

      Wilkins, Oscar G., et al. "Creation of de novo cryptic splicing for ALS and FTD precision medicine." Science 386.6717 (2024): 61-69.

      Thank you for pointing out Wilkins et al recent publication, we now refer to it as well. 

      (3) Please discuss the relationship between your model and this deep learning model. You will also need to change the following sentence: "Since the splicing sequence design task is novel, there are no prior implementations to reference."

      We revised this statement and now refer to several recent publications that propose similar design tasks.  

      (4) I would suggest adding a histogram of PSI values - they appear to be mostly close to 1 or 0.

      PSI values are indeed typically close to either 0 or 1. This is a known phenomenon illustrated in previous studies of splicing (e.g. Shen et al NAR 2012 ). We are not sure what is meant by the comment to add a histogram but we made sure to point this out in the main text: 

      “...Still, those statistics are dominated by extreme values, such that 33.2\% are smaller than 0.15 and 56.0\% are higher than 0.85. Furthermore, most cassette exons do not change between a given tissue pair (only 14.0\% of the samples in the dataset, \ie a cassette exon measured across two tissues, exhibit ΔΨ| ≥ 0.15).”

      (5) Part of the improvement of TrASPr over Pangolin could be the result of a more extensive dataset.

      Please see above responses and new analysis.

      (6) In the discussion of the roles of alternative splicing, protein diversity is mentioned, but I suggest you also mention the importance of alternative splicing as a regulatory mechanism:

      Lewis, Benjamin P., Richard E. Green, and Steven E. Brenner. "Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans." Proceedings of the National Academy of Sciences 100.1 (2003): 189-192.

      Thank you for the suggestion. We added that point and citation. 

      (7) Line 96: You use dPSI without defining it (although quite clear that it should be Delta PSI).

      Fixed.

      (8) Pretrained transformers: Have you trained separate transformers on acceptor and donor sites, or a single splice junction transformer?

      Single splice junction pre-training.

      (9) "TrASPr measures the probability that the splice site in the center of Se is included in some tissue" - that's not my understanding of what TrASPr is designed to do.

      We revised the above sentence to make it more precise: “Given a genomic sequence context S<sub>e</sub> = (s<sub>e</sub>,...,s<sub>e</sub>), made of  a cassette exon e and flanking intronic/exonic regions, TrASPr predicts for tissue c the fraction of transcripts where exon e is included or skipped over, ΔΨ-<sub>e,c,c’</sub>.”

      (10) Please include the version of the human genome annotations that you used. 

      We used GENCODE v40 human genome hg38- this is now included in the Data section. 

      (11) I did not see a description of the RBP-AE component in the methods section. A bit more detail on the model would be useful as well.

      Please see above details about replacing RBP-AE with a simpler linear PCA “RBP-State” encoding. We added details about how the PCA was performed to the Methods section.

      (12) Typos, grammar:

      -   Fix the following sentence: ATP13A2, a lysosomal transmembrane cation transporter, linked to an early-onset form of Parkinson's Disease (PD) when 306 loss-of-function mutations disrupt its function.

      Sentence was fixed to now read: “The first example is of a brain cerebellum-specific cassette exon skipping event predicted by TrASPr in the ATP13A2 gene (aka PARK9). ATP13A2 is a lysosomal transmembrane cation transporter, for which loss of function mutation has been linked to early-onset of Parkinson’s Disease (PD)”.

      -   Line 501: "was set to 4e−4"(the - is a superscript). 

      Fixed

      -   A couple of citations are missing in lines 580 and 581.

      Thank you for catching this error. Citations in line 580, 581 were fixed.

      (13) Paper title: Generative modeling for RNA splicing predictions and design - it would read better as "Generative modeling for RNA splicing prediction and design", as you are solving the problems of splicing prediction and splicing design.  

      Thank you for the suggestion. We updated the title and removed the plural form.

      Reviewer #2 (Recommendations for the authors):

      (1) Appendices are not very common in biology journals. It is also not clear what purpose the appendix serves exactly - it seems to repeat some of the things said earlier. Consider merging it into the methods or the main text. 

      We merged the appendices into the Methods section and removed redundancy.

      (2) L112, "For instance, the model could be tasked with designing a new version of the cassette exon, restricted to no more than N edit locations and M total base changes." How are N and M different? Is there a difference between an edit location and a base change? 

      Yes, N is the number of locations (one can think of it as a start position) of various lengths (e.g. a SNP is of length 1) and the total number of positions edited is M. The text now reads “For instance, the model could be tasked with designing a new version of the cassette exon, restricted to no more than  $N$ edit locations (\ie start position of one or more consecutive bases) and $M$ total base changes.”

      (3) L122: "DEN was developed for a distinct problem". What prevents one from adapting DEN to your sequence design task? The method should be generic. I do not see what "differs substantially" means here. (Finally, wasn't DEN developed for the task you later refer to as "alternative splice site" (as opposed to "splice site selection")? Use consistent terminology. And in L236 you use "splice site variation" - is that also the same?).

      Indeed, our original description was not clear/precise enough. DEN was designed and trained for two tasks: APA, and 5’ alternative splice site usage. The terms “selection”, “usage”, and “variation” were indeed used interchangeably in different locations and the reviewer was right, noting the lack of precision. We have now revised the text to make sure the term “relative usage” is used. 

      Nonetheless, we hold DEN was indeed defined for different tasks. See figures from Figure 2A, 6A of Linder et al 2020 (the reference was also incorrect as we cited the preprint and not the final paper):

      In both cases DEN is trying to optimize a short region for selecting an alternative PA site (left) or a 5’ splice site (right). This work focused on an MPRA dataset of short synthetic sequences inserted in the designated region for train/test. We hold this is indeed a different type of data and task then the one we focus on here. Yes, one can potentially adopt DEN for our task, but this is beyond the scope of this paper. Finally, we note that a more closely related algorithm recently proposed is Ledidi (Schreiber et al 2025) which was posted as a pre-print. Similar to BOS, Ledidi tries to optimize a given sequence and adopt it with a few edits for a given task. Regardless, we updated the main text to make the differences between DEN and the task we defined here for BOS more clear, and we also added a reference to Ledidi and other recent works in the discussion section.

      (4) L203, exons with DeltaPSI very close to 0.15 are going to be nearly impossible to classify (or even impossible, considering that the DeltaPSI measurements are not perfect). Consider removing such exons to make the task more feasible.

      Yes, this is how it was done. As described in more details below, we defined changing samples as ones where the change was >= 0.15 and non-changing as ones where the change in PSI was < 0.05 to avoid ambiguous cases affecting the classification task.  

      (5) L230, RBP-AE is not explained in sufficient detail (and does not appear in the methods, apparently). It is not clear how exactly it is trained on each new cellular condition.

      Please see response in the opening of this document and Q11 from

      Reviewer 1 

      (6) L230, "significantly improving": the r value actually got worse; it is therefore not clear you can claim any significant improvement. Please mention that fact in the text.

      This is a fair point. We note that we view the “a” statistic as potentially more interesting/relevant here as the Pearson “r” is dominated by points being generally close to 0/1.  Regardless, revisiting this we realized one can also make a point that the term “significant” is imprecise/misplaced since there is no statistical test done here (side note: given the amount of points, a simple null of same distribution yes/no would pass significance but we don’t think this is an interesting/relevant test here). Also, we note that with the transition to PCA instead of RBP-AE we actually get improvements in both a and r values, both for the ENCODE samples shown in Figure 3a and the two new GTEX tissues we tested (see above). We now changed the text to simply state: 

      “...As shown in Figure 3a, this latent space representation allows TrSAPr to generalize from the six GTEX tissues to unseen conditions, including unseen GTEX tissues (top row), and ENCODE cell lines (bottom row). It improves prediction accuracy compared to TrASPr lacking PCA (eg a=88.5% vs a=82.3% for ENCODE cell lines), though naturally training on the additional GTEX and ENCODE conditions can lead to better performance  (eg a=91.7%, for ENCODE, Figure 3a left column).”

      (7) L233, "Notably, previous splicing codes focused solely on cassette exons", Rosenberg et al. focused solely on alternative splice site choice.

      Right - we removed that sentence.. 

      (8) L236, "trained TrASPr on datasets for 3' and 5' splice site variations". Please provide more details on this task. What is the input to TrASPr and what is the prediction target (splice site usage, PSI of alternative isoforms)? What datasets are used for this task?

      The data for this data was the same GTEx tissue data processed, just for alternative 3’ and 5’ splice sites events. We revised the description of this task in the main task and added information in the Methods section. The data is also included in the repo.

      (9) L243, "directly from genomic sequences", and conservation?

      Yes, we changed the sentence to read “...directly from genomic sequences combined with related features” 

      (10) L262, what is the threshold for significant splicing changes?

      The threshold is 0.15 We updated the main text to read the following:

      The total number of mutations hitting each of the 1198 genomic positions across the 6106 sequences is shown in \FIG{mut_effect}b (left), while the distribution of effects ($|\Delta \Psi|$) observed across those 6106 samples is shown in \FIG{mut_effect}b (right). To this data we applied three testing schemes. The first is a standard 5-fold CV where 20\% of combinations of point mutations were hidden in every fold while the second test involved 'unseen mutation' (UM) where we hide any sample that includes mutations in specific positions for a total of 1480 test samples. As illustrated by the CDF in \FIG{mut_effect}b, most samples (each sample may involve multiple positions mutated) do not involve significant splicing changes. Thus, we also performed a third test using only  the 883 samples were mutations cause significant changes ($|\Delta \Psi|\geq 0.15 $). 

      (11) L266, Pangolin performance is only provided for one of the settings (and it is not clear which). Please provide details of its performance in all settings.

      The description was indeed not clear. Pangolin’s performance was similar to SpliceAI as mentioned above but retraining it on the CD19 data yielded much closer performance to TrASPr. We include all the matching tests for Pangolin after retraining in Figure 4 Supp Figure 1. 

      (12) Please specify "n=" in all relevant plots. 

      Fixed.

      (13) Figure 3a, "The tissues were first represented as tokens, and new cell line results were predicted based on the average over conditions during training." Please explain this procedure in more detail. What are these tokens and how are they provided to the model? Are the cell line predictions the average of the predictions for the training tissues?

      Yes, we compared to simply the average over the predictions for the training tissues for that specific event as baseline to assess improvements (see related work pointing for the need to have similar baselines in DL for genomics in https://pubmed.ncbi.nlm.nih.gov/33213499/). Regarding the tokens - we encode each tissue type as a possible value and feed the two tissues as two tokens to the transformer.

      (14) Figure 4b, the total count in the histogram is much greater than 6106. Please explain the dataset you're using in more detail, and what exactly is shown here.

      We updated the text to read: 

      “...we used 6106 sequence samples where each sample may have multiple positions mutated (\ie mutation combinations) in exon 2 of CD19 and its flanking introns and exons (Cortes et al 2022). The total number of mutations hitting each of the 1198 genomic positions across the 6106 sequences is shown in Figure 4b (left).”

      (15) Figure 5a, how are the prediction thresholds (TrASPr passed, TrASPr stringent, and TrASPr very stringent) defined?

      Passed: dpsi>0.1, Stringent: dpsi>0.15, Very stringent: dpsi>0.2 This is now included in the main text.

      (16) L417, please include more detail on the relative size of TrASPr compared to other models (e.g. number of parameters, required compute, etc.).

      SpliceAI is a general-purpose splicing predictor with 32-layer deep residual neural network to capture long-range dependencies in genomic sequences. Pangolin is a deep learning model specifically designed for predicting tissue-specific splicing with similar architecture as SpliceAI. The implementation of SpliceAI that can be found here https://huggingface.co/multimolecule/spliceai involves an ensemble of 5 such models for a total of ~3.5M parameters. TrASPr, has 4 BERT transformers (each 6 layers and 12 heads) and MLP a top of those for a total of ~189M parameters. Evo 2, a genomic ‘foundation’ model has 40B parameters, DNABERT has ~86M (a single BERT with 12 layers and 12 heads), and Borzoi has 186M parameters (as stated in https://www.biorxiv.org/content/10.1101/2025.05.26.656171v2).  We note that the difference here is not just in model size but also the amount of data used to train the model. We edited the original L417 to reflect that.

      (17) L546, please provide more detail on the VAE. What is the dimension of the latent representation?

      We added more details in the Methods section like the missing dimension (256) and definitions for P(Z) and P(S). 

      (18) Consider citing (and possibly comparing BOS to) Ghari et al., NeurIPS 2024 ("GFlowNet Assisted Biological Sequence Editing").

      Added.

      (19) Appendix Figure 2, and corresponding main text: it is not clear what is shown here. What is dPSI+ and dPSI-? What pairs of tissues are you comparing? Spearman correlation is reported instead of Pearson, which is the primary metric used throughout the text.

      The dPSI+ and dPSI- sets were indeed not well defined in the original submission. Moreover, we found our own code lacked consistency due to different tests executed at different times/by different people. We apologize for this lack of consistency and clarity which we worked to remedy in the revised version. To answer the reviewer’s question, given two tissues ($c,c'$), dPSI+ and dPSI- is for correctly classifying the exons that are significantly differentially included or excluded. Specifically, differential included exons are those for which  $\Delta \Psi_{e,c1,c2} = \Psi_\Psi_{e,c1} - \Psi_{e,c2}  \geq 0.15$, compared to those that are not  ($\Delta \Psi_{e,c1,c2} < 0.05). Similarly, dPSI- is for correctly classifying the exons that are significantly differentially excluded in the first tissue or included in the second tissue ($\Delta \Psi_{e,c1,c2} = \Psi_\Psi_{e,c1} - \Psi_{e,c2}  \leq -0.15$) compared to those that are not  ($\Delta \Psi_{e,c1,c2} > -0.05). This means dPSI+ and dPSI- are dependent on the order of c1, c2. In addition, we also define a direction/order agnostic test for changing vs non changing events i.e. $|\Delta \Psi_{e,c1,c2}| \geq 0.15$ vs $|\Delta \Psi_{e,c1,c2}| < 0.05$. These test definitions are consistent with previous publications (e.g. Barash et al Nature 2010, Jha et al 2017) and also answer different biological questions: For example “Exons that go up in brain” and “Exons that go up in Liver” can reflect distinct mechanisms, while changing exons capture a model’s ability to identify regulated exons even if the direction of prediction may be wrong. The updated Appendix Figure 2 is now in the main text as Figure 2d and uses Pearson, while AUPRC and AUROC refer to the changing vs no-changing classification task described above such that we avoid dPSI+ and dPSI- when summarizing in this table over 3 pairs of tissues . Finally, we note that making sure all tests comply with the above definition also resulted in an update to Figure 2b/c labels and values, where TrASPr’s improvements over Pangolin reaches up to 1.8fold in AUPRC compared to 2.4fold in the earlier version. We again apologize for having a lack of clarity and consistent evaluations in the original submission.

      (20) Minor typographical comments:

      -   Some plots could use more polishing (e.g., thicker stroke, bigger font size, consistent style (compare 4a to the other plots)...).

      Agreed. While not critical for the science itself we worked to improve figure polishing in the revision to make those more readable and pleasant. 

      -   Consider using 2-dimensional histograms instead of the current kernel density plots, which tend to over-smooth the data and hide potentially important details. 

      We were not sure what the exact suggestion is here and opted to leave the plots as is.

      -   L53: dPSI_{e, c, c'} is never formally defined. Is it PSI_{e, c} - PSI_{e, c'} or vice versa?  

      Definition now included (see above).

      -   L91: Define/explain "transformer" and provide reference. 

      We added the explanation and related reference of the transformer in the introduction section and BERT in the method section.  

      -   L94: exons are short. Are you referring here to the flanking introns? Please explain. 

      We apologize for the lack of clarity. We are referring to a cassette exon alternative splicing event as is commonly defined by the splice junctions involved that is from the 5’ SS of the upstream exon to the 3’ SS of the downstream exon. The text now reads:

      “...In contrast, 24% of the cassette exons analyzed in this study span a region between the flanking exons' upstream 3' and downstream 5' splice sites that are larger than 10 kb.”

      -   L132: It's unclear whether a single, shared transformer or four different transformers (one for each splice site) are being pre-trained. One would at least expect 5' and 3' splice sites to have a different transformer. In Methods, L506, it seems that each transformer is pre-trained separately. 

      We updated the text to read:

      “We then center a dedicated transformer around each of the splice sites of the cassette exon and its upstream and downstream (competing) exons (four separate transformers for four splice sites in total).”

      -   L471: You explain here that it is unclear what tasks 'foundation' models are good for. Also in L128, you explain that you are not using a 'foundation' model. But then in L492, you describe the BERT model you're using as a foundation model! 

      Line 492 was simply a poor choice of wording as “foundation” is meant here simply as the “base component”. We changed it accordingly.

      -   L169, "pre-training ... BERT", explain what exactly this means. Is it using masking? Is it self-supervised learning? How many splice sites do you provide? Also explain more about the BERT architecture and provide references. 

      We added more details about the BERT architecture and training in the Methods section.

      -   L186 and later, the values for a and r provided here and in the below do not correspond to what is shown in Figure 2. 

      Fixed, thank you for noticing this.

      -   L187,188: What exactly do you mean by "events" and "samples"? Are they the same thing? If so, are they (exon, tissue) pairs? Please use consistent terminology. Moreover, when you say "changing between two conditions": do you take all six tissues whenever there is a 0.15 spread in PSI among them? Or do you take just the smallest PSI tissue and the largest PSI tissue when there is a 0.15 spread between them? Or something else altogether?

      Reviewer #2 is yet again correct that the definitions were not precise. A “sample” involves a specific exon skipping “event” measured in two tissues.  The text now reads: 

      “....most cassette exons do not change between a given tissue pair (only 14.0% of the samples in the dataset, i.e., a cassette exon measured across two tissues, exhibit |∆Ψ| ≥ 0.15). Thus, when we repeat this analysis only for samples involving exons that exhibited a change in inclusion (|∆Ψ| ≥ 0.15) between at least two tissues, performance degrades for all three models, but the differences between them become more striking (Figure 2a, right column).”

      -   Figure 1a, explain the colors in the figure legend. The 3D effect is not needed and is confusing (ditto in panel C).

      Color explanation is now added: “exons and introns are shown as blue rectangles and black lines. The blue dashed line indicates the inclusive pattern and the red junction indicates an alternative splicing pattern.” 

      These are not 3D effects but stacks to indicate multiple events/cases. We agree these are not needed in Fig1a to illustrate types of AS and removed those. However, in Fig1c and matching caption we use the stacks to  indicate HT data captures many such LSVs over which ML algorithms can be trained. 

      -   Figure 1b, this cartoon seems unnecessary and gives the wrong impression that this paper explores mechanistic aspects of splicing. The only relevant fact (RBPs serving as splicing factors) can be explained in the text (and is anyway not really shown in this figure).

      We removed Figure 1b cartoon.

      -   Figure 1c, what is being shown by the exon label "8"? 

      This was meant to convey exon ID, now removed to simplify the figure. 

      -   Figure 1e, left, write "Intron Len" in one line. What features are included under "..."? Based on the text, I did not expect more features.

      Also, the arrows emanating from the features do not make sense. Is "Embedding" a layer? I don't think so. Do not show it as a thin stripe. Finally, what are dPSI'+ and dPSI'-? are those separate outputs? are those logits of a classification task?

      We agree this description was not good and have updated it in the revised version. 

      -   Figure 1e, the right-hand side should go to a separate figure much later, when you introduce BOS.

      We appreciate the suggestion. However, we feel that Figure 1e serves as a visual representation of the entire framework. Just like we opted to not turn this work into two separate papers (though we fully agree it is a valid option that would also increase our publication count), we also prefer to leave this unified visual representation as is.

      -   Figure 2, does the n=2456 refer to the number of (exons, tissues) pairs? So each exon contributes potentially six times to this plot? Typo "approximately". 

      The “n” refers to the number of samples which is a cassette event measured in two tissues. The same cassette event may appear in multiple samples if it was confidently quantified in more than two tissues. We updated the caption to reflect this and corrected the typo.

      -   Figure 2b, typo "differentially included (dPSI+) or excluded" .

      Fixed.

      -   L221, "the DNABERT" => "DNABERT".

      Fixed.

      -   L232, missing percent sign.

      -    

      Fixed.

      -   L246, "see Appendix Section 2 for details" seems to instead refer to the third section of the appendix.

      We do not have this as an Appendix, the reference has been updated.

      -   Figure 3, bottom panels, PSI should be "splice site usage"? 

      PSI is correct here - we hope the revised text/definitions make it more clear now.

      -   Figure 3b: typo: "when applied to alternative alternative 3'".

      Fixed.

      -   p252, "polypyrimidine" (no capitalization).

      Fixed.

      -   Strange capitalization of tissue names (e.g., "Brain-Cerebellum"). The tissue is called "cerebellum" without capitalization.

      We used EBV (capital) for the abbreviation and lower case for the rest.

      -   Figure 4c: "predicted usage" on the left but "predicted PSI" on the right. 

      Right. We opted to leave it as is since Pangolin and SpliceAI do predict their definition of “usage” and not directly PSI, we just measure correlations to observed PSI as many works have done in the past. 

      -   Figure 4 legend typo: "two three".

      Fixed.

      -   L351, typo: "an (unsupervised)" (and no need to capitalize Transformer).

      Fixed.

      -   L384, "compared to other tissues at least" => "compared to other tissues of at least".

      Fixed.

      -   L549, P(Z) and P(S) are not defined in the text.

      Fixed.

      -   L572, remove "Subsequently". Add missing citations at the end of the paragraph.

      Fixed.

      -   L580-581, citations missing.

      Fixed.

      -   L584-585, typo: "high confidince predictions"

      Fixed.

      -   L659-660, BW-M and B-WM are both used. Typo?

      Fixed.

      -   L895, "calculating the average of these two", not clear; please rewrite.

      Fixed.

      -   L897, "Transformer" and "BERT", do these refer to the same thing? Be consistent.  

      BOS is a transformer and not a BERT but TrASPr uses the BERT architecture. BERT is a type of transformer as the reviewer is surely well aware so the sentence is correct. Still, to follow the reviewer’s recommendation for consistency/clarity we changed it here to state BERT.

      -   Appendix Figure 5: The term dPSI appears to be overloaded to also represent the difference between predicted PSI and measured PSI, which is inconsistent with previous definitions. 

      Indeed! We thank the reviewer again for their sharp eye and attention to details that we missed. We changed Supp Figure 5, now Figure 4 Supplementary Figure 2, to |PSI’-PSI| and defined those as the difference between TrASPr’s predictions (PSI’) and MAJIQ based PSI quantifications.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer 1

      The authors should clarify the statement regarding the expression in horizontal cells (lines 170-172). In line 170, it is stated that GFP was observed in horizontal cells. Since GFP is fused to Cx36, the observation of GFP in horizontal cells would suggest the expression of Cx36-GFP.

      We believe that there appears to be a misunderstanding. GFP is observed in horizontal cells, because the test AAV construct, which consists of the HKamac promoter and a downstream GFP sequence, was used to validate the promoter specificity in wildtype animals. This was just a test to confirm that HKamac is indeed active in AII amacrine cells as previously described by Khabou et al. 2023. This construct was not used for the large scale BioID screen. For these experiments, V5-dGBP-Turbo was expressed under the control of the HKamac promoter as illustrated in Figure 2A.

      Fig 7: the legend is missing the descriptions for panels A-C.

      We apologize for this mistake. We have missed the label “(A-C)” and added it to the legend.

      Supplemental files are not referenced in the manuscript.

      We have added a reference for these files in line 221-226.

      Reviewer 2

      Supplementary Files 1 and 2 are presented as two replicates of the zebrafish proteomic datasets, but they appear to be identical.

      This appears to be a misunderstanding. These two replicates contain slightly different hits, although the most abundant candidates are identical.

      Reviewer 3

      Thank you for the positive comments

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      We thank the reviewers and editors for this peer review. Following the editorial assessment and specific review comments, in this revision we have included new analysis to support the validity of the behavioral task (Reviewer #2). We have improved data presentation by including 1) data points from individual animals (Reviewer #1, #3), 2) updated histology showing the expression of hM4Di in LC neurons as well as LC terminals in the mPFC (Reviewer #3), and 3) more detailed descriptions of methodology and data analysis (Reviewer #1, #2, #3).

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) Planned t-tests should be performed in both control and experimental animals to determine if the number of trials needed to reach criterion on the ID is lower than on the ED. Based on the data analyses showing no difference among the control group, the data could be pooled to demonstrate that the task is valid. Reporting all p-values using 2 decimal points and standard language e.g., p < 0.001 would greatly improve the readability of the data. 

      Thank you for this suggestion. As pointed out by this reviewer, more trials to reach performance criterion in EDS than IDS is indicative of successful acquisition and switching of the attentional sets. Upon closer examination of the behavioral data, we exclude several sessions where more trials were taken in IDS than in EDS, and our conclusions that DREADD inhibition of the LC or LC input to the mPFC impaired rule switching in EDS remain robust (e.g., new Fig. 1e, 1h). We also pool control and test data (Fig. 1e, 1h, new Supp. Fig. 1a, 1b) to demonstrate the validity of this task (new Supp. Fig. 1c, IDS vs. EDS in the control group, 10 ± 1 trials vs. 16 ± 1 trials, P < 1e-3). The validity of set shifting is also supported by the new Fig. 1c.  

      We report p values using 2 decimal points and standard language as suggested by this reviewer.

      Relevant to the comments from Reviewer #1 in the public review, we now show individual data points on the bar charts (new Fig. 1e, 1h).  

      (2) It may also be helpful to provide the average time between CNO infusion and onset of the ED as well as information about when maximal effects are expected after these treatments.

      Systemic CNO injections were administered immediately after IDS, and we waited approximately one hour before proceeding to EDS. Maximal effects of systemic CNO activation were reported to occur after 30 minutes and last for at least 4-6 hours. Both control and test groups received the CNO injections in the same manner. This is now better described in Methods.  

      Reviewer #3 (Recommendations for the authors):

      (1) Add better histology images showing colocalization of TH and HM4Di. Quantification of colocalization would be optimal.

      We now include better histology images (new Fig. 1d) and have quantified the colocalization of TH and HM4Di in the main text (line 115-116).  

      (2) If possible, images showing HM4Di expression in mPFC axon terminals would be useful. If these are colocalized with TH immunostaining, that would increase confidence in their identity. This would be much more useful than the images provided in Figure 1C.

      We now include new image to show hM4Di expression (mCherry) in LC terminals in the mPFC (new Fig. 1f). However, due to technical limitations (species of the primary antibody), we did not co-stain with TH.

      (3) Include behavior of mice from the miniscope experiment in Figure 2 to show they are similar to those from Figure 1.

      This is now included in Supp. Fig. 1b.

      (4) More details about the processing and segmentation of miniscope data would be helpful (e.g., how many neurons were identified from each animal?). 

      We use standard preprocessing and segmentation pipelines in Inscopix data processing software (version 1.6), which includes modules for motion correction and signal extraction. Briefly, raw imaging videos underwent preprocessing, including a x4 spatial down sampling to reduce file size and processing time. No temporal down sampling was performed. The images were then cropped to eliminate post-registration borders and areas where cells were not visible. Prior to the calculation of the dF/F0 traces, lateral movement was corrected. For ROI identification, we used a constrained non-negative matrix factorization algorithm optimized for endoscopic data (CNMF-E) to extract fluorescence traces from ROIs. We identified 128 ± 31 neurons after manual selection, depending on recording quality and field of view. Number of neurons acquired from each animal are now included in Methods. This is now further elaborated in Methods (line 405415).  

      (5) Add more methodological detail for how cell tuning was analyzed, including how z-scoring was performed (across the entire session?), and how neurons in each category were classified. 

      We have expanded the Methods section to clarify how cell tuning was analyzed (line 419430). Calcium traces were z-scored on a per-neuron basis across the entire session. For each neuron, we computed trial-averaged activity aligned to specific task events (e.g., digging in one of the two ramekins available). A neuron was classified as responsive if its activity showed a significant difference (p < 0.05) between two conditions within the defined time window in the ROC analysis.

      (6) For data from Figure 2F it would be very useful to plot data from individual mice in addition to this aggregated representation.

      We now include data from individual mice in Supp. Table 1.

      (7) I think it would be helpful to move some parts of Figure S1 to the main Figure 1, in particular the table from S1A. 

      Fig. S1 is now part of the new Fig. 1.

      (8) Clarify whether Figure S2 is an independent replication, as implied, or whether the same test data is shown twice in two separate figures (In Figure 1b and Supplementary Figure 2).

      The test group in Fig. S2 (new Fig. S1) is the same as the test group in Fig. 1b (new Fig. 1e), but the control group is a separate cohort. This is now clarified in the figure legends.  

      (9) The authors should add a limitations section to the discussion where they specifically discuss the caveats involved in relating their results specifically to NE. This should include the possible involvement of co-transmitters and off-target expression of Cre in other populations.

      Thank you for this comment. Previous pharmacology and lesion studies showed that LC input or NE content in the mPFC was specifically required for EDS-type switching processes (Lapiz, M.D. et al., 2006; Tait, D.S. et al. 2007; McGaughy, J. et al. 2008), in light of which we interpret our mPFC neurophysiological effects with LC inhibition as at least partially mediated by the direct LC-NE input.  When discussing the limitations of our study, we now explicitly acknowledge the potential involvement of co-transmitters released by LC neurons (line 253-256).  

      (10) The authors should provide details about the TH antibody uses for IHC

      We now include more details in immunohistochemistry (line 384-388).

      (11) Throughout, it would be helpful to include datapoints from individual animals - these are included in some supplementary figures, but are missing in a number of the main plots.

      Reviewer #1 made a similar comment, and we now include individual data points in the figures (e.g., Fig. 1e, 1h).

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This study introduces a novel method for estimating spatial spectra from irregularly sampled intracranial EEG data, revealing cortical activity across all spatial frequencies, which supports the global and integrated nature of cortical dynamics. The study showcases important technical innovations and rigorous analyses, including tests to rule out potential confounds; however, the lack of comprehensive theoretical justification and assumptions about phase consistency across time points renders the strength of evidence incomplete. The dominance of low spatial frequencies in cortical phase dynamics continues to be of importance, and further elaboration on the interpretation and justification of the results would strengthen the link between evidence and conclusions.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The paper uses rigorous methods to determine phase dynamics from human cortical stereotactic EEGs. It finds that the power of the phase is higher at the lowest spatial phase.

      Strengths:

      Rigorous and advanced analysis methods.

      Weaknesses:

      The novelty and significance of the results are difficult to appreciate from the current version of the paper.

      (1) It is very difficult to understand which experiments were analysed, and from where they were taken, reading the abstract. This is a problem both for clarity with regard to the reader and for attribution of merit to the people who collected the data.

      We now explicitly state the experiments that were used, lines 715-716.

      (2) The finding that the power is higher at the lowest spatial phase seems in tune with a lot of previous studies. The novelty here is unclear and it should be elaborated better.

      It is not generally accepted in neuroscience that power is higher at lowest spatial frequencies, and recent research concludes that traveling waves at this scale may be the result of artefactual measurement (Orczyk et al., 2022; Hindriks et al., 2014; Zhigalov & Jensen,2023). The question we answer is therefore timely and a source of controversy to researchers analysing TWs in cortex. While, in our view, the previous literature points in the direction of our conclusions (notably the work of Freeman et. al. 2003; 2000; Barrie et al. 1996), it is not conclusive at the scale we are interested in, specifically >8cm, and certainly not convincing to the proponents of ‘artefactual measurement’.

      We have added to a sentence to make this explicit in the abstract, lines 20-22. Please also note previous text at the end of the introduction, lines 140-148 and in the first paragraph of the discussion, lines 563-569.

      I could not understand reading the paper the advantage I would have if I used such a technique on my data. I think that this should be clear to every reader.

      We have made the core part of the code available on github (line 1154), which should simplify adoption of the technique. We have urged, in the Discussion (lines 653-663), why habitual measurement of SF spectra is desirable, since the same task measured with EEG, sEEG or ECoG does not encompass the same spatial scales, and researchers may be comparing signals with different functional properties. Until reliable methods for estimating SF are available, not dependent on the layout of the recording array, data cannot be analysed to resolve this question. Publication of our results and methods will help this process along.

      (3) It seems problematic to trust in a strong conclusion that they show low spatial frequency dynamics of up to 15-20 cm given the sparsity of the arrays. The authors seem to agree with this concern in the last paragraph of page 12. 

      The new surrogate testing supports our conclusions. The sEEG arrays would not normally be a first choice to estimate SF spectra, for reasons of their sparsity, which may be why such estimates have not been done before. Yet, this is the research challenge that we sought to solve, and a problem for which there was no ready method to hand. Nevertheless, it is a problem that urgently needed to be solved given the current debate on the origin of large-scale TWs. We have now included detailed surrogate testing of real data plus varying strength model waves (Figure 6A and Supplementary Figure 4). We believe this should convince the reader that we are measuring the spatial frequency spectrum with sufficient accuracy to answer the central research question.

      They also say that it would be informative to repeat the analyses presented here after the selection of more participants from all available datasets. It begs the question of why this was not done. It should be done if possible.

      We have now doubled the number of participants in the main analyses. Since each participant comprises a test of the central hypothesis, now the hypothesis test now has 23 replications (Supplementary Figures 2 and 3). There were four failures to reach significance due to under-powered tests, i.e., not enough contacts. This is sufficient test of the hypothesis and, in our opinion, not the primary obstacle to scientific acceptance of our results. The main obstacle is providing convincing tests that the method is accurate, and this is what we have focussed on. Publication of python code and the detailed methods described here enable any interested researcher to extend our method to other datasets.

      (4) Some of the analyses seem not to exploit in full the power of the dataset. Usually, a figure starts with an example participant but then the analysis of the entire dataset is not as exhaustive. For example, in Figure 6 we have a first row with the single participants and then an average over participants. One would expect quantifications of results from each participant (i.e. from the top rows of GFg 6) extracting some relevant features of results from each participant and then showing the distribution of these features across participants. This would complement the subject average analysis.

      The results are now clearly split into sections, where we first deal with all the single participant analyses, then the surrogate testing to confirm the basic results, then the participant aggregate results (Figure 7 and Supplementary Figure 7). The participant aggregate results reiterate the basic findings for the single participants. The key finding is straightforward (SF power decreases with SF) and required only one statistical analysis per subject.

      (5) The function of brain phase dynamics at different frequencies and scales has been examined in previous papers at frequencies and scales relevant to what the authors treat. The authors may want to be more extensive with citing relevant studies and elaborating on the implications for them. Some examples below:

      Womelsdorf T, et alScience. 2007

      Besserve M et al. PloS Biology 2015

      Nauhaus I et al Nat Neurosci 2009

      We have added two paragraphs to the discussion, in response to the reviewer suggestion (lines 606-623). These paragraphs place our high TF findings in the context of previous research.

      Reviewer #2 (Public review):

      Summary:

      In this paper, the authors analyze the organization of phases across different spatial scales. The authors analyze intracranial, stereo-electroencephalogram (sEEG) recordings from human clinical patients. The authors estimate the phase at each sEEG electrode at discrete temporal frequencies. They then use higher-order SVD (HOSVD) to estimate the spatial frequency spectrum of the organization of phase in a data-driven manner. Based on this analysis, the authors conclude that most of the variance explained is due to spatially extended organizations of phase, suggesting that the best description of brain activity in space and time is in fact a globally organized process. The authors' analysis is also able to rule out several important potential confounds for the analysis of spatiotemporal dynamics in EEG.

      Strengths:

      There are many strengths in the manuscript, including the authors' use of SVD to address the limitation of irregular sampling and their analyses ruling out potential confounds for these signals in the EEG.

      Weaknesses:

      Some important weaknesses are not properly acknowledged, and some conclusions are overinterpreted given the evidence presented.

      The central weakness is that the analyses estimate phase from all signal time points using wavelets with a narrow frequency band (see Methods - "Numerical methods"). This step makes the assumption that phase at a particular frequency band is meaningful at all times; however, this is not necessarily the case. Take, for example, the analysis in Figure 3, which focuses on a temporal frequency of 9.2 Hz. If we compare the corresponding wavelet to the raw sEEG signal across multiple points in time, this will look like an amplitude-modulated 9.2 Hz sinusoid to which the raw sEEG signal will not correspond at all. While the authors may argue that analyzing the spatial organization of phase across many temporal frequencies will provide insight into the system, there is no guarantee that the spatial organization of phase at many individual temporal frequencies converges to the correct description of the full sEEG signal. This is a critical point for the analysis because while this analysis of the spatial organization of phase could provide some interesting results, this analysis also requires a very strong assumption about oscillations, specifically that the phase at a particular frequency (e.g. 9.2 Hz in Figure 3, or 8.0 Hz in Figure 5) is meaningful at all points in time. If this is not true, then the foundation of the analysis may not be precisely clear. This has an impact on the results presented here, specifically where the authors assert that "phase measured at a single contact in the grey matter is more strongly a function of global phase organization than local". Finally, the phase examples given in Supplementary Figure 5 are not strongly convincing to support this point.

      “using wavelets with a narrow frequency band … this analysis also requires a very strong assumption about oscillations, specifically that the phase at a particular frequency (e.g. 9.2 Hz in Figure 3, or 8.0 Hz in Figure 5) is meaningful at all points in time”

      Our method uses very short time-window Morlet wavelets to avoid the assumptions of oscillations, i.e., long-lasting sinusoids in the signal, in the sense of sinusoidal waveforms, or limit cycles extending in time. Cortical TWs can only last one or two cycles (Alexander et al., 2006), requiring methods that are compact in the time domain to avoid underreporting the desired phenomena. Additionally, the short time-window Morlet wavelets have low frequency resolution, so they are robust with respect to shifts in frequency between sites. We now discuss this issue explicitly in the Methods (lines 658-674). This means the phase estimation methods used in the manuscript precisely do not have the problem of assuming narrow-band oscillations in the signal. The methods are also robust to the exact shape of the waveforms; the signal needs be only approximately sinusoidal; to rise and fall. This means the Fourier variant we use does not introduce ringing artefact that can be introduced using longer timeseries methods, such as FFT.

      “This step makes the assumption that phase at a particular frequency band is meaningful at all times”

      This important consideration is entrenched in our choice of methods. By way of explanatory background, we point out that this step is not the final step. Aggregation methods can be used to distinguish between signal and noise. In the simple case, event-locked time-series of phase can be averaged. This would allow consistent (non-noise) phase relations to be preserved, while the inconsistent (including noise) phase relations would be washed out. This is part of the logic behind all such aggregation procedures, e.g., phase-locking, coherence. SVD has the advantage of capturing consistent relations in this sense, but without loss of information as occurs in averaging (up to the choice of number of singular vectors in the final model). Specifically, maps of the spatial covariances in phase are captured in the order of the variance explained. Noise (in the sense conveyed by the reviewer) in the phase measurements will not contribute to highest rank singular vectors. SVD is commonly used to remove noise, and that is one of its purposes here. This point can be seen by considering the very smooth singular vectors derived from MEG (Figure 3F) in this new version of the manuscript. These maps of phase gradients pull out only the non-noisy relations, even as their weighted sums reproduce any individual sample to any desired accuracy.

      To summarize, the next step (of incorporating the phase measure into the SVD) neatly bypasses the issue of non-meaningful phase quantification. This is one of the reasons why we do not undertake the spatial frequency estimates on the raw matrices of estimated phase.

      We now include a new sub-paragraph on this topic in the methods, lines 831-838.

      In addition, we have reworded the first description of the methods with a new paragraph at the end of the introduction, which better balances the description of the steps involved. The two sentences (lines 162-166 highlight the issue of concern to the reviewer.

      “there is no guarantee that the spatial organization of phase at many individual temporal frequencies converges to the correct description of the full sEEG signal.”

      The correct description of the full sEEG signal is beyond the scope of the present research. Our main goal, as stated, is to show that the hypothesis that ‘extra-cranial measurements of TWs is the result of projection from localized activity’ is not supported by the evidence of spatial patterns of activity in the cortex. Since this activity can be accessed as single frequency band (especially if localized sources create the large-scale patterns), analysis of SF on a TF-by-TF basis is sufficient.

      “This has an impact on the results presented here, specifically where the authors assert that "phase measured at a single contact in the grey matter is more strongly a function of global phase organization than local".

      We agree with the reviewer, even though we expect that the strongest influences on local phase are due to other cortical signals in the same band. The implicit assumption of the focus on bands of the same temporal frequency is now made explicit in the abstract (lines 31-34).

      A sentence addressing this issue had been added to the first paragraph of the discussion (lines 579-582).

      Inclusion of cross-frequency interactions would likely require a highly regular measurement array over the scales of interest here, i.e., the noise levels inherent in the spatial organization of sEEG contacts would not support such analyses.

      “Finally, the phase examples given in Supplementary Figure 5 are not strongly convincing to support this point.”

      We have removed the phase examples that were previously in Supplementary Figure 5 (and Figure 5 in the previous version of the main text), since further surrogate testing and modelling (Supplementary Figure 11) shows the LSVs from irregular arrays will inevitably capture mixtures of low and high SF signals. The final section of the Methods explains this effect in some detail. Instead, the new version of the manuscript relies on new surrogate testing to validate our methods.

      Another weakness is in the discussion on spatial scale. In the analyses, the authors separate contributions at (approximately) > 15 cm as macroscopic and < 15 cm as mesoscopic. The problem with the "macroscopic" here is that 15 cm is essentially on the scale of the whole brain, without accounting for the fact that organization in sub-systems may occur. For example, if a specific set of cortical regions, spanning over a 10 cm range, were to exhibit a consistent organization of phase at a particular temporal frequency (required by the analysis technique, as noted above), it is not clear why that would not be considered a "macroscopic" organization of phase, since it comprises multiple areas of the brain acting in coordination. Further, while this point could be considered as mostly semantic in nature, there is also an important technical consideration here: would spatial phase organizations occurring in varying subsets of electrodes and with somewhat variable temporal frequency reliably be detected? If this is not the case, then could it be possible that the lowest spatial frequencies are detected more often simply because it would be difficult to detect variable organizations in subsets of electrodes?

      The motivation for our study was to show that large-scale TWs measured outside the cortex cannot be the result of more localized activity being ‘projected up’. In this case, the temporal frequency of the artefactual waves would be the same as the localized sources, so the criticism does not apply.

      “while this point could be considered as mostly semantic in nature”

      We have changed the terminology in the paper to better coincide with standard usage. Macroscopic now refers to >1cm, while we refer to >8cm as large-scale.

      “15 cm is essentially on the scale of the whole brain, without accounting for the fact that organization in sub-systems may occur.”

      We can assume that subtle frequency variation (e.g., within an alpha phase binding) is greatest at the largest scales of cortex, or at least not less varying than measurements within regions. This means that not considering frequency-drift effects will not inflate low spatial frequency power over high spatial frequency power. Even so, the power spectrum we estimated is approximately 1/SF, so that unmeasured cross-frequency effects in binding (causal influences on local phase) would have to overcome the strength of this relation for this criticism to apply, which seems unlikely.

      “would spatial phase organizations occurring in varying subsets of electrodes and with somewhat variable temporal frequency reliably be detected?”

      See our previous comments about the low temporal frequency resolution of two cycle Morlet wavelets. The answer is yes, up to the range approximated by half-power bandwidth, which is large in the case of this method (see lines 760-764).

      Another weakness is disregarding the potential spike waveform artifact in the sEEG signal in the context of these analyses. Specifically, Zanos et al. (J Neurophysiol, 2011) showed that spike waveform artifacts can contaminate electrode recordings down to approximately 60 Hz. This point is important to consider in the context of the manuscript's results on spatial organization at temporal frequencies up to 100 Hz. Because the spike waveform artifact might affect signal phase at frequencies above 60 Hz, caution may be important in interpreting this point as evidence that there is significant phase organization across the cortex at these temporal frequencies.

      We have now added a sentence on this issue to the discussion (lines 600-602).

      However, our reading of the Zanos et al. paper is that the low temporal frequency (60-100Hz) contribution of spikes and spike patterns is negligible compared to genuine post-synaptic membrane fluctuations (see their Figure 3). These considerations come more strongly into play when correlations between LFP and spikes are calculated or spike triggered averaging is undertaken, since then a signal is being partly correlated with itself, or, partly averaged over the supposedly distinct signal with which it was detected.

      A last point is that, even though the present results provide some insight into the organization of phase across the human brain, the analyses do not directly link this to spiking activity. The predictive power that these spatial organizations of phase could provide for spiking activity - even if the analyses were not affected by the distortion due to the narrow-frequency assumption - remains unknown. This is important because relating back to spiking activity is the key factor in assessing whether these specific analyses of phase can provide insight into neural circuit dynamics. This type of analysis may be possible to do with the sEEG recordings, as well, by analyzing high-gamma power (Ray and Maunsell, PLoS Biology, 2011), which can provide an index of multi-unit spiking activity around the electrodes.

      “even if the analyses were not affected by the distortion due to the narrow-frequency assumption”

      See our earlier comment about narrow TFs; this is not the case in the present work.

      The spiking activity analysis would be an interesting avenue for future research. It appears the 1000Hz sampling frequency in the present data is not sufficient for method described in Ray & Maunsell (2011). On a related topic, we have shown that large-scale traveling waves in the MEG and 8cm waves in ECoG can both be used to predict future localized phase at a single sensor/contact, two cycles into the future (Alexander et al., 2019). This approach could be used to predict spiking activity, by combining it with the reviewer’s suggestion. However, the current manuscript is motivated by the argument that measured large-scale extra-cranial TWs are merely projections of localized cortical activity. Since spikes do not arise in this argument, we feel it is outside the scope of the present research. We have added this suggestion to the discussion as a potential line of future research (lines 686-688).

      Reviewer #3 (Public review):

      Summary:

      The authors propose a method for estimation of the spatial spectra of cortical activity from irregularly sampled data and apply it to publicly available intracranial EEG data from human patients during a delayed free recall task. The authors' main findings are that the spatial spectra of cortical activity peak at low spatial frequencies and decrease with increasing spatial frequency. This is observed over a broad range of temporal frequencies (2-100 Hz).

      Strengths:

      A strength of the study is the type of data that is used. As pointed out by the authors, spatial spectra of cortical activity are difficult to estimate from non-invasive measurements (EEG and MEG) due to signal mixing and from commonly used intracranial measurements (i.e. electrocorticography or Utah arrays) due to their limited spatial extent. In contrast, iEEG measurements are easier to interpret than EEG/MEG measurements and typically have larger spatial coverage than Utah arrays. However, iEEG is irregularly sampled within the threedimensional brain volume and this poses a methodological problem that the proposed method aims to address.

      Weaknesses:

      The used method for estimating spatial spectra from irregularly sampled data is weak in several respects.

      First, the proposed method is ad hoc, whereas there exist well-developed (Fourier-based) methods for this. The authors don't clarify why no standard methods are used, nor do they carry out a comparative evaluation.

      We disagree that the method is ad hoc, though the specific combination of SVD and multiscale differencing is novel in its application to sEEG. The SVD method has been used to isolate both ~30cm TWs in MEG and EEG (Alexander et al., 2013; 2016), as well as 8cm waves in ECoG (Alexander et al., 2013; 2019). In our opening examples in the results now reiterate these previous related findings, by way of example analysis of MEG data (Figure 3). This will better inform the reader on the extent of continuity of the method from previous research.

      Standard FFT has been used after interpolating between EEG electrodes to produce a uniform array (Alamia et al., 2023). There exist well-developed Fourier methods for nonuniform grids, such as simple interpolation, the butterfly algorithm, wavefield extrapolation and multi-scale vector field techniques. However, the problems for which these methods are designed require non-sparse sampling or less irregular arrays. The sEEG contacts (reduced in number to grey matter contacts) are well outside the spatial irregularity range of any Fourierrelated methods that we are aware of, particularly at the broad range of spatial scales of interest here (2cm up to 24cm). This would make direct comparison of these specialized Fourier method to our novel methods, in the sEEG, something of a straw-man comparison.

      We now include a summary paragraph in the introduction, which is a brief review of Fourier methods designed to deal with non-uniform sampling (lines 159-162).

      Second, the proposed method lacks a theoretical foundation and hinges on a qualitative resemblance between Fourier analysis and singular value decomposition.

      We have improved our description of the theoretical relation between Fourier analysis and SVD (additional material at lines 839-861 and 910-922). In fact, there are very strong links between the two methods, and now it should be clearer that our method does not rely on a mere qualitative resemblance.

      Third, the proposed method is not thoroughly tested using simulated data. Hence it remains unclear how accurate the estimated power spectra actually are.

      We now include a new surrogate testing procedure, which takes as inputs the empirical data and a model signal (of known spatial frequency) in various proportions. Thus, we test both the impact of small amount of surrogate signal on the empirical signal, and the impact of ‘noise’ (in the form of a small amount of empirical signal) added to the well-defined surrogate signal.

      In addition, there are a number of technical issues and limitations that need to be addressed or clarified (see recommendations to the authors).

      My assessment is that the conclusions are not completely supported by the analyses. What would convince me, is if the method is tested on simulated cortical activity in a more realistic set-up. I do believe, however, that if the authors can convincingly show that the estimated spatial spectra are accurate, the study will have an impact on the field. Regarding the methodology, I don't think that it will become a standard method in the field due to its ad hoc nature and well-developed alternatives.

      Simulations of cortical activity do not seem the most direct way to achieve this goal. The first author has published in this area (Liley et. al., 1999; Wright et al., 2001), and such simulations, for both bulk and neuronally based simulations, readily display traveling wave activity at low spatial frequencies (indeed, this was the origin of the present scientific journey). The manuscript outlines these results in the introduction, as well as theoretical treatments proposing the same. Several other recent studies have highlighted the appearance of largescale travelling waves using connectome-based models (https://www.biorxiv.org/content/10.1101/2025.07.05.663278v1; https://www.nature.com/articles/s41467-024-47860-x), which we do not include in the manuscript for reasons of brevity. In short, the emergence of TW phenomenon in models is partly a function of the assumptions put into them (i.e., spatial damping, boundary conditions, parameterization of connection fields) and would therefore be inconclusive in our view.

      Instead, we rely on the advantages provided by the way our central research question has been posed: that the spatial frequency distribution of grey matter signal can determine whether extra-cranial TWs are artefactual. The newly introduced surrogate methods reflect this advantage by directly adding ground truth spatial frequency components to individual sample measurements. This is a less expensive option than making cortical simulations to achieve the same goal.

      For the same reasons, we include testing of the methods using real cortical signals with MEG arrays (for which we could test the effects of increasing sparseness of contacts, test the effects of average referencing, and also construct surrogate time-series with alternative spectra).

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Major points

      Methods, Page 18: "... using notch filters to remove the 50Hz line signal and its harmonics ...": The sEEG data appear to have been recorded in North America, where the line frequency is 60 Hz. Is this perhaps a typo, or was a 50 Hz notch filter in fact applied here (which would be a mistake)?

      This has now been fixed in the text to read 60Hz. This is the notch filter that was applied.

      Minor points

      (1) While the authors do state that they are analyzing the "spatial frequency spectrum of phase dynamics" in the abstract, this could be more clearly emphasized. Specifically, the difference between signal power at different spatial frequencies (as analyzed by a standard Fourier analysis) and the organization of phase in space (as done here) could be more clearly distinguished.

      We now address this point explicitly on lines 167-172. We now include at the end of the results additional analyses where the TF power is included. This means that the effects of including signal power at different temporal frequencies can be directly compared to our main analysis of the SF spectrum of the phase dynamics.

      (2) Figure 1A-C: It was not immediately clear what the lengths provided in these panels (e.g."> 40 cm cortex", "< 10 cm", "< 30 cm") were meant to indicate. This could be made clearer.

      Now fixed in the caption.

      (3) Figure 2A: If this is surrogate data to explain the analysis technique, it would be helpful to note explicitly at this point.

      This Figure has been completely reworked, and now the status of the examples (from illustrative toy models to actual MEG data) should be clearer.

      (4) Figure 4A: Why change from "% explained variance" for the example data in Figure 2C to arbitrary units at this point?

      This has now been explicitly stated in the methods (lines 1033-1036).

      (5) Page 15: "This means either the results were biased by a low pass filter, or had a maximum measurable...": If the authors mean that the low-pass filter is due to spatial blurring of neural activity in the EEG signal, it would be helpful to state that more directly at this point.

      Now stated directly, lines 567-568.

      (6) Page 23: "...where |X| is the complex magnitude of X...": The modulus operation is defined on a complex number, yet here is applied to a vector of complex numbers. If the operation is elementwise, it should be defined explicitly.

      ‘Elementwise’ is now stated explicitly (line 1020).

      Reviewer #3 (Recommendations for the authors):

      In the submitted manuscript, the authors propose a method to estimate spatial (phase) spectra from irregularly sampled oscillatory cortical activity. They apply the method to intracranial (iEEG) data and argue that cortical activity is organized into global waves up to the size of the entire cortex. If true, this finding is certainly of interest, and I can imagine that it has profound implications for how we think about the functional organization of cortical activity.

      We have added a section to the discussion outlining the most radical of these implications: what does it mean to do source localization when non-local signals dominate? Lines 670-681.

      The manuscript is well-written, with comprehensive introduction and discussion sections, detailed descriptions of the results, and clear figures. However, the proposed method comprised several ad hoc elements and is not well-founded mathematically, its performance is not adequately assessed, and its limitations are not sufficiently discussed. As such, the study failed to convince (me) of the correctness of the main conclusions.

      We now have a direct surrogate testing of the method. We have also improved the mathematical explanation to show that the link between Fourier analysis and SVD is not ad hoc, but well understood in both literatures. We had addressed explicitly in the text all of the limitations raised by the reviewers.

      Major comments

      (1) The main methodological contribution of the study is summarized in the introduction section:

      "The irregular sampling of cortical spatial coordinates via stereotactic EEG was partly overcome by the resampling of the phase data into triplets corresponding to the vertices of approximately equilateral triangles within the cortical sheet."

      There exist well-established Fourier methods for handling irregularly sampled data so it is unclear why the authors did not resort to these and instead proposed a rather ad hoc method without theoretical justification (see next comment).

      We have re-reviewed the literature on non-uniform Fourier analysis. We now briefly review the Fourier methods for handling irregularly sampled data (lines 155-162) and conclude that none of the existing methods can deal with the degree of irregularity, and especially sparsity, found for the grey-matter sEEG contacts.

      (2) In the Appendix, the authors write:

      "For appropriate signals, i.e., those with power that decreases monotonically with frequency, each of the first few singular vectors, v_k, is an approximate complex sinusoid with wavenumber equal to k."

      I don't think this is true in general and if it is, there must be a formal argument that proves it. Furthermore, is it also true for irregularly sampled data? And in more than one spatial dimension? Moreover, it is also unclear exactly how the spatial Fourier spectrum is estimated from the SVD.

      In response to these reviewer queries, we now spend considerably more time in the conceptual set-up of the manuscript, giving examples of where SVD can be used to estimate the Fourier spectrum. We have now unpacked the word ‘appropriate’ and we are now more exact in our phrasing. This is laid out in lines 843-850 of the manuscript. In addition, the methods now describe the mathematical links between Fourier analysis and SVD (lines 851861 and 910-922).

      The authors write:

      "The spatial frequency spectrum can therefore be estimated using SVD by summing over the singular values assigned to each set of singular vectors with unique (or by binning over a limited range of) spatial frequencies. This procedure is illustrated in Figure 1A-C."

      First, the singular vectors are ordered to decreasing values of the corresponding singular values. Hence, if the singular values are used to estimate spectral power, the estimated spectrum will necessarily decrease with increasing spatial frequency (as can be seen in Figure 2C). Then how can traveling waves be detected by looking for local maxima of the estimated power spectra?

      TWs are not detected by looking for local maxima in the spectra. Our work has focussed on the global wave maps derived from the SVD of phase (i.e., k=1-3), which also explain most of the variance in phase. This is now mentioned in the caption to Figure 3 (lines 291-294).

      Second, how are spatial frequencies assigned to the different singular vectors? The proposed method for estimating spatial power spectra from irregularly sampled data seems rather ad hoc and it is not at all clear if, and under what conditions, it works and how accurate it is.

      The new version of the manuscript uses a combination of the method previously presented (the multi-scale differencing) and the method previously outlined in the supplementary materials (doing complex-valued SVD on the spatial vectors of phase). We hope that along with the additional expository material in the methods the new version is clearer and seems less ad hoc to the reviewer. Certainly, there are deep and well-understood links between Fourier analysis and SVD, and we hope we have brought these into focus now.

      (3) The authors define spatial power spectra in three-dimensional Euclidean space, whereas the actual cortical activity occurs on a two-dimensional sheet (the union of two topological 2spheres). As such, it is not at all clear how the estimated wavelengths in three-dimensional space relate to the actual wavelengths of the cortical activity.

      We define spatial power spectra on the folded cortical sheet, rather than Cartesian coordinates. We use geodesic distances in all cases where a distance measurement is required. We have included two new figures (Figure 5 and Supplementary Figure1) showing the mapping of the triangles onto the cortical sheet, which should bring this point home.

      (4) The authors' analysis of the iEEG data is subject to a caveat that is not mentioned in the manuscript: As a reference for the local field potentials, the average white-matter signal was used and this can lead to artifactual power at low spatial frequencies. This is because fluctuations in the reference signal are visible as standing waves in the recording array. This might also explain the observation that

      "A surprising finding was that the shape of the spatial frequency spectrum did not vary much with temporal frequency."

      because fluctuations in the reference signal are expected to have power at all temporal frequencies (1/f spectrum). When superposed with local activity at the recording electrodes, this leads to spurious power at low spatial frequencies. Can the authors exclude this interpretation of the results?

      The new version of the manuscript deals explicitly with this potential confound (lines 454467). First, the artefactual global synchrony due to the reference signal (the DC component in our spatial frequency spectra of phase) is at a distinct frequency from the lowest SF of interest here. The lowest spatial frequency is a function of the maximum spatial range of the recording array and not overlapping in our method with the DC component, despite the loss of SF resolution due to the noise of the spatial irregularity of the recording array. This can be seen from consideration of the SF tuning (Figure 4) for the MEG wave maps shown in Figure 3, and the spectra generated for sparse MEG arrays in Supplementary Figure 5. Additionally, this question led us to a series of surrogate tests which are now included in the manuscript. We used MEG to test for the effects of average reference, since in this modality the reference free case is available. The results show that even after imposing a strong and artefactual global synchrony, the method is highly robust to inflation of the DC component, which either way does not strongly influence the SF estimates in the range of interest (4c/m to 12c/m for the case of MEG).

      (5) Related to the previous comment: Contrary to the authors' claims, local field potentials are susceptible to volume conduction, particularly when average references are used (see e.g. https://www.cell.com/neuron/fulltext/S0896-6273(11)00883-X)

      Methods exist to mitigate these effects (e.g. taking first- or second-order spatial differences of the signals). I think this issue deserves to be discussed.

      We have reviewed this research and do not find it to be a problem. The authors cited by the reviewer were concerned with unacknowledged volume conduction up to 1 cm for LFP. The maximum spatial frequency we report here is 50c/m, or equivalent to 2cm. While the intercontact distance on the sEEG electrodes was 0.5cm, in practice the smallest equilateral triangles (i.e., between two electrodes) to be found in the grey matter was around 2cm linear size. We make no statements about SF in the 1cm range. We do now cite this paper and mention this short-range volume conduction (lines 602-605). The method of taking derivatives has the same problems as source localization methods. They remove both artefactual correlations (volume conduction) and real correlations (the low SF interactions of interest here). We mention this now at lines 667-669. In addition, our method to remove negative SF components from the LSVs ameliorates the effects of average referencing. There are now more details in the Methods about this step (lines 924-947), as well as a new supplementary figure illustrating its effects on signal with a known SF spectrum (MEG, supplementary Figure 6).

      (6) Could the authors add an analysis that excludes the possibility that the observed local maxima in the spectra are a necessary consequence of the analysis method, rather than reflecting true maxima in the spectra? A (possibly) similar effect can be observed in ordinary Fourier spectra that are estimated from zero-mean signals: Because the signals have zero mean, the power spectrum at frequency zero is close to zero and this leads to an artificial local maximum at low frequencies.

      We acknowledge the reviewer’s mathematical point. We do not agree that it could be an issue, though it is important to rule it out definitively. First, removing the DC component will only produce an artefactual low SF peak if the power at low SF is high. This may occur in the reviewer’s example only because temporal frequency has a ~1/f spectrum. If the true spectrum is flat, or increasing in power with f, no such artificial low SF will be produced (see Supplementary Figure 5G). Additionally,

      (1) The DC component is well separated from the low SF components in our method;

      (2) We now include several surrogate methods which show that our method finds the correct spectral distribution and is not just finding a maximum at low SFs due to the suggested effect (subtraction of the DC component). Analysis of separated wave maps in MEG (Figures 3 & 4) shows the expected peaks in SF, increasing in peak SF for each family of maps when wavenumber increases (roughly three k=1 maps, three k=2 etc.). A specific surrogate test for this query was also undertaken by creating a reverse SF spectrum in MEG phase data, in which the spectrum goes linearly with f over the SF range of interest, rather than the usual 1/f. Our method correctly finds the former spectrum (Supplementary Figure 5). Additionally, we tested for the effects of introducing the average reference and the effects of our method to remove the DC component of the phase SF spectrum (Supplementary Figure 6). We can definitively rule out the reviewer’s concern.

      A related issue (perhaps) is the observation that the location of the maximum (i.e. the peak spatial frequency of cortical activity) depends on array size: If cortical activity indeed has a characteristic wavelength (in the sense of its spectrum having a local maximum) would one not expect it to be independent of array size?

      This is only true when making estimates for relatively clean sinusoidal signals, and not from broad-band signals. Fourier analysis and our related SVD methods are very much dependent on maximum array size used to measure cortical signals. This is why the first frequency band (after the DC component) in Fourier analysis is always at a frequency equivalent to 1/array_size, even if the signal is known to contain lower frequency components. We now include a further illustration of this in Figure 3, a more detailed exposition of this point in the methods, and in Supplementary Figure 11 we provide a more detailed example of the relation between Fourier analysis and SVD when grids with two distinct scales are used.

      In short, it is not possible, mathematically, to measure wavelengths greater than the array size in broad-band data. This is now stated explicitly in the manuscript (lines 143-144). A common approach in Neuroscience research is to first do narrowband filtering, then use a method that can accurately estimate ‘instantaneous’ phase change, such as the Hilbert transform. This is not possible for highly irregular sEEG arrays.

      (7) The proposed method of estimating wavelength from irregularly sampled threedimensional iEEG data involves several steps (phase-extraction, singular value decomposition, triangle definition, dimension reduction, etc.) and it is not at all clear that the concatenation of all these steps actually yields accurate estimates.

      Did the authors use more realistic simulations of cortical activity (i.e. on the convoluted cortical sheet) to verify that the method indeed yields accurate estimates of phase spectra?

      We now included detailed surrogate testing, in which varying combinations of sEEG phase data and veridical surrogate wavelengths are added together.

      See our reply from the public reviewer comments. We assess that real neurophysiological data (here, sEEG plus surrogate and MEG manipulated in various ways) is a more accurate way to address these issues. In our experience, large scale TWs appear spontaneously in realistic cortical simulations, and we now cite the relevant papers in the manuscript (line 53).

      Minor comments

      (1) Perhaps move the first paragraph of the results section to the Introduction (it does not describe any results).

      So moved.

      (2) The authors write:

      "The stereotactic EEG contacts in the grey matter were re-referenced using the average of low-amplitude white matter contacts"

      Does this mean that the average is taken over a subset of white-matter contacts (namely those with low amplitude)? Or do the authors refer to all white-matter contacts as "low-amplitude"? And had contacts at different needles different references? Or where the contacts from all needles pooled?

      A subset of white-matter contacts was used for re-referencing, namely those 50% with lowest amplitude signals. This subset was used to construct a pooled, single, average reference. We have rephrased the sentences referring to this procedure to improve clarity (line 202 and 743745).

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors scrutinized differences in C-terminal region variant profiles between Rett syndrome patients and healthy individuals and pinpointed that subtle genetic alternation can cause benign or pathogenic output, which harbours important implications in Rett syndrome diagnosis and proposes a therapeutic strategy. This work will be beneficial to clinicians and basic scientists who work on Rett syndrome, and carries the potential to be applied to other Mendelian rare diseases.

      Strengths:

      Well-designed genetic and molecular experiments translate genetic differences into functional and clinical changes. This is a unique study resolving subtle changes in sequences that give rise to dramatic phenotypic consequences.

      Weaknesses:

      There are many base-editing and protein-expression changes throughout the manuscript, and they cause confusion. It would be helpful to readers if authors could provide a simple summary diagram at the end of the paper.

      We thank Reviewer #1 for their encouraging comments. As suggested, we will include a summary figure of the genetic changes we have made, and the resulting expression and phenotypic consequences.

      Reviewer #2 (Public review):

      Summary:

      This study by Guy and Bird and colleagues is a natural follow-up to their 2018 Human Molecular Genetics paper, further clarifying the molecular basis of C-terminal deletions (CTDs) in MECP2 and how they contribute to Rett syndrome. The authors combine human genetic data with well-designed experiments in embryonic stem cells, differentiated neurons, and knock-in mice to explain why some CTD mutations are disease-causing while others are harmless. They show that pathogenic mutations create a specific amino acid motif at the C-terminus, where +2 frameshifts produce a PPX ending that greatly reduces MeCP2 protein levels (likely due to translational stalling) whereas +1 frameshifts generating SPRTX endings are well tolerated.

      Strengths:

      This is a comprehensive and rigorous study that convincingly pinpoints the molecular mechanism behind CTD pathogenicity, with strong agreement between the cell-based and animal data. The authors also provide a proof of principle that modifying the PPX termination codon can restore MeCP2-CTD protein levels and rescue symptoms in mice. In addition, they demonstrate that adenine base editing can correct this defect in cultured cells and increase MeCP2-CTD protein levels. Overall, this is a well-executed study that provides important mechanistic and translational insight into a clinically important class of MECP2 mutations.

      Weaknesses:

      The adenine base editing to change the termination codon is shown to be feasible in generated cell lines, but has yet to be shown in vivo in animal models.

      We thank Reviewer #2 for their positive comments. We agree that an in vivo study demonstrating effective DNA base editing in our CTD-1 mouse model is the obvious next step, and this work is in progress. However, given the ever-increasing use of pre- and neonatal screening for genetic diseases, we felt it important to disseminate our findings as soon as possible. The family pedigree in Figure 3C is a clear demonstration of this need.

      Reviewer #3 (Public review):

      Summary:

      Guy et al. explored the variation in the pathogenicity of carboxy-terminal frameshift deletions in the X-linked MECP2 gene. Loss-of-function variants in MECP2 are associated with Rett syndrome, a severe neurodevelopmental disorder. Although 100's of pathogenic MECP2 variants have been found in people with Rett syndrome, 8 recurrent point mutations are found in ~65% of disease cases, and frameshift insertions/deletions (indels) variants resulting in production of carboxy-terminal truncated (CTT) MeCP2 protein account for ~10% of cases. Many of these occur in a "deletion prone region" (DPR) between c.1110-1210, with common recurrent deletions c.1157-1197del (CTD1) and c.1164_1207del (CTD2). While two major protein functional domains have been defined in MeCP2, the methyl-binding domain (MBD) and the NCoR interacting domain (NID), the functional role of the carboxy-terminal domain (CTD, beyond the NID, predicted to have a disordered protein structure) has not been identified, and previous work by this group and others demonstrated that a Mecp2 "minigene" lacking the CTD retains MeCP2 function suggesting that the CTD is dispensable. This raises an important question: If the CTD is dispensable, what is the pathogenic basis of the various CTT frameshift variants? Prior work from this group demonstrated that genetically engineered mice expressing the CTD1 variant had decreased expression of Mecp2 RNA and MeCP2 protein and decreased survival, but those expressing the CTD2 variant had normal Mecp2 RNA and protein and survival. However, they noted that differences between the mouse and human coding sequences resulted in different terminal sequences between the two common CTD, with CTD1 ending in -PPX in both mouse and human, but CTD2 ending in -PPC in human but -SPX in mouse, and in the previous paper they demonstrated in humanized mouse ES cells (edited to have the same -PPX termination) containing the CTD2 deletion resulted in decreased Mecp2 RNA and protein levels. This previous work provides the underlying hypotheses that they sought to explore, which is that the pathological basis of disease causing CTD relates to the formation of truncated proteins that end with a specific amino acid sequence (-PPX), which leads to decreased mRNA and protein levels, whereas tolerated, non-pathogenic CTD do not lead to production of truncated proteins ending in this sequence and retain normal mRNA/protein expression.

      In this manuscript, they evaluate missense variants, in-frame deletions, and frame shift deletions within the DPR from the aggregated Genome Aggregated Database (gnomAD) and find that the "apparently" normal individuals within gnomAD had numerous tolerated missense variants and in-frame deletions within this region, as well as frameshift deletions (in hemizygous males) in the defined region. All of the gnomAD deletions within this region resulted in terminal amino acid sequences -SPRTX (due to +1 frameshift), whereas nearly all deletion variants in this region from people with Rett syndrome (from the Clinvar copy of the former RettBase database) had a terminal -PPX sequence, due to a +2 frameshift. They hypothesized that terminal proline codons causing ribosomal stalling and "nonsense mediated decay like" degradation of mRNA (with subsequent decreased protein expression) was the basis of the specific pathogenicity of the +2 frameshift variants, and that utilizing adenine base editors (ABE) to convert the termination codon to a tryptophan could correct this issue. They demonstrate this by engineering the change into mouse embryonic stem cell lines and mouse lines containing the CTD1 deletion and show that this change normalized Mecp2 mRNA and protein levels and mouse phenotypes. Finally, they performed an initial proof-of-concept in an inducible HEK cell line and showed the ability of targeted ABE to edit the correct adenine and cause production of the expected larger truncated Mecp2 protein from CTD1 constructs.

      The findings of this manuscript provide a level of support for their hypothesis about the pathogenicity versus non-pathogenicity of some MECP2 CTT intragenic deletions and provide preliminary evidence for a novel therapeutic approach for Rett syndrome; however, limitations in their analysis do not fully support the broader conclusions presented.

      Strengths:

      (1) Utilization of publicly available databases containing aggregated genetic sequencing data from adult cohorts (gnomAD) and people with Rett syndrome (Clinvar copy of RettBase) to compare differences in the composition of the resulting terminal amino acid sequences resulting from deletions presumed to be pathogenic (n+2) versus presumed to be tolerated (n+1).

      (2) Evaluation of a unique human pedigree containing an n+1 deletion in this region that was reported as pathogenic, with demonstration of inheritance of this from the unaffected father and presence within other unaffected family members.

      (3) Development of a novel engineered mouse model of a previously assumed n+1 pathogenic variant to demonstrate lack of detrimental effect, supporting that this is likely a benign variant and not causative of Rett syndrome.

      (4) Creation and evaluation of novel cell lines and mouse models to test the hypothesis that the pathogenicity of the n+2 deletion variants could be altered by a single base change in the frameshifted stop codon.

      (5) Initial proof-of-concept experiments demonstrating the potential of ABE to correct the pathogenicity of these n+2 deletion variants.

      Weaknesses:

      (1) While the use of the large aggregated gnomAD genetic data benefits from the overall size of the data, the presence of genetic variants within this collection does not inherently mean that they are "neutral" or benign. While gnomAD does not include children, it does include aggregated data from a variety of projects targeting neuropsychiatric (and other conditions), so there is information in gnomAD from people with various medical/neuropsychiatric conditions. The authors do make some acknowledgement of this and argue that the presence of intragenic deletion variants in their region of interest in hemizygous males indicates that it is highly likely that these are tolerated, non-pathogenic variants. Broadly, it is likely true that gnomAD MECP2 variants found in hemizygous males are unlikely to cause Rett syndrome in heterozygous females, it does not necessarily mean that these variants have no potential to cause other, milder, neuropsychiatric disorders. As a clear example, within gnomAD, there is a hemizygous male with the rs28934908 C>T variant that results in p.A140V (p.A152V in e1 transcript numbering convention). This pathogenic variant has been found in a number of pedigrees with an X-linked intellectual disability pattern, in which males have a clear neurodevelopmental disorder and heterozygous females have mild intellectual disability (see PMIDs 12325019, 24328834 as representative examples of a large number of publications describing this). Thus, while their claim that hemizygous deletion variants in gnomAD are unlikely to cause Rett syndrome, that cannot make the definitive statement that they are not pathogenic and completely benign, especially when only found in a very small number of individuals in gnomAD.

      (2) The authors focus exclusively on deletions within the "DPR", they define as between c.1110-1210 and say that these deletions account for 10% of Rett syndrome cases. However, the published studies that are the basis for this 10% estimate include all genetic variants (frameshift deletions, insertions, complex insertion/deletions, nonsense variants) resulting in truncations beyond the NID. For example, Bebbington 2010 (PMID: 19914908), which includes frameshift indels as early as c.905 and beyond c.1210. Further specific examples from RettBase are described below, but the important point is that their evaluation of only frameshift variants within c.1110-1210 is not truly representative of the totality of genetic variants that collectively are considered CTT and account for 10% of Rett cases.

      (3) The authors say that they evaluated the putative pathogenic variants contained within RettBase (which is no longer available, but the data were transferred to Clinvar) for all cases with Classic Rett syndrome and de novo deletion variants within their defined DPR domain. Looking at the data from the Clinvar copy of RettBase, there are a number (n=143) of c-terminal truncating variants (either frameshift or nonsense) present beyond the NID, but the authors only discuss 14 deletion frameshift variants in this manuscript. A number of these variants have molecular features that do not fall into the pathogenic classification proposed by the authors and are not addressed in the manuscript and do not support the generalization of the conclusions presented in this manuscript, especially the conclusion that the determination of pathogenicity of all c-terminal truncating variants can be determined according to their proposed n+2 rule, or that all of the 10% of people with Rett syndrome and c-terminal truncating variants could be treated by using a base editor to correct the -PPX termination codon.

      (4) The HEK-based system utilized is convenient for doing the initial experiments testing ABE; however, it represents an artificial system expressing cDNA without splicing. Canonical NMD is dependent on splicing, and while non-canonical "NMD-like" processes are less well understood, a concern is whether the artificial system used can adequately predict efficacy in a native setting that includes introns and splicing.

      We thank reviewer #3 for their constructive comments. A number of these relate to our analysis of databases of pathogenic (RettBASE) and non-pathogenic (gnomAD) databases. We disagree with their assertion that we are looking at only a small subset of RTT CTD mutations. We detail 14 different RTT CTDs in the manuscript, but these include the 3 most frequently occurring, which alone account for 121 RTT cases in RettBASE.

      We used the original RettBASE database for our analysis, which contained significantly more information than was transferred to Clinvar. We may not have made this sufficiently clear and will remedy this during revision of the manuscript.

      We stress that RettBASE contained many non-RTT causing mutations. For this reason, we employed stringent selection criteria to define a high-confidence set of RTT CTD alleles. Importantly, this set was chosen before any investigation of reading frame or C-terminal amino acid sequence. Our stringent set was selected based on three criteria: location within the C-terminal deletion prone region (CT-DPR), a diagnosis of Classical RTT and at least one case where that mutation had been shown to be absent from both parents (i.e. that it was a de novo mutation). This excluded a large number of CTD alleles which fitted the +2 frameshift/PPX ending category as well as some in other categories. There are good reasons to believe that the vast majority of genuinely pathogenic RTT CTD mutations do fall into this class.

      Concerning gnomAD CTDs, we chose to restrict our detailed analysis to those which are present in the hemizygous state, to exclude individuals which mask a pathogenic mutation due to skewed X-inactivation. Data from all zygosities are shown in Fig. 3, SF1.

      We will revise the manuscript to include tables of all extracted data relevant to this region, from both gnomAD and RettBASE, along with analysis of a less stringent set of RettBASE CTDs for reading frame and C-terminal amino acid sequence. We hope this will make clear the strength of the evidence for our conclusions.

      We agree with Reviewer #3 that inclusions of variants in gnomAD does not exclude the possibility that they may cause medical/psychiatric conditions other than RTT. This point is already mentioned in the Discussion, but we plan to emphasise it further. The pedigree included in the paper, as well as others that we have learned of, argue that loss of the C-terminus of MeCP2 has few if any phenotypic consequences, but more cases are needed to robustly assess this conclusion.

      We disagree that our HEK cell-based system is not suitable for testing efficacy of reagents for use on endogenous alleles in vivo. The editing process is not dependent on splicing, and we have shown in this manuscript that making this single base change has the same effect on an endogenous knock-in allele (CTD1 X>W) or a cDNA-based transgene (Flp-In T-REx CTD1 + base editing), namely, to increase the amount of truncated MeCP2 produced.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      Englert et al. proposed a functional connectome-based Hopfield artificial neural network (fcHNN) architecture to reveal attractor states and activity flows across various conditions, including resting state, task-evoked, and pathological conditions. The fcHNN can reconstruct characteristics of resting-state and task-evoked brain activities. Additionally, the fcHNN demonstrates differences in attractor states between individuals with autism and typically developing individuals.

      Strengths:

      (1) The study used seven datasets, which somewhat ensures robust replication and validation of generalization across various conditions.

      (2) The proposed fcHNN improves upon existing activity flow models by mimicking artificial neural networks, thereby enhancing the representational ability of the model. This advancement enables the model to more accurately reconstruct the dynamic characteristics of brain activity.

      (3) The fcHNN projection offers an interesting visualization, allowing researchers to observe attractor states and activity flow patterns directly.

      We are grateful to the reviewer for highlighting the robustness of our findings across multiple datasets and for appreciating the novelty and representational advantages of our fcHNN model (which has been renamed to fcANN in the revised manuscript).

      Weaknesses:

      (1) The fcHNN projection can offer low-dimensional dynamic visualizations, but its interpretability is limited, making it difficult to make strong claims based on these projections. The interpretability should be enhanced in the results and discussion.

      We thank the reviewer for these important points. We agree that the interpretability of the low-dimensional projection is limited. In the revised manuscript, we have reframed the fcANN projection primarily as a visualization tool (see e.g. line 359) and moved the corresponding part of Figure 2 to the Supplementary Material (Supplementary Figure 2). We have also implemented a substantial revision of the manuscript, which now directly links our analysis to the novel theoretical framework of self-orthogonalizing attractor networks (Spisak & Friston, 2025), opening several new avenues in terms of interpretation and shedding light on the computational principles underlying attractor dynamics in the brain (see the revised introduction and the new section “Theoretical background”, starting at lines 128, but also the Mathematical Appendices 1-2 in the Supplementary Material for a comprehensive formal derivation). As part of these efforts, we now provide evidence for the brain’s functional organization approximating a special, computationally efficient class of attractor networks, the so-called Kanter-Sompolinsky projector network (Figure 2A-C, line 346, see also our answer to your next comment). This is exactly, what the theoretical framework of free-energy-minimizing attractor networks predicts.

      (2) The presentation of results is not clear enough, including figures, wording, and statistical analysis, which contributes to the overall difficulty in understanding the manuscript. This lack of clarity in presenting key findings can obscure the insights that the study aims to convey, making it challenging for readers to fully grasp the implications and significance of the research.

      We have thoroughly revised the manuscript for clarity in wording, figures (see e.g. lines 257, 482, 529 in the Results and lines 1128, 1266, 1300, 1367 in the Methods). We carefully improved statistical reporting and ensured that we always report test statistics, effect sizes and clearly refer to the null modelling approach used (e.g. lines 461, 542, 550, 565, 573, 619, as well as Figures 2-4). As absolute effect sizes, in many analyses, do not have a straightforward interpretation, we provided Glass’ , as a standardized effect size measure, expressing the distance of the true observation from the null distribution as a ratio of the null standard deviation. To further improve clarity, we now clearly define our research questions and the corresponding analyses and null models in the revised manuscript, both in the main text and in two new tables (Tables 1 and 2). We denoted research questions and null model with Q1-7 and NM1-5, respectively and refer to them at multiple instances when detailing the analyses and the results.

      Reviewer #2 (Public Review):

      Summary:

      Englert et al. use a novel modelling approach called functional connectome-based Hopfield Neural Networks (fcHNN) to describe spontaneous and task-evoked brain activity and the alterations in brain disorders. Given its novelty, the authors first validate the model parameters (the temperature and noise) with empirical resting-state function data and against null models. Through the optimisation of the temperature parameter, they first show that the optimal number of attractor states is four before fixing the optimal noise that best reflects the empirical data, through stochastic relaxation. Then, they demonstrate how these fcHNN-generated dynamics predict task-based functional activity relating to pain and self-regulation. To do so, they characterise the different brain states (here as different conditions of the experimental pain paradigm) in terms of the distribution of the data on the fcHNN projections and flow analysis. Lastly, a similar analysis was performed on a population with autism condition. Through Hopfield modeling, this work proposes a comprehensive framework that links various types of functional activity under a unified interpretation with high predictive validity.

      Strengths:

      The phenomenological nature of the Hopfield model and its validation across multiple datasets presents a comprehensive and intuitive framework for the analysis of functional activity. The results presented in this work further motivate the study of phenomenological models as an adequate mechanistic characterisation of large-scale brain activity.

      Following up on Cole et al. 2016, the authors put forward a hypothesis that many of the changes to the brain activity, here, in terms of task-evoked and clinical data, can be inferred from the resting-state brain data alone. This brings together neatly the idea of different facets of brain activity emerging from a common space of functional (ghost) attractors.

      The use of the null models motivates the benefit of non-linear dynamics in the context of phenomenological models when assessing the similarity to the real empirical data.

      We thank the reviewer for recognizing the comprehensive and intuitive nature of our framework and for acknowledging the strength of our hypothesis that diverse brain activity facets emerge from a common resting state attractor landscape.

      Weaknesses:

      While the use of the Hopfield model is neat and very well presented, it still begs the question of why to use the functional connectome (as derived by activity flow analysis from Cole et al. 2016). Deriving the functional connectome on the resting-state data that are then used for the analysis reads as circular.

      We agree that starting from functional couplings to study dynamics is in stark contrast with the common practice of estimating the interregional couplings based on structural connectome data. We now explicitly discuss how this affects the scope of the questions we can address with the approach, with explicit notes on the inability of this approach to study the structure-function coupling and its limitations in deriving mechanistic insights at the level of biophysical implementation.

      Line 894:

      “The proposed approach is not without limitations. First, as the proposed approach does not incorporate information about anatomical connectivity and does not explitly model biophysical details. Thus, in its present form, the model is not suitable to study the structure-function coupling and cannot yiled mechanistic explanations underlying (altered) polysynaptic connections, at the level of biophysical details.”

      We are confident, however, that our approach is not circular. At the high level, our approach can be considered as a function-to-function generative model, with twofold aims.

      First, we link large-scale brain dynamics to theoretical artificial neural network models and show that the functional connectome display characteristics that render it as an exceptionally “well-behaving” attractor network (e.g. superior convergence properties, as contrasted against appropriate respective null models). In the revised manuscript, we have significantly improved upon this aspect by explicitly linking the fcANN model to the theoretical framework of self-orthogonalizing attractor networks (Spisak & Friston, 2025) (see the revised introduction and the new section “Theoretical background”, starting at lines 128, but also the Mathematical Appendices 1-2 in the Supplementary Material for a comprehensive formal derivation). As part of these efforts, we now provide evidence for the brain’s functional organization approximating a special, computationally efficient class of attractor networks, the so-called Kanter-Sompolinsky projector network (Figure 2A-C, line 346, see also our answer to your next comment). This is exactly, what the theoretical framework of free-energy-minimizing attractor networks predicts. This result is not circular, as the empirical model does not use the key mechanism (the Hebbian/anti-Hebbian learning rule) that induces self-orthogonalization in the theoretical framework. We clarify this in the revised manuscript, e.g. in line 736.

      Second, we benchmark ability of the proposed function-to-function generative model to predict unseen data (new datasets) or data characteristics that are not directly encompassed in the connectivity matrix (e.g. non-Gaussian conditional dependencies, temporal autocorrelation, dynamical responses to perturbations on the system). These benchmarks are constructed against well defined null models, which provide reasonable references. We have now significantly improved the discussion of these null models in the revised manuscript (Tables 1 and 2, lines 257). We not only show, that our model - when reconstructing resting state dynamics - can generalize to unseen data over and beyond what is possible with the baseline descriptive measure (e.g. covariance measures and PCA), but also demonstrate the ability of the framework to reconstruct the effects of perturbations on this dynamics (such as task-evoked changes), based solely on the resting state data form another sample.

      If the fcHNN derives the basins of four attractors that reflect the first two principal components of functional connectivity, it perhaps suffices to use the empirically derived components alone and project the task and clinical data on it without the need for the fcHNN framework.

      We are thankful for the reviewer for highlighting this important point, which encouraged us to develop a detailed understanding of the origins of the close alignment between attractors and principal components (eigenvectors of the coupling matrix) and the corresponding (approximate) orthogonality. Here, we would like to emphasize that the attractor-eigenvector correspondence is by no means a general feature of any arbitrary attractor network. In fact, such networks are a very special class of attractor neural networks (the so-called Kanter-Sompolinsky projector neural network (Kanter & Sompolinsky, 1987)), with a high degree of computational efficiency, maximal memory capacity and perfect memory recall. It has been rigorously shown that in such networks, the eigenvectors of the coupling matrix (i.e. PCA on the timeseries data) and the attractors become equivalent (Kanter & Sompolinsky, 1987). This in turn made us ask the question, what are the learning and plasticity rules that drive attractor networks towards developing approximately orthogonal attractors? We found that this is a general tendency of networks obeying the free energy principle ( Figure 2A-C, line 346, see also our answer to your next comment). The formal derivation of this framework in now presented in an accompanying theoretical piece (Spisak & Friston, 2025). In the revised manuscript, we provide a short, high-level overview of these results (in the Introduction form line 55 and in the new section “Theoretical background”, line 128, but also the Mathematical Appendices 1-2 in the Supplementary Material for a comprehensive formal derivation). According to this new theoretical model, attractor states can be understood as a set of priors (in the Bayesian sense) that together constitute an optimal orthogonal basis, equipping the update process (which is akin to a Markov-chain Monte Carlo sampling) to find posteriors that generalize effectively within the spanned subspace. Thus, in sum, understanding brain function in terms of attractor dynamics - instead of PCA-like descriptive projections - provides important links towards a Bayesian interpretation of brain activity. At the same time, the eigenvector-attractor correspondence also explains, why descriptive decomposition approaches, like PCA or ICA are so effective at capturing the dynamics of the system, at the first place.

      As presented here, the Hopfield model is excellent in its simplicity and power, and it seems suited to tackle the structure-function relationship with the power of going further to explain task-evoked and clinical data. The work could be strengthened if that was taken into consideration. As such the model would not suffer from circularity problems and it would be possible to claim its mechanistic properties. Furthermore, as mentioned above, in the current setup, the connectivity matrix is based on statistical properties of functional activity amongst regions, and as such it is difficult to talk about a certain mechanism. This contention has for example been addressed in the Cole et al. 2016 paper with the use of a biophysical model linking structure and function, thus strengthening the mechanistic claim of the work.

      We agree that investigating how the structural connectome constraints macro-scale dynamics is a crucial next step. Linking our results with the theoretical framework of self-orthogonalizing attractor networks provides a principled approach to this, as the “self-orthogonalizing” learning rule in the accompanying theoretical work provides the opportunity to fit attractor networks with structural constraints to functional data, shedding light on the plastic processes which maintain the observed approximate orthogonality even in the presence of these structural constraints. We have revised the manuscript to clarify that our phenomenological approach is inherently limited in its ability to answer mechanistic questions at the level of biophysical details (lines 894) and discuss this promising direction as follows:

      Lines 803:

      “A promising application of this is to consider structural brain connectivity (as measured by diffusion MRI) as a sparsity constraint for the coupling weights and then train the fcANN model to match the observed resting-state brain dynamics. If the resulting structural-functional ANN model is able to closely match the observed functional brain substate dynamics, it can be used as a novel approach to quantify and understand the structural functional coupling in the brain”.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) The statistical analyses are poorly described throughout the manuscript. The authors should provide more details on the statistical methods used for each comparison, as well as the corresponding statistics and degrees of freedom, rather than solely reporting p-values.

      We thank the reviewer for pointing this out. We have revised the manuscript to include the specific test statistics, precise p-values and raw effect sizes for all reported analyses to ensure full transparency and replicability, see e.g. lines 461, 542, 550, 565, 573, 619, as well as Figures 2-4. Additionally, as absolute effect sizes - in many analyses - do not have a straightforward interpretation, we provided Glass’ Δ, as a standardized effect size measure, expressing the distance of the true observation from the null distribution as a ratio of the null standard deviation.

      We have also improved the description of the statistical methods used in the manuscript (lines 1270, 1306, 1339, 1367, 1404) and added two overview tables (Tables 1 and 2) that summarize the methodological approaches and the corresponding null models.

      Furthermore, we have fully revised the analysis corresponding to noise optimization. We only retained null model 2 (covariance-matched Gaussian) in the main text and on Figure 3, and moved model 1 (spatial phase randomization) into the Supplementary Material (Supplementary Figure 6) and is less appropriate for this analysis (trivially significant in all cases). Furthermore, as test statistic, no we use a Wasserstein distance between the 122-dimensional empirical and the simulated data (instead of focusing on the 2-dimensional projection). This analysis now directly quantifies the capacity of the fcANN model to capture non-Gaussian conditionals in the data.

      (2) The convergence procedure is not clearly explained in the manuscript. Is this an optimization procedure to minimize energy? If so, the authors should provide more details about the optimizer used.

      We apologize for the lack of clarity. The convergence is not an optimization procedure per se, in a sense that it does not involve any external optimizer. It is simply the repeated (deterministic) application of the same update rule also known from Hopfield networks or Boltzmann machines. However, as detailed in the accompanying theoretical paper, this update rule (or inference rule) inherently solves and optimization problem: it performs gradient descent on the free energy landscape of the network. As such, it is guaranteed to converge to a local free energy minimum in the deterministic case. We have clarified this process in the Results and Methods sections as follows:

      Line 161:

      “Inference arises from minimizing free energy with respect to the states \sigma. For a single unit, this yields a local update rule homologous to the relaxation dynamics in Hopfield networks”.

      Line 181:

      “In the basis framework (Spisak & Friston, 2025), inference is a gradient descent on the variational free energy landscape with respect to the states σ and can be interpreted as a form of approximate Bayesian inference, where the expected value of the state σ<sub>i</sub> is interpreted as the posterior mean given the attractor states currently encoded in the network (serving as a macro-scale prior) and the previous state, including external inputs (serving as likelihood in the Bayesian sense)”.

      Line 1252:

      “As the inference rule was derived as a gradient descent on free energy, iterations monotonically decrease the free energy function and therefore converge to a local free‑energy minimum without any external optimizer. Thus, convergence does not require any optimization procedure with an external optimizer. Instead, it arises as the fixed point of repeated local inference updates, which implement gradient descent on free energy in the deterministic symmetric case.”

      (3) In Figure 2G, the beta values range from 0.035 to 0.06, but they are reported as 0.4 in the main text and the Supplementary Figure. Please clarify this discrepancy.

      We are grateful to the reviewer for spotting this typo. The correct value for β is 0.04, as reported in the Methods section. We have corrected this inconsistency in the revised manuscript and as well as in Supplementary Figure 5.

      (4) Line 174: What type of null model was used to evaluate the impact of the beta values? The authors did not provide details on this anywhere in the manuscript.

      We apologize for this omission. The null model is based on permuting the connectome weights while retaining the matrix symmetry, which destroys the specific topological structure but preserves the overall weight distribution. We have now clarified this at multiple places in the revised manuscript (lines 432, Table 1-2, Figure 2), and added new overview tables (Tables 1 and 2) to summarize the methodological approaches and the corresponding null models.

      (5) Figure 3B: It appears that the authors only demonstrate the reproducibility of the “internal” attractor across different datasets. What about other states?

      Thank you for noticing this. We now visualize all attractor states in Figure 3B (note that these essentially consist of two symmetric pairs).

      (6) Figure 3: What does “empirical” represent in Figure 3? Is it PCA? If the “empirical” method, which is a much simpler method, can achieve results similar to those of the fcHNN in terms of state occupancy, distribution, and activity flow, what are the benefits of the proposed method? Furthermore, the authors claim that the explanatory power of the fcHNN is higher than that of the empirical model and shows significant differences. However, from my perspective, this difference is not substantial (37.0% vs. 39.9%). What does this signify, particularly in comparison to PCA?

      This is a crucial point that is now a central theme of our revised manuscript. The reviewer is correct that the “empirical” method is PCA. PCA - by identifying variance-heavy orthogonal directions - aims to explain the highest amount of variance possible in the data (with the assumption of Gaussian conditionals). While empirical attractors are closely aligned to the PCs (i.e. eigenvectors of the inverse covariance matrix, as shown in the new analysis Q1), the alignment is only approximate. We basically take advantage of this small “gap” to quantify, weather attractor states are a better fit to the unseen data than the PCs. Obviously, due to the otherwise strong PC-attractor correspondence, this is expected to be only a small improvement. However, it is an important piece of evidence for the validity of our framework, as it shows that attractors are not just a complementary, perhaps “noisier” variety of the PCs, but a “substrate” that generalizes better to unseen data than the PCs themselves. We have revised the manuscript to clarify this point (lines 528).

      Reviewer #2 (Recommendations For The Authors):

      For clarity, it might be useful to define and use consistently certain key terms. Connectome often refers to structural (anatomical) connectivity unless defined specifically this should be considered, in Figure 1B title for example Brain state often refers to different conditions ie autism, neurotypical, sleep, etc... see for review Kringelbach et al. 2020, Cell Reports. When referring to attractors of brain activity they might be called substates.

      We thank the reviewer for these helpful suggestions. We have carefully revised the manuscript to ensure our terminology is precise and consistent. We now explicitly refer to the “functional connectome” (including the title) and avoid using the too general term “brain state” and use “substates” instead.

      In Figure 2 some terms are not defined. Noise is sigma in the text but elpsilon in the figure. Only in methods, the link becomes clear. Perhaps define epsilon in the caption for clarity. The same applies to μ in the methods. It is only described above in the methods, I suggest repeating the epsilon definition for clarity

      We appreciate this feedback and apologize for the inconsistency. We have revised all figures and the Methods section to ensure that all mathematical symbols (including ε, σ, and μ) are clearly and consistently defined upon their first appearance and in all figure captions. For instance, noise level is now consistently referred to as ϵ. We improved the consistency and clarity for other terms, too, including:

      functional connectome-based Hopfiled network (fcHNN) => functional connectivity-based attractor network (fcANN);

      temperature => inverse temperature;

      And improved grammar and language throughout the manuscript.

      References

      Kanter, I., & Sompolinsky, H. (1987). Associative recall of memory without errors. Physical Review A, 35(1), 380–392. 10.1103/physreva.35.380

      Spisak T & Friston K (2025). Self-orthogonalizing attractor neural networks emerging from the free energy principle. arXiv preprint arXiv:2505.22749.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      Zhou and colleagues developed a computational model of replay that heavily builds on cognitive models of memory in context (e.g., the context-maintenance and retrieval model), which have been successfully used to explain memory phenomena in the past. Their model produces results that mirror previous empirical findings in rodents and offers a new computational framework for thinking about replay.

      Strengths:

      The model is compelling and seems to explain a number of findings from the rodent literature. It is commendable that the authors implement commonly used algorithms from wakefulness to model sleep/rest, thereby linking wake and sleep phenomena in a parsimonious way. Additionally, the manuscript's comprehensive perspective on replay, bridging humans and non-human animals, enhanced its theoretical contribution.

      Weaknesses:

      This reviewer is not a computational neuroscientist by training, so some comments may stem from misunderstandings. I hope the authors would see those instances as opportunities to clarify their findings for broader audiences.

      (1) The model predicts that temporally close items will be co-reactivated, yet evidence from humans suggests that temporal context doesn't guide sleep benefits (instead, semantic connections seem to be of more importance; Liu and Ranganath 2021, Schechtman et al 2023). Could these findings be reconciled with the model or is this a limitation of the current framework?

      We appreciate the encouragement to discuss this connection. Our framework can accommodate semantic associations as determinants of sleep-dependent consolidation, which can in principle outweigh temporal associations. Indeed, prior models in this lineage have extensively simulated how semantic associations support encoding and retrieval alongside temporal associations. It would therefore be straightforward to extend our model to simulate how semantic associations guide sleep benefits, and to compare their contribution against that conferred by temporal associations across different experimental paradigms. In the revised manuscript, we have added a discussion of how our framework may simulate the role of semantic associations in sleep-dependent consolidation.

      “Several recent studies have argued for dominance of semantic associations over temporal associations in the process of human sleep-dependent consolidation (Schechtman et al., 2023; Liu and Ranganath 2021; Sherman et al., 2025), with one study observing no role at all for temporal associations (Schechtman et al., 2023). At first glance, these findings appear in tension with our model, where temporal associations drive offline consolidation. Indeed, prior models have accounted for these findings by suppressing temporal context during sleep (Liu and Ranganath 2024; Sherman et al., 2025). However, earlier models in the CMR lineage have successfully captured the joint contributions of semantic and temporal associations to encoding and retrieval (Polyn et al., 2009), and these processes could extend naturally to offline replay. In a paradigm where semantic associations are especially salient during awake learning, the model could weight these associations more and account for greater co-reactivation and sleep-dependent memory benefits for semantically related than temporally related items. Consistent with this idea, Schechtman et al. (2023) speculated that their null temporal effects likely reflected the task’s emphasis on semantic associations. When temporal associations are more salient and task-relevant, sleep-related benefits for temporally contiguous items are more likely to emerge (e.g., Drosopoulos et al., 2007; King et al., 2017).”

      The reviewer’s comment points to fruitful directions for future work that could employ our framework to dissect the relative contributions of semantic and temporal associations to memory consolidation.

      (2) During replay, the model is set so that the next reactivated item is sampled without replacement (i.e., the model cannot get "stuck" on a single item). I'm not sure what the biological backing behind this is and why the brain can't reactivate the same item consistently.

      Furthermore, I'm afraid that such a rule may artificially generate sequential reactivation of items regardless of wake training. Could the authors explain this better or show that this isn't the case?

      We appreciate the opportunity to clarify this aspect of the model. We first note that this mechanism has long been a fundamental component of this class of models (Howard & Kahana 2002). Many classic memory models (Brown et al., 2000; Burgess & Hitch, 1991; Lewandowsky & Murdock 1989) incorporate response suppression, in which activated items are temporarily inhibited. The simplest implementation, which we use here, removes activated items from the pool of candidate items. Alternative implementations achieve this through transient inhibition, often conceptualized as neuronal fatigue (Burgess & Hitch, 1991; Grossberg 1978). Our model adopts a similar perspective, interpreting this mechanism as mimicking a brief refractory period that renders reactivated neurons unlikely to fire again within a short physiological event such as a sharp-wave ripple. Importantly, this approach does not generate spurious sequences. Instead, the model’s ability to preserve the structure of wake experience during replay depends entirely on the learned associations between items (without these associations, item order would be random). Similar assumptions are also common in models of replay. For example, reinforcement learning models of replay incorporate mechanisms such as inhibition to prevent repeated reactivations (e.g., Diekmann & Cheng, 2023) or prioritize reactivation based on ranking to limit items to a single replay (e.g., Mattar & Daw, 2018). We now discuss these points in the section titled “A context model of memory replay”

      “This mechanism of sampling without replacement, akin to response suppression in established context memory models (Howard & Kahana 2002), could be implemented by neuronal fatigue or refractory dynamics (Burgess & Hitch, 1991; Grossberg 1978). Non-repetition during reactivation is also a common assumption in replay models that regulate reactivation through inhibition or prioritization (Diekmann & Cheng 2023; Mattar & Daw 2018; Singh et al., 2022).”

      (3) If I understand correctly, there are two ways in which novelty (i.e., less exposure) is accounted for in the model. The first and more talked about is the suppression mechanism (lines 639-646). The second is a change in learning rates (lines 593-595). It's unclear to me why both procedures are needed, how they differ, and whether these are two different mechanisms that the model implements. Also, since the authors controlled the extent to which each item was experienced during wakefulness, it's not entirely clear to me which of the simulations manipulated novelty on an individual item level, as described in lines 593-595 (if any).

      We agree that these mechanisms and their relationships would benefit from clarification. As noted, novelty influences learning through two distinct mechanisms. First, the suppression mechanism is essential for capturing the inverse relationship between the amount of wake experience and the frequency of replay, as observed in several studies. This mechanism ensures that items with high wake activity are less likely to dominate replay. Second, the decrease in learning rates with repetition is crucial for preserving the stochasticity of replay. Without this mechanism, the model would increase weights linearly, leading to an exponential increase in the probability of successive wake items being reactivated back-to-back due to the use of a softmax choice rule. This would result in deterministic replay patterns, which are inconsistent with experimental observations.

      We have revised the Methods section to explicitly distinguish these two mechanisms:

      “This experience-dependent suppression mechanism is distinct from the reduction of learning rates through repetition; it does not modulate the update of memory associations but exclusively governs which items are most likely to initiate replay.”

      We have also clarified our rationale for including a learning rate reduction mechanism:

      “The reduction in learning rates with repetition is important for maintaining a degree of stochasticity in the model’s replay during task repetition, since linearly increasing weights would, through the softmax choice rule, exponentially amplify differences in item reactivation probabilities, sharply reducing variability in replay.”

      Finally, we now specify exactly where the learning-rate reduction applied, namely in simulations where sequences are repeated across multiple sessions:

      “In this simulation, the learning rates progressively decrease across sessions, as described above.“

      As to the first mechanism - experience-based suppression - I find it challenging to think of a biological mechanism that would achieve this and is selectively activated immediately before sleep (somehow anticipating its onset). In fact, the prominent synaptic homeostasis hypothesis suggests that such suppression, at least on a synaptic level, is exactly what sleep itself does (i.e., prune or weaken synapses that were enhanced due to learning during the day). This begs the question of whether certain sleep stages (or ultradian cycles) may be involved in pruning, whereas others leverage its results for reactivation (e.g., a sequential hypothesis; Rasch & Born, 2013). That could be a compelling synthesis of this literature. Regardless of whether the authors agree, I believe that this point is a major caveat to the current model. It is addressed in the discussion, but perhaps it would be beneficial to explicitly state to what extent the results rely on the assumption of a pre-sleep suppression mechanism.

      We appreciate the reviewer raising this important point. Unlike the mechanism proposed by the synaptic homeostasis hypothesis, the suppression mechanism in our model does not suppress items based on synapse strength, nor does it modify synaptic weights. Instead, it determines the level of suppression for each item based on activity during awake experience. The brain could implement such a mechanism by tagging each item according to its activity level during wakefulness. During subsequent consolidation, the initial reactivation of an item during replay would reflect this tag, influencing how easily it can be reactivated.

      A related hypothesis has been proposed in recent work, suggesting that replay avoids recently active trajectories due to spike frequency adaptation in neurons (Mallory et al., 2024). Similarly, the suppression mechanism in our model is critical for explaining the observed negative relationship between the amount of recent wake experience and the degree of replay.

      We discuss the biological plausibility of this mechanism and its relationship with existing models in the Introduction. In the section titled “The influence of experience”, we have added the following:

      “Our model implements an activity‑dependent suppression mechanism that, at the onset of each offline replay event, assigns each item a selection probability inversely proportional to its activation during preceding wakefulness. The brain could implement this by tagging each memory trace in proportion to its recent activation; during consolidation, that tag would then regulate starting replay probability, making highly active items less likely to be reactivated. A recent paper found that replay avoids recently traversed trajectories through awake spike‑frequency adaptation (Mallory et al., 2025), which could implement this kind of mechanism. In our simulations, this suppression is essential for capturing the inverse relationship between replay frequency and prior experience. Note that, unlike the synaptic homeostasis hypothesis (Tononi & Cirelli 2006), which proposes that the brain globally downscales synaptic weights during sleep, this mechanism leaves synaptic weights unchanged and instead biases the selection process during replay.”

      (4) As the manuscript mentions, the only difference between sleep and wake in the model is the initial conditions (a0). This is an obvious simplification, especially given the last author's recent models discussing the very different roles of REM vs NREM. Could the authors suggest how different sleep stages may relate to the model or how it could be developed to interact with other successful models such as the ones the last author has developed (e.g., C-HORSE)? 

      We appreciate the encouragement to comment on the roles of different sleep stages in the manuscript, especially since, as noted, the lab is very interested in this and has explored it in other work. We chose to focus on NREM in this work because the vast majority of electrophysiological studies of sleep replay have identified these events during NREM. In addition, our lab’s theory of the role of REM (Singh et al., 2022, PNAS) is that it is a time for the neocortex to replay remote memories, in complement to the more recent memories replayed during NREM. The experiments we simulate all involve recent memories. Indeed, our view is that part of the reason that there is so little data on REM replay may be that experimenters are almost always looking for traces of recent memories (for good practical and technical reasons).

      Regarding the simplicity of the distinction between simulated wake and sleep replay, we view it as an asset of the model that it can account for many of the different characteristics of awake and NREM replay with very simple assumptions about differences in the initial conditions. There are of course many other differences between the states that could be relevant to the impact of replay, but the current target empirical data did not necessitate us taking those into account. This allows us to argue that differences in initial conditions should play a substantial role in an account of the differences between wake and sleep replay.

      We have added discussion of these ideas and how they might be incorporated into future versions of the model in the Discussion section:

      “Our current simulations have focused on NREM, since the vast majority of electrophysiological studies of sleep replay have identified replay events in this stage. We have proposed in other work that replay during REM sleep may provide a complementary role to NREM sleep, allowing neocortical areas to reinstate remote, already-consolidated memories that need to be integrated with the memories that were recently encoded in the hippocampus and replayed during NREM (Singh et al., 2022). An extension of our model could undertake this kind of continual learning setup, where the student but not teacher network retains remote memories, and the driver of replay alternates between hippocampus (NREM) and cortex (REM) over the course of a night of simulated sleep. Other differences between stages of sleep and between sleep and wake states are likely to become important for a full account of how replay impacts memory. Our current model parsimoniously explains a range of differences between awake and sleep replay by assuming simple differences in initial conditions, but we expect many more characteristics of these states (e.g., neural activity levels, oscillatory profiles, neurotransmitter levels, etc.) will be useful to incorporate in the future.”

      Finally, I wonder how the model would explain findings (including the authors') showing a preference for reactivation of weaker memories. The literature seems to suggest that it isn't just a matter of novelty or exposure, but encoding strength. Can the model explain this? Or would it require additional assumptions or some mechanism for selective endogenous reactivation during sleep and rest?

      We appreciate the encouragement to discuss this, as we do think the model could explain findings showing a preference for reactivation of weaker memories, as in Schapiro et al. (2018). In our framework, memory strength is reflected in the magnitude of each memory’s associated synaptic weights, so that stronger memories yield higher retrieved‑context activity during wake encoding than weaker ones. Because the model’s suppression mechanism reduces an item’s replay probability in proportion to its retrieved‑context activity, items with larger weights (strong memories) are more heavily suppressed at the onset of replay, while those with smaller weights (weaker memories) receive less suppression. When items have matched reward exposure, this dynamic would bias offline replay toward weaker memories, therefore preferentially reactivating weak memories. 

      In the section titled “The influence of experience”, we updated a sentence to discuss this idea more explicitly: 

      “Such a suppression mechanism may be adaptive, allowing replay to benefit not only the most recently or strongly encoded items but also to provide opportunities for the consolidation of weaker or older memories, consistent with empirical evidence (e.g., Schapiro et al. 2018; Yu et al., 2024).”

      (5) Lines 186-200 - Perhaps I'm misunderstanding, but wouldn't it be trivial that an external cue at the end-item of Figure 7a would result in backward replay, simply because there is no potential for forward replay for sequences starting at the last item (there simply aren't any subsequent items)? The opposite is true, of course, for the first-item replay, which can't go backward. More generally, my understanding of the literature on forward vs backward replay is that neither is linked to the rodent's location. Both commonly happen at a resting station that is further away from the track. It seems as though the model's result may not hold if replay occurs away from the track (i.e. if a0 would be equal for both pre- and post-run).

      In studies where animals run back and forth on a linear track, replay events are decoded separately for left and right runs, identifying both forward and reverse sequences for each direction, for example using direction-specific place cell sequence templates. Accordingly, in our simulation of, e.g., Ambrose et al. (2016), we use two independent sequences, one for left runs and one for right runs (an approach that has been taken in prior replay modeling work). Crucially, our model assumes a context reset between running episodes, preventing the final item of one traversal from acquiring contextual associations with the first item of the next. As a result, learning in the two sequences remains independent, and when an external cue is presented at the track’s end, replay predominantly unfolds in the backward direction, only occasionally producing forward segments when the cue briefly reactivates an earlier sequence item before proceeding forward.

      We added a note to the section titled “The context-dependency of memory replay” to clarify this:

      “In our model, these patterns are identical to those in our simulation of Ambrose et al. (2016), which uses two independent sequences to mimic the two run directions. This is because the drifting context resets before each run sequence is encoded, with the pause between runs acting as an event boundary that prevents the final item of one traversal from associating with the first item of the next, thereby keeping learning in each direction independent.”

      To our knowledge, no study has observed a similar asymmetry when animals are fully removed from the track, although both types of replay can be observed when animals are away from the track. For example, Gupta et al. (2010) demonstrated that when animals replay trajectories far from their current location, the ratio of forward vs. backward replay appears more balanced. We now highlight this result in the manuscript and explain how it aligns with the predictions of our model:

      “For example, in tasks where the goal is positioned in the middle of an arm rather than at its end, CMR-replay predicts a more balanced ratio of forward and reverse replay, whereas the EVB model still predicts a dominance of reverse replay due to backward gain propagation from the reward. This contrast aligns with empirical findings showing that when the goal is located in the middle of an arm, replay events are more evenly split between forward and reverse directions (Gupta et al., 2010), whereas placing the goal at the end of a track produces a stronger bias toward reverse replay (Diba & Buzsaki 2007).” 

      Although no studies, to our knowledge, have observed a context-dependent asymmetry between forward and backward replay when the animal is away from the track, our model does posit conditions under which it could. Specifically, it predicts that deliberation on a specific memory, such as during planning, could generate an internal context input that biases replay: actively recalling the first item of a sequence may favor forward replay, while thinking about the last item may promote backward replay, even when the individual is physically distant from the track.

      We now discuss this prediction in the section titled “The context-dependency of memory replay”:

      “Our model also predicts that deliberation on a specific memory, such as during planning, could serve to elicit an internal context cue that biases replay: actively recalling the first item of a sequence may favor forward replay, while thinking about the last item may promote backward replay, even when the individual is physically distant from the track. While not explored here, this mechanism presents a potential avenue for future modeling and empirical work.”

      (6) The manuscript describes a study by Bendor & Wilson (2012) and tightly mimics their results. However, notably, that study did not find triggered replay immediately following sound presentation, but rather a general bias toward reactivation of the cued sequence over longer stretches of time. In other words, it seems that the model's results don't fully mirror the empirical results. One idea that came to mind is that perhaps it is the R/L context - not the first R/L item - that is cued in this study. This is in line with other TMR studies showing what may be seen as contextual reactivation. If the authors think that such a simulation may better mirror the empirical results, I encourage them to try. If not, however, this limitation should be discussed.

      Although our model predicts that replay is triggered immediately by the sound cue, it also predicts a sustained bias toward the cued sequence. Replay in our model unfolds across the rest phase as multiple successive events, so the bias observed in our sleep simulations indeed reflects a prolonged preference for the cued sequence.

      We now discuss this issue, acknowledging the discrepancy:

      “Bendor and Wilson (2012) found that sound cues during sleep did not trigger immediate replay, but instead biased reactivation toward the cued sequence over an extended period of time. While the model does exhibit some replay triggered immediately by the cue, it also captures the sustained bias toward the cued sequence over an extended period.”

      Second, within this framework, context is modeled as a weighted average of the features associated with items. As a result, cueing the model with the first R/L item produces qualitatively similar outcomes as cueing it with a more extended R/L cue that incorporates features of additional items. This is because both approaches ultimately use context features unique to the two sides.

      (7) There is some discussion about replay's benefit to memory. One point of interest could be whether this benefit changes between wake and sleep. Relatedly, it would be interesting to see whether the proportion of forward replay, backward replay, or both correlated with memory benefits. I encourage the authors to extend the section on the function of replay and explore these questions.

      We thank the reviewer for this suggestion. Regarding differences in the contribution of wake and sleep to memory, our current simulations predict that compared to rest in the task environment, sleep is less biased toward initiating replay at specific items, leading to a more uniform benefit across all memories. Regarding the contributions of forward and backward replay, our model predicts that both strengthen bidirectional associations between items and contexts, benefiting memory in qualitatively similar ways. Furthermore, we suggest that the offline learning captured  by our teacher-student simulations reflects consolidation processes that are specific to sleep.

      We have expanded the section titled The influence of experience to discuss these predictions of the model: 

      “The results outlined above arise from the model's assumption that replay strengthens bidirectional associations between items and contexts to benefit memory. This assumption leads to several predictions about differences across replay types. First, the model predicts that sleep yields different memory benefits compared to rest in the task environment: Sleep is less biased toward initiating replay at specific items, resulting in a more uniform benefit across all memories. Second, the model predicts that forward and backward replay contribute to memory in qualitatively similar ways but tend to benefit different memories. This divergence arises because forward and backward replay exhibit distinct item preferences, with backward replay being more likely to include rewarded items, thereby preferentially benefiting those memories.”

      We also updated the “The function of replay” section to include our teacher-student speculation:

      “We speculate that the offline learning observed in these simulations corresponds to consolidation processes that operate specifically during sleep, when hippocampal-neocortical dynamics are especially tightly coupled (Klinzing et al., 2019).”

      (8) Replay has been mostly studied in rodents, with few exceptions, whereas CMR and similar models have mostly been used in humans. Although replay is considered a good model of episodic memory, it is still limited due to limited findings of sequential replay in humans and its reliance on very structured and inherently autocorrelated items (i.e., place fields). I'm wondering if the authors could speak to the implications of those limitations on the generalizability of their model. Relatedly, I wonder if the model could or does lead to generalization to some extent in a way that would align with the complementary learning systems framework.

      We appreciate these insightful comments. Traditionally, replay studies have focused on spatial tasks with autocorrelated item representations (e.g., place fields). However, an increasing number of human studies have demonstrated sequential replay using stimuli with distinct, unrelated representations. Our model is designed to accommodate both scenarios. In our current simulations, we employ orthogonal item representations while leveraging a shared, temporally autocorrelated context to link successive items. We anticipate that incorporating autocorrelated item representations would further enhance sequence memory by increasing the similarity between successive contexts. Overall, we believe that the model generalizes across a broad range of experimental settings, regardless of the degree of autocorrelation between items. Moreover, the underlying framework has been successfully applied to explain sequential memory in both spatial domains, explaining place cell firing properties (e.g., Howard et al., 2004), and in non-spatial domains, such as free recall experiments where items are arbitrarily related. 

      In the section titled “A context model of memory replay”, we added this comment to address this point:

      “Its contiguity bias stems from its use of shared, temporally autocorrelated context to link successive items, despite the orthogonal nature of individual item representations. This bias would be even stronger if items had overlapping representations, as observed in place fields.”

      Since CMR-replay learns distributed context representations where overlap across context vectors captures associative structure, and replay helps strengthen that overlap, this could indeed be viewed as consonant with complementary learning systems integration processes. 

      Reviewer #2 (Public Review):

      This manuscript proposes a model of replay that focuses on the relation between an item and its context, without considering the value of the item. The model simulates awake learning, awake replay, and sleep replay, and demonstrates parallels between memory phenomenon driven by encoding strength, replay of sequence learning, and activation of nearest neighbor to infer causality. There is some discussion of the importance of suppression/inhibition to reduce activation of only dominant memories to be replayed, potentially boosting memories that are weakly encoded. Very nice replications of several key replay findings including the effect of reward and remote replay, demonstrating the equally salient cue of context for offline memory consolidation.

      I have no suggestions for the main body of the study, including methods and simulations, as the work is comprehensive, transparent, and well-described. However, I would like to understand how the CMRreplay model fits with the current understanding of the importance of excitation vs inhibition, remembering vs forgetting, activation vs deactivation, strengthening vs elimination of synapses, and even NREM vs REM as Schapiro has modeled. There seems to be a strong association with the efforts of the model to instantiate a memory as well as how that reinstantiation changes across time. But that is not all this is to consolidation. The specific roles of different brain states and how they might change replay is also an important consideration.

      We are gratified that the reviewer appreciated the work, and we agree that the paper would benefit from comment on the connections to these other features of consolidation.

      Excitation vs. inhibition: CMR-replay does not model variations in the excitation-inhibition balance across brain states (as in other models, e.g., Chenkov et al., 2017), since it does not include inhibitory connections. However, we posit that the experience-dependent suppression mechanism in the model might, in the brain, involve inhibitory processes. Supporting this idea, studies have observed increased inhibition with task repetition (Berners-Lee et al., 2022). We hypothesize that such mechanisms may underlie the observed inverse relationship between task experience and replay frequency in many studies. We discuss this in the section titled “A context model of memory replay”:

      “The proposal that a suppression mechanism plays a role in replay aligns with models that regulate place cell reactivation via inhibition (Malerba et al., 2016) and with empirical observations of increased hippocampal inhibitory interneuron activity with experience (Berners-Lee et al., 2022). Our model assumes the presence of such inhibitory mechanisms but does not explicitly model them.”

      Remembering/forgetting, activation/deactivation, and strengthening/elimination of synapses: The model does not simulate synaptic weight reduction or pruning, so it does not forget memories through the weakening of associated weights. However, forgetting can occur when a memory is replayed less frequently than others, leading to reduced activation of that memory compared to its competitors during context-driven retrieval. In the Discussion section, we acknowledge that a biologically implausible aspect of our model is that it implements only synaptic strengthening: 

      “Aspects of the model, such as its lack of regulation of the cumulative positive weight changes that can accrue through repeated replay, are biologically implausible (as biological learning results in both increases and decreases in synaptic weights) and limit the ability to engage with certain forms of low level neural data (e.g., changes in spine density over sleep periods; de Vivo et al., 2017; Maret et al., 2011). It will be useful for future work to explore model variants with more elements of biological plausibility.” Different brain states and NREM vs REM: Reviewer 1 also raised this important issue (see above). We have added the following thoughts on differences between these states and the relationship to our prior work to the Discussion section:

      “Our current simulations have focused on NREM, since the vast majority of electrophysiological studies of sleep replay have identified replay events in this stage. We have proposed in other work that replay during REM sleep may provide a complementary role to NREM sleep, allowing neocortical areas to reinstate remote, already-consolidated memories that need to be integrated with the memories that were recently encoded in the hippocampus and replayed during NREM (Singh et al., 2022). An extension of our model could undertake this kind of continual learning setup, where the student but not teacher network retains remote memories, and the driver of replay alternates between hippocampus (NREM) and cortex (REM) over the course of a night of simulated sleep. Other differences between stages of sleep and between sleep and wake states are likely to become important for a full account of how replay impacts memory. Our current model parsimoniously explains a range of differences between awake and sleep replay by assuming simple differences in initial conditions, but we expect many more characteristics of these states (e.g., neural activity levels, oscillatory profiles, neurotransmitter levels, etc.) will be useful to incorporate in the future.”

      We hope these points clarify the model’s scope and its potential for future extensions.

      Do the authors suggest that these replay systems are more universal to offline processes beyond episodic memory? What about procedural memories and working memory?

      We thank the reviewer for raising this important question. We have clarified in the manuscript:

      “We focus on the model as a formulation of hippocampal replay, capturing how the hippocampus may replay past experiences through simple and interpretable mechanisms.”

      With respect to other forms of memory, we now note that:

      “This motor memory simulation using a model of hippocampal replay is consistent with evidence that hippocampal replay can contribute to consolidating memories that are not hippocampally dependent at encoding (Schapiro et al., 2019; Sawangjit et al., 2018). It is possible that replay in other, more domain-specific areas could also contribute (Eichenlaub et al., 2020).”

      Though this is not a biophysical model per se, can the authors speak to the neuromodulatory milieus that give rise to the different types of replay?

      Our work aligns with the perspective proposed by Hasselmo (1999), which suggests that waking and sleep states differ in the degree to which hippocampal activity is driven by external inputs. Specifically, high acetylcholine levels during waking bias activity to flow into the hippocampus, while low acetylcholine levels during sleep allow hippocampal activity to influence other brain regions. Consistent with this view, our model posits that wake replay is more biased toward items associated with the current resting location due to the presence of external input during waking states. In the Discussion section, we have added a comment on this point:

      “Our view aligns with the theory proposed by Hasselmo (1999), which suggests that the degree of hippocampal activity driven by external inputs differs between waking and sleep states: High acetylcholine levels during wakefulness bias activity into the hippocampus, while low acetylcholine levels during slow-wave sleep allow hippocampal activity to influence other brain regions.”

      Reviewer #3 (Public Review):

      In this manuscript, Zhou et al. present a computational model of memory replay. Their model (CMR-replay) draws from temporal context models of human memory (e.g., TCM, CMR) and claims replay may be another instance of a context-guided memory process. During awake learning, CMR replay (like its predecessors) encodes items alongside a drifting mental context that maintains a recency-weighted history of recently encoded contexts/items. In this way, the presently encoded item becomes associated with other recently learned items via their shared context representation - giving rise to typical effects in recall such as primacy, recency, and contiguity. Unlike its predecessors, CMR-replay has built-in replay periods. These replay periods are designed to approximate sleep or wakeful quiescence, in which an item is spontaneously reactivated, causing a subsequent cascade of item-context reactivations that further update the model's item-context associations.

      Using this model of replay, Zhou et al. were able to reproduce a variety of empirical findings in the replay literature: e.g., greater forward replay at the beginning of a track and more backward replay at the end; more replay for rewarded events; the occurrence of remote replay; reduced replay for repeated items, etc. Furthermore, the model diverges considerably (in implementation and predictions) from other prominent models of replay that, instead, emphasize replay as a way of predicting value from a reinforcement learning framing (i.e., EVB, expected value backup).

      Overall, I found the manuscript clear and easy to follow, despite not being a computational modeller myself. (Which is pretty commendable, I'd say). The model also was effective at capturing several important empirical results from the replay literature while relying on a concise set of mechanisms - which will have implications for subsequent theory-building in the field.

      With respect to weaknesses, additional details for some of the methods and results would help the readers better evaluate the data presented here (e.g., explicitly defining how the various 'proportion of replay' DVs were calculated).

      For example, for many of the simulations, the y-axis scale differs from the empirical data despite using comparable units, like the proportion of replay events (e.g., Figures 1B and C). Presumably, this was done to emphasize the similarity between the empirical and model data. But, as a reader, I often found myself doing the mental manipulation myself anyway to better evaluate how the model compared to the empirical data. Please consider using comparable y-axis ranges across empirical and simulated data wherever possible.

      We appreciate this point. As in many replay modeling studies, our primary goal is to provide a qualitative fit that demonstrates the general direction of differences between our model and empirical data, without engaging in detailed parameter fitting for a precise quantitative fit. Still, we agree that where possible, it is useful to better match the axes. We have updated figures 2B and 2C so that the y-axis scales are more directly comparable between the empirical and simulated data. 

      In a similar vein to the above point, while the DVs in the simulations/empirical data made intuitive sense, I wasn't always sure precisely how they were calculated. Consider the "proportion of replay" in Figure 1A. In the Methods (perhaps under Task Simulations), it should specify exactly how this proportion was calculated (e.g., proportions of all replay events, both forwards and backwards, combining across all simulations from Pre- and Post-run rest periods). In many of the examples, the proportions seem to possibly sum to 1 (e.g., Figure 1A), but in other cases, this doesn't seem to be true (e.g., Figure 3A). More clarity here is critical to help readers evaluate these data. Furthermore, sometimes the labels themselves are not the most informative. For example, in Figure 1A, the y-axis is "Proportion of replay" and in 1C it is the "Proportion of events". I presumed those were the same thing - the proportion of replay events - but it would be best if the axis labels were consistent across figures in this manuscript when they reflect the same DV.

      We appreciate these useful suggestions. We have revised the Methods section to explain in detail how DVs are calculated for each simulation. The revisions clarify the differences between related measures, such as those shown in Figures 1A and 1C, so that readers can more easily see how the DVs are defined and interpreted in each case. 

      Reviewer #4/Reviewing Editor (Public Review):

      Summary:

      With their 'CMR-replay' model, Zhou et al. demonstrate that the use of spontaneous neural cascades in a context-maintenance and retrieval (CMR) model significantly expands the range of captured memory phenomena.

      Strengths:

      The proposed model compellingly outperforms its CMR predecessor and, thus, makes important strides towards understanding the empirical memory literature, as well as highlighting a cognitive function of replay.

      Weaknesses:

      Competing accounts of replay are acknowledged but there are no formal comparisons and only CMR-replay predictions are visualized. Indeed, other than the CMR model, only one alternative account is given serious consideration: A variant of the 'Dyna-replay' architecture, originally developed in the machine learning literature (Sutton, 1990; Moore & Atkeson, 1993) and modified by Mattar et al (2018) such that previously experienced event-sequences get replayed based on their relevance to future gain. Mattar et al acknowledged that a realistic Dyna-replay mechanism would require a learned representation of transitions between perceptual and motor events, i.e., a 'cognitive map'. While Zhou et al. note that the CMR-replay model might provide such a complementary mechanism, they emphasize that their account captures replay characteristics that Dyna-replay does not (though it is unclear to what extent the reverse is also true).

      We thank the reviewer for these thoughtful comments and appreciate the opportunity to clarify our approach. Our goal in this work is to contrast two dominant perspectives in replay research: replay as a mechanism for learning reward predictions and replay as a process for memory consolidation. These models were chosen as representatives of their classes of models because they use simple and interpretable mechanisms that can simulate a wide range of replay phenomena, making them ideal for contrasting these two perspectives.

      Although we implemented CMR-replay as a straightforward example of the memory-focused view, we believe the proposed mechanisms could be extended to other architectures, such as recurrent neural networks, to produce similar results. We now discuss this possibility in the revised manuscript (see below). However, given our primary goal of providing a broad and qualitative contrast of these two broad perspectives, we decided not to undertake simulations with additional individual models for this paper.

      Regarding the Mattar & Daw model, it is true that a mechanistic implementation would require a mechanism that avoids precomputing priorities before replay. However, the "need" component of their model already incorporates learned expectations of transitions between actions and events. Thus, the model's limitations are not due to the absence of a cognitive map.

      In contrast, while CMR-replay also accumulates memory associations that reflect experienced transitions among events, it generates several qualitatively distinct predictions compared to the Mattar & Daw model. As we note in the manuscript, these distinctions make CMR-replay a contrasting rather than complementary perspective.

      Another important consideration, however, is how CMR replay compares to alternative mechanistic accounts of cognitive maps. For example, Recurrent Neural Networks are adept at detecting spatial and temporal dependencies in sequential input; these networks are being increasingly used to capture psychological and neuroscientific data (e.g., Zhang et al, 2020; Spoerer et al, 2020), including hippocampal replay specifically (Haga & Fukai, 2018). Another relevant framework is provided by Associative Learning Theory, in which bidirectional associations between static and transient stimulus elements are commonly used to explain contextual and cue-based phenomena, including associative retrieval of absent events (McLaren et al, 1989; Harris, 2006; Kokkola et al, 2019). Without proper integration with these modeling approaches, it is difficult to gauge the innovation and significance of CMR-replay, particularly since the model is applied post hoc to the relatively narrow domain of rodent maze navigation.

      First, we would like to clarify our principal aim in this work is to characterize the nature of replay, rather than to model cognitive maps per se. Accordingly, CMR‑replay is not designed to simulate head‐direction signals, perform path integration, or explain the spatial firing properties of neurons during navigation. Instead, it focuses squarely on sequential replay phenomena, simulating classic rodent maze reactivation studies and human sequence‐learning tasks. These simulations span a broad array of replay experimental paradigms to ensure extensive coverage of the replay findings reported across the literature. As such, the contribution of this work is in explaining the mechanisms and functional roles of replay, and demonstrating that a model that employs simple and interpretable memory mechanisms not only explains replay phenomena traditionally interpreted through a value-based lens but also accounts for findings not addressed by other memory-focused models.

      As the reviewer notes, CMR-replay shares features with other memory-focused models. However, to our knowledge, none of these related approaches have yet captured the full suite of empirical replay phenomena, suggesting the combination of mechanisms employed in CMR-replay is essential for explaining these phenomena. In the Discussion section, we now discuss the similarities between CMR-replay and related memory models and the possibility of integrating these approaches:

      “Our theory builds on a lineage of memory-focused models, demonstrating the power of this perspective in explaining phenomena that have often been attributed to the optimization of value-based predictions. In this work, we focus on CMR-replay, which exemplifies the memory-centric approach through a set of simple and interpretable mechanisms that we believe are broadly applicable across memory domains. Elements of CMR-replay share similarities with other models that adopt a memory-focused perspective. The model learns distributed context representations whose overlaps encodes associations among items, echoing associative learning theories in which overlapping patterns capture stimulus similarity and learned associations (McLaren & Mackintosh 2002). Context evolves through bidirectional interactions between items and their contextual representations, mirroring the dynamics found in recurrent neural networks (Haga & Futai 2018; Levenstein et al., 2024). However, these related approaches have not been shown to account for the present set of replay findings and lack mechanisms—such as reward-modulated encoding and experience-dependent suppression—that our simulations suggest are essential for capturing these phenomena. While not explored here, we believe these mechanisms could be integrated into architectures like recurrent neural networks (Levenstein et al., 2024) to support a broader range of replay dynamics.”

      Recommendations For The Authors

      Reviewer #1 (Recommendations For The Authors):

      (1) Lines 94-96: These lines may be better positioned earlier in the paragraph.

      We now introduce these lines earlier in the paragraph.

      (2) Line 103 - It's unclear to me what is meant by the statement that "the current context contains contexts associated with previous items". I understand why a slowly drifting context will coincide and therefore link with multiple items that progress rapidly in time, so multiple items will be linked to the same context and each item will be linked to multiple contexts. Is that the idea conveyed here or am I missing something? I'm similarly confused by line 129, which mentions that a context is updated by incorporating other items' contexts. How could a context contain other contexts?

      In the model, each item has an associated context that can be retrieved via Mfc. This is true even before learning, since Mfc is initialized as an identity matrix. During learning and replay, we have a drifting context c that is updated each time an item is presented. At each timestep, the model first retrieves the current item’s associated context cf by Mfc, and incorporates it into c. Equation #2 in the Methods section illustrates this procedure in detail. Because of this procedure, the drifting context c is a weighted sum of past items’ associated contexts. 

      We recognize that these descriptions can be confusing. We have updated the Results section to better distinguish the drifting context from items’ associated context. For example, we note that:

      “We represent the drifting context during learning and replay with c and an item's associated context with cf.”

      We have also updated our description of the context drift procedure to distinguish these two quantities: 

      “During awake encoding of a sequence of items, for each item f, the model retrieves its associated context cf via Mfc. The drifting context c incorporates the item's associated context cf and downweights its representation of previous items' associated contexts (Figure 1c). Thus, the context layer maintains a recency weighted sum of past and present items' associated contexts.”

      (3) Figure 1b and 1d - please clarify which axis in the association matrices represents the item and the context.

      We have added labels to show what the axes represent in Figure 1.

      (4) The terms "experience" and "item" are used interchangeably and it may be best to stick to one term.

      We now use the term “item” wherever we describe the model results. 

      (5) The manuscript describes Figure 6 ahead of earlier figures - the authors may want to reorder their figures to improve readability.

      We appreciate this suggestion. We decided to keep the current figure organization since it allows us to group results into different themes and avoid redundancy. 

      (6) Lines 662-664 are repeated with a different ending, this is likely an error.

      We have fixed this error.

      Reviewer #3 (Recommendations For The Authors):

      Below, I have outlined some additional points that came to mind in reviewing the manuscript - in no particular order.

      (1) Figure 1: I found the ordering of panels a bit confusing in this figure, as the reading direction changes a couple of times in going from A to F. Would perhaps putting panel C in the bottom left corner and then D at the top right, with E and F below (also on the right) work?

      We agree that this improves the figure. We have restructured the ordering of panels in this figure. 

      (2) Simulation 1: When reading the intro/results for the first simulation (Figure 2a; Diba & Buszaki, 2007; "When animals traverse a linear track...", page 6, line 186). It wasn't clear to me why pre-run rest would have any forward replay, particularly if pre-run implied that the animal had no experience with the track yet. But in the Methods this becomes clearer, as the model encodes the track eight times prior to the rest periods. Making this explicit in the text would make it easier to follow. Also, was there any reason why specifically eight sessions of awake learning, in particular, were used?

      We now make more explicit that the animals have experience with the track before pre-run rest recording:

      “Animals first acquire experience with a linear track by traversing it to collect a reward. Then, during the pre-run rest recording, forward replay predominates.”

      We included eight sessions of awake learning to match with the number of sessions in Shin et al. (2017), since this simulation attempts to explain data from that study. After each repetition, the model engages in rest. We have revised the Methods section to indicate the motivation for this choice: 

      “In the simulation that examines context-dependent forward and backward replay through experience (Figs. 2a and 5a), CMR-replay encodes an input sequence shown in Fig. 7a, which simulates a linear track run with no ambiguity in the direction of inputs, over eight awake learning sessions (as in Shin et al. 2019)”

      (3) Frequency of remote replay events: In the simulation based on Gupta et al, how frequently overall does remote replay occur? In the main text, the authors mention the mean frequency with which shortcut replay occurs (i.e., the mean proportion of replay events that contain a shortcut sequence = 0.0046), which was helpful. But, it also made me wonder about the likelihood of remote replay events. I would imagine that remote replay events are infrequent as well - given that it is considerably more likely to replay sequences from the local track, given the recency-weighted mental context. Reporting the above mean proportion for remote and local replay events would be helpful context for the reader.

      In Figure 4c, we report the proportion of remote replay in the two experimental conditions of Gupta et al. that we simulate. 

      (4) Point of clarification re: backwards replay: Is backwards replay less likely to occur than forward replay overall because of the forward asymmetry associated with these models? For example, for a backwards replay event to occur, the context would need to drift backwards at least five times in a row, in spite of a higher probability of moving one step forward at each of those steps. Am I getting that right?

      The reviewer’s interpretation is correct: CMR-replay is more likely to produce forward than backward replay in sleep because of its forward asymmetry. We note that this forward asymmetry leads to high likelihood of forward replay in the section titled “The context-dependency of memory replay”: 

      “As with prior retrieved context models (Howard & Kahana 2002; Polyn et al., 2009), CMR-replay encodes stronger forward than backward associations. This asymmetry exists because, during the first encoding of a sequence, an item's associated context contributes only to its ensuing items' encoding contexts. Therefore, after encoding, bringing back an item's associated context is more likely to reactivate its ensuing than preceding items, leading to forward asymmetric replay (Fig. 6d left).”

      (5) On terminating a replay period: "At any t, the replay period ends with a probability of 0.1 or if a task-irrelevant item is reactivated." (Figure 1 caption; see also pg 18, line 635). How was the 0.1 decided upon? Also, could you please add some detail as to what a 'task-irrelevant item' would be? From what I understood, the model only learns sequences that represent the points in a track - wouldn't all the points in the track be task-relevant?

      This value was arbitrarily chosen as a small value that allows probabilistic stopping. It was not motivated by prior modeling or a systematic search. We have added: “At each timestep, the replay period ends either with a stop probability of 0.1 or if a task-irrelevant item becomes reactivated. (The choice of the value 0.1 was arbitrary; future work could explore the implications of varying this parameter).” 

      In addition, we now explain in the paper that task irrelevant items “do not appear as inputs during awake encoding, but compete with task-relevant items for reactivation during replay, simulating the idea that other experiences likely compete with current experiences during periods of retrieval and reactivation.”

      (6) Minor typos:

      Turn all instances of "nonlocal" into "non-local", or vice versa

      "For rest at the end of a run, cexternal is the context associated with the final item in the sequence. For rest at the end of a run, cexternal is the context associated with the start item." (pg 20, line 663) - I believe this is a typo and that the second sentence should begin with "For rest at the START of a run".

      We have updated the manuscript to correct these typos. 

      (7) Code availability: I may have missed it, but it doesn't seem like the code is currently available for these simulations. Including the commented code in a public repository (Github, OSF) would be very useful in this case.

      We now include a Github link to our simulation code: https://github.com/schapirolab/CMR-replay.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews: 

      Reviewer #1 (Public review): 

      Summary: 

      The manuscript by Raices et al., provides some novel insights into the role and interactions between SPO-11 accessory proteins in C. elegans. The authors propose a model of meiotic DSBs regulation, critical to our understanding of DSB formation and ultimately crossover regulation and accurate chromosome segregation. The work also emphasizes the commonalities and species-specific aspects of DSB regulation. 

      Strengths: 

      This study capitalizes on the strengths of the C. elegans system to uncover genetic interactions between a lSPO-11 accessory proteins. In combination with physical interactions, the authors synthesize their findings into a model, which will serve as the basis for future work, to determine mechanisms of DSB regulation. 

      Weaknesses: 

      The methodology, although standard, still lacks some rigor, especially with the IPs. 

      Reviewer #2 (Public review): 

      Summary: 

      Meiotic recombination initiates with the formation of DNA double-strand break (DSB) formation, catalyzed by the conserved topoisomerase-like enzyme Spo11. Spo11 requires accessory factors that are poorly conserved across eukaryotes. Previous genetic studies have identified several proteins required for DSB formation in C. elegans to varying degrees; however, how these proteins interact with each other to recruit the DSB-forming machinery to chromosome axes remains unclear. 

      In this study, Raices et al. characterized the biochemical and genetic interactions among proteins that are known to promote DSB formation during C. elegans meiosis. The authors examined pairwise interactions using yeast two-hybrid (Y2H) and co-immunoprecipitation and revealed an interaction between a chromatin-associated protein HIM-17 and a transcription factor XND-1. They further confirmed the previously known interaction between DSB-1 and SPO-11 and showed that DSB-1 also interacts with a nematodespecific HIM-5, which is essential for DSB formation on the X chromosome. They also assessed genetic interactions among these proteins, categorizing them into four epistasis groups by comparing phenotypes in double vs. single mutants. Combining these results, the authors proposed a model of how these proteins interact with chromatin loops and are recruited to chromosome axes, offering insights into the process in C. elegans compared to other organisms. 

      Weaknesses: 

      This work relies heavily on Y2H, which is notorious for having high rates of false positives and false negatives. Although the interactions between HIM-17 and XND-1 and between DSB-1 and HIM-5 were validated by co-IP, the significance of these interactions was not tested in vivo. Cataloging Y2H and genetic interactions does not yield much more insight. The model proposed in Figure 4 is also highly speculative. 

      Reviewer #3 (Public review): 

      The goal of this work is to understand the regulation of double-strand break formation during meiosis in C. elegans. The authors have analyzed physical and genetic interactions among a subset of factors that have been previously implicated in DSB formation or the number of timing of DSBs: CEP-1, DSB-1, DSB-2, DSB-3, HIM-5, HIM-17, MRE-11, REC-1, PARG-1, and XND-1. 

      The 10 proteins that are analyzed here include a diverse set of factors with different functions, based on prior analyses in many published studies. The term "Spo11 accessory factors" has been used in the meiosis literature to describe proteins that directly promote Spo11 cleavage activity, rather than factors that are important for the expression of meiotic proteins or that influence the genome-wide distribution or timing of DSBs. Based on this definition, the known SPO-11 accessory factors in C. elegans include DSB-1, DSB2, DSB-3, and the MRN complex (at least MRE-11 and RAD-50). These are all homologs of proteins that have been studied biochemically and structurally in other organisms. DSB-1 & DSB-2 are homologs of Rec114, while DSB-3 is a homolog of Mei4. Biochemical and structural studies have shown that Rec114 and Mei4 directly modulate Spo11 activity by recruiting Spo11 to chromatin and promoting its dimerization, which is essential for cleavage. The other factors analyzed in this study affect the timing, distribution, or number of RAD-51 foci, but they likely do so indirectly. As elaborated below, XND-1 and HIM-17 are transcription factors that modulate the expression of other meiotic genes, and their role in DSB formation is parsimoniously explained by this regulatory activity. The roles of HIM-5 and REC-1 remain unclear; the reported localization of HIM-5 to autosomes is consistent with a role in transcription (the autosomes are transcriptionally active in the germline, while the X chromosome is largely silent), but its loss-of-function phenotypes are much more limited than those of HIM-17 and XND-1, so it may play a more direct role in DSB formation. The roles of CEP-1 (a Rad53 homolog) and PARG-1 are also ambiguous, but their homologs in other organisms contribute to DNA repair rather than DSB formation. 

      We appreciate the reviewer’s clarification. However, the definition of Spo11 accessory factors varies across the literature. Only Keeney and colleagues define these as proteins that physically associate with and activate Spo11 to catalyze DSB formation (Keeney, Lange & Mohibullah, 2014; Lam & Keeney, 2015). In contrast, other authors have used the term more broadly to refer to proteins that promote or regulate Spo11-dependent DSB formation, without necessarily implying a direct interaction with Spo11 (e.g., Panizza et al., 2011; Robert et al., 2016; Stanzione et al., 2016; Li et al., 2021; Lange et al., 2016). Thus, our usage of the term follows this broader functional definition.

      An additional significant limitation of the study, as stated in my initial review, is that much of the analysis here relies on cytological visualization of RAD-51 foci as a proxy for DSBs. RAD-51 associates transiently with DSB sites as they undergo repair and is thus limited in its ability to reveal details about the timing or abundance of DSBs since its loading and removal involve additional steps that may be influenced by the factors being analyzed. 

      We agree with the reviewer that counting RAD-51 foci provides only an indirect measure of SPO-11–dependent DSBs, as RAD-51 marks sites of repair rather than the breaks themselves. However, we would like to clarify that our current study does not rely on RAD51 foci quantification for any of the analyses or conclusions presented. None of the figures or datasets in this manuscript are based on RAD-51 cytology. Instead, our conclusions are drawn from genetic interactions, biochemical assays, and protein–protein interaction analyses.

      The paper focuses extensively on HIM-5, which was previously shown through genetic and cytological analysis to be important for breaks on the X chromosome. The revised manuscript still claims that "HIM-5 mediates interactions with the different accessory factors sub-groups, providing insights into how components on the DNA loops may interact with the chromosome axis." The weak interactions between HIM-5 and DSB-1/2 detected in the Y2H assay do not convincingly support such a role. The idea that HIM-5 directly promotes break formation is also inconsistent with genetic data showing that him5 mutants lack breaks on the X chromosomes, while HIM-5 has been shown to be is enriched on autosomes. Additionally, as noted in my comment to the authors, the localization data for HIM-5 shown in this paper are discordant with prior studies; this discrepancy should be addressed experimentally. 

      We appreciate the reviewer’s concerns regarding the interpretation of HIM-5 function.  The weak Y2H interactions between HIM-5 and DSB-1 are not interpreted as direct biochemical evidence of a strong physical interaction, but rather as a potential point of regulatory connection between these pathways. Importantly, these Y2H data are further supported by co-immunoprecipitation experiments, genetic interactions, and the observed mislocalization of HIM-5 in the absence of DSB-1. Together, these complementary results strengthen our conclusion that HIM-5 functionally associates with DSB-promoting complexes.

      Regarding HIM-5 localization, the pattern we observe using both anti-GFP staining of the eaIs4 transgene (Phim-5::him-5::GFP) and anti-HA staining of the HIM-5::HA strain is consistent with that reported by McClendon et al. (2016), who validated the same eaIs4 transgene. Although the pattern difers slightly from Meneely et al. (2012), that used a HIM5 antibody that is no longer functional and that has been discontinued by the commercial source. In this prior study, a weak signal was detected in the mitotic region and late pachytene, but stronger signal was seen in early to mid-pachytene. Our imaging— optimized for low background and stable signal—similarly shows robust HIM-5 localization in early and mid-pachytene, supporting the reliability of our GFP and HA-tagged analyses.

      The recent analysis of DSB formation in C. elegans males (Engebrecht et al; PloS Genetics; PMID: 41124211) shows that in absence of him-5 there is a significant reduction of CO designation (measured as COSA-1 foci) on autosomes. This study strongly supports a direct and general role for HIM-5 in crossover formation— on both autosomes and on the hermaphrodite X.

      This paper describes REC-1 and HIM-5 as paralogs, based on prior analysis in a paper that included some of the same authors (Chung et al., 2015; DOI 10.1101/gad.266056.115). In my initial review I mentioned that this earlier conclusion was likely incorrect and should not be propagated uncritically here. Since the authors have rebutted this comment rather than amending it, I feel it is important to explain my concerns about the conclusions of previous study. Chung et al. found a small region of potential homology between the C. elegans rec-1 and him-5 genes and also reported that him-5; rec-1 double mutants have more severe defects than either single mutant, indicative of a stronger reduction in DSBs. Based on these observations and an additional argument based on microsynteny, they concluded that these two genes arose through recent duplication and divergence. However, as they noted, genes resembling rec-1 are absent from all other Caenorhabditis species, even those most closely related to C. elegans. The hypothesis that two genes are paralogs that arose through duplication and divergence is thus based on their presence in a single species, in the absence of extensive homology or evidence for conserved molecular function. Further, the hypothesis that gene duplication and divergence has given rise to two paralogs that share no evident structural similarity or common interaction partners in the few million years since C. elegans diverged from its closest known relatives is implausible. In contrast, DSB-1 and DSB-2 are both homologs of Rec114 that clearly arose through duplication and divergence within the Caenorhabditis lineage, but much earlier than the proposed split between REC-1 and HIM-5. Two genes that can be unambiguously identified as dsb-1 and dsb-2 are present in genomes throughout the Elegans supergroup and absent in the Angaria supergroup, placing the duplication event at around 18-30 MYA, yet DSB-1 and DSB-2 share much greater similarity in their amino acid sequence, predicted structure, and function than HIM-5 and REC-1. Further, Raices place HIM-5 and REC-1 in different functional complexes (Figure 3B). 

      We respectfully disagree with the reviewer’s characterization of the relationship between HIM-5 and REC-1. Our use of the term “paralog” follows the conclusions of Chung et al. (2015), a peer-reviewed study that provided both sequence and microsynteny evidence supporting this relationship. While we acknowledge that the degree of sequence conservation is limited, the evolutionary scenario proposed by Chung et al. remains the only published framework addressing this question. Further the degree of homology between either HIM-5 or REC-1 and the ancestral locus are similar to that observed for DSB-1 and DSB-2 with REC-114 (Hinman et al., 2021). We therefore retain the use of the term “paralog” in reference to these genes. Importantly, our conclusions regarding their distinct molecular and functional roles are independent of this classification.

      The authors acknowledge that HIM-17 is a transcription factor that regulates many meiotic genes. Like HIM-17, XND-1 is cytologically enriched along the autosomes in germline nuclei, suggestive of a role in transcription. The Reinke lab performed ChIP-seq in a strain expressing an XND-1::GFP fusion protein and showed that it binds to promoter regions, many of which overlap with the HIM-17-regulated promoters characterized by the Ahringer lab (doi: 10.1126/sciadv.abo4082). Work from the Yanowitz lab has shown that XND-1 influences the transcription of many other genes involved in meiosis (doi: 10.1534/g3.116.035725) and work from the Colaiacovo lab has shown that XND-1 regulates the expression of CRA-1 (doi: 10.1371/journal.pgen.1005029). Additionally, loss of HIM-17 or XND-1 causes pleiotropic phenotypes, consistent with a broad role in gene regulation. Collectively, these data indicate that XND-1 and HIM-17 are transcription factors that are important for the proper expression of many germline-expressed genes. Thus, as stated above, the roles of HIM-17 and XND-1 in DSB formation, as well as their effects on histone modification, are parsimoniously explained by their regulation of the expression of factors that contribute more directly to DSB formation and chromatin modification. I feel strongly that transcription factors should not be described as "SPO-11 accessory factors." 

      The ChIP analysis of XND-1 binding sites (using the XND-1::GFP transgene we provided to the Reinke lab) was performed, and Table S3 in the Ahringer paper suggests it is found at germline promoters, although the analysis is not actually provided. We completely agree that at least a subset of XND-1 functions is explained by its regulation of transcriptional targets (as we previously showed for HIM-5). However, like the MES proteins, a subset of which are also autosomal and impact X chromosome gene expression, XND-1 could also be directly regulating chromatin architecture which could have profound effects on DSB formation.  As stated in our prior comments, precedent for the involvement of a chromatin factor in DSB formation is provided by yeast Spp1. 

      Recommendations for the authors: 

      Editor comments: 

      As you can see, the reviewers have additional comments, and the authors can include revisions to address those points prior to publicizing 'a version of record' (e.g. hatching rate assay mentioned by reviewer #1). This type of study, trying to catalog interactions of many factors, inevitably has loose ends, but in my opinion, it does not reduce the value of the study, as long as statements are not misleading. I suggest that the authors address issues by making changes to the main text. After the next round of adjustments by authors, I feel that it will be ready for a version of record, based on the spirit of the current eLife publication model. 

      Reviewer #1 (Recommendations for the authors): 

      I still have concerns about the HIM-17 IP and immunoblot probing with XND-1 antibodies. While the newly provided whole extract immunoblot clearly shows a XND-1 specific band that goes away in the mutant extracts, there is additional bands that are recognized - the pattern looks different than in the input in Figure 1B. Additionally, there is still a band of the corresponding size in the IPs from extracts not containing the tagged allele of HIM-17, calling into question whether XND-1 is specifically pulled down. 

      The authors did not include the hatching rate as pointed out in the original reviews. In the rebuttal: 

      "Great question. I guess we need to do this while back out for review. If anyone has suggestions of what to say here. Clearly we overlooked this point but do have the strain." 

      We thank the reviewer for this suggestion. We had intended to include a hatching analysis; however, during the course of this work we discovered that our him-17 stock had acquired an additional linked mutation(s) that altered its phenotype and led to inconsistent results. This strain was used to rederive the him-17; eaIs4 double mutant after our original did not survive freeze/thaw. Given the abnormal behavior observed in this line, we concluded that proceeding with the hatching assays could yield unreliable data. We are currently reestablishing a verified him-17 strain, but in the interest of accuracy and reproducibility, we have restricted our analysis in this manuscript to validated datasets derived from confirmed strains.

      Reviewer #2 (Recommendations for the authors): 

      The authors have addressed most of the previous concerns and substantially improved the manuscript. The new data demonstrate that HIM-5 localization depends on DSB-1, and together with the Y2H and Co-PI results, strengthen the link between HIM-5 and the DSBforming machinery in C. elegans. The remaining points are outlined below: 

      Specific comments: 

      The font size of texts and labels in the Figure is very small and is hardly legible. Please enlarge them and make them clearly visible (Fig 1A, 1B, 2A, 2B, 2C, 2D, 2E, 3A, 3B, 3C, 3D, 3F)

      Done

      Although the authors have addressed the specificity of the XND-1 antibody, it remains unclear whether the boxed band is specific to the him-17::3xHA IP, since the same band appears in the control IP, albeit with lower intensity (Fig 1B). Is the ~100 kDa band in the him-17::3xHA IP a modified form XND-1? While antibody specificity was previously demonstrated by IF using xnd-1 mutants, it would be ideal to confirm this on a western blot as well. 

      A Western Blot performed using whole cell extracts and probed with the anti- XND-1 antibody has been provided in the revised version of the manuscript (Fig. S1A). This confirms that the antibody specifically recognizes XND-1 protein. We believe that the ~100 kDa band mentioned by the reviewer is likely to be a non-specific cross reaction band detected by the antibody, since an identical band of the same mW was also detected in xnd-1 null mutants (Fig. S1A).

      Regarding the IP negative controls, we are firmly convinced the boxed band to be specific, and the fact that a (very) low intensity band is also found in the negative control should not infringe the validity of the HIM-17-XND-1 specific interaction. There is a constellation of similar examples present across the literature, as it is widely acknowledged amongst biochemists that some proteins may “stick” to the beads due their intrinsic biochemical properties despite usage of highly stringent IP buffers. However, the high level of enrichment detected in the IP (as also underlined by the reviewer) corroborates that XND-1 specifically immunoprecipitates with HIM-17 despite a low, non-specific binding to the HA beads is present. If interaction between XND-1 and HIM-17 was non-specific, we logically would have found the band in the IP and the band in the negative control to be of very similar intensity, which is clearly not the case. 

      Although co-IP assays are generally considered not a strictly quantitative assay, we want to emphasize that a comparable amount of nuclear extract was employed in both samples as also evidenced by the inputs, in which it is also possible to see that if anything, slightly less  nuclear extracts were employed in the him-17::3xHA; him-5::GFP::3xFLAG vs. the him5::GFP::3xFLAG negative control, corroborating the above mentioned points.

      Lastly, it is crucial to mention that mass spectrometry analyses performed on HIM17::3xHA pulldowns show XND-1 as a highly enriched interacting protein (Blazickova et al.; 2025 Nature Comms.), which strongly supports our co-IP results.

      The subheading "HIM-5 is the essential factor for meiotic breaks in the X chromosome" does not accurately represent the work described in the Results or in Figure 1. I disagree with the authors' response to the earlier criticism. The issue is not merely semantic. The data do not demonstrate that HIM-5 is required for DSB formation on the X chromosome - this conclusion can only be inferred. What Figure 1 shows is that XND-1 and HIM-17 interact, and that pie-1p-driven HIM-5 expression can partially rescue meiotic defects of him-17 mutants. This supports the conclusion that him-5 is a target of HIM-17/XND-1 in promoting CO formation on the X chromosome. However, the data provide no direct evidence for the claim stated in the subheading. I strongly encourage authors to revise the subheading to more accurately represent the findings presented in the paper. 

      After considering the reviewer’s comments, we have revised the subheading to more accurately describe our findings.

      In Fig1C, please fix the typo in the last row - "pie1p::him5-::GFP" to "pie-1p::him- 5::GFP".

      Done

      In Fig 2C, "p" is missing from the label on the right for Phim-5::him-5::GFP.

      Done

      In Fig 3I, bring the labels (DSB-1/2/3) at the lower right to the front.

      Done

      In Concluding Remarks, please fix the typo "frequently".

      Done

      Reviewer #3 (Recommendations for the authors): 

      The experiments that analyze HIM-5 in dsb-1 mutants should be repeated using antibodies against the endogenous HIM-5 antibody, and localization of the HIM-5::HA and HIM-5::GFP proteins should be compared directly to antibody staining. This work uses an epitopetagged protein and a GFP-tagged protein to analyze the localization of HIM-5, while prior work (Meneely et al., 2012) used an antibody against the endogenous protein. In Figures 2 and S4 of this paper, neither HIM-5::HA nor HIM-5::GFP appears to localize strongly to chromatin, and autosomal enrichment of HIM-5, as previously reported for the endogenous protein based on antibody staining, is not evident. Moreover, HIM-5::GFP and HIM-5::HA look different from each other, and neither resembles the low-resolution images shown in Figure 6 in Meneely et al 2012, which showed nuclear staining throughout the germline, including in the mitotic zone, and also in somatic sheath cells. Given the differences in localization between the tagged transgenes and the endogenous protein, it is important to analyze the behavior of the endogenous, untagged protein. A minor issue: a wild-type control should also be shown for HIM-5::HA in Figure S4. 

      Wild type control added to figure S4

      Evidence that XND-1 and HIM-17 form a complex is weak; it is supported by the Y2H and co-IP data but opposed by functional analysis or localization. The diversity of proteins found in the Co-IP of HIM-17::GFP (Table S2) indicate that these interactions are unlikely to be specific. The independent localization of these proteins to chromatin is clear evidence that they do not form an obligate complex; additionally, they have been found to regulate distinct (although overlapping) sets of genes. The predicted structure generated by Alphafold3 has very low confidence and should not be taken as evidence for an interaction.The newly added argument about the lack of apparently overlap between HIM-17 and XND1 due to the distance between the HA tag on HIM-17 and XND-1 is flawed and should be removed - the extended C-terminus in the predicted AlphaFold3 C-terminus of HIM-17 has been interpreted as if it were a structured domain. Moreover, the predicted distance of 180 Å (18 nm) is comparable to the distance between a fluorophore on a secondary antibody and the epitope recognized by the primary antibody (~20-25 nm) and is far below than the resolution limit of light microscopy. 

      We appreciate the reviewer’s thoughtful comment. The evidence supporting a physical interaction between XND-1 and HIM-17 is not only shown by our co-IP experiments, but it has also been recently shown in an independent study where MS analyses were conducted on HIM-17::3xHA pull downs to identify novel HIM-17 interactors (Blazickova et al.; 2025 Nature Comms). As shown in the data provided in this study, also under these experimental settings XND-1 was identified as a highly enriched putative HIM-17 interactor. We do acknowledge that their chromatin localization patterns are distinct and they regulate overlapping but not identical sets of genes, however, it is worth noting that protein–protein interactions in meiosis are often transient or context-dependent, and may not necessarily result in co-localization detectable by microscopy. In line with this, in the same work cited above, a similar situation for BRA-2 and HIM-17 was reported, as they were shown to interact biochemically despite the absence of overlapping staining patterns. 

      Minor issues: 

      The images shown in Panel D in Figure 1 seem to have very different resolutions; the HTP3/HIM-17 colocalization image is particularly blurry/low-resolution and should be replaced. The contrast between blue and green cannot be seen clearly; colors with stronger contrast should be used, and grayscale images should also be shown for individual channels. High-resolution images should probably be included for all of the factors analyzed here to facilitate comparisons.

    1. Author response:

      Reviewer #1:

      We thank the reviewer for this important point. Beyond long reaction times, we did not originally exclude participants based on low EMA variability. We agree this is a relevant concern, particularly given the need to add small random noise to some EMA series for model convergence. In the revised manuscript, we will assess additional indicators of careless responding, including within-person EMA variability (e.g., standard deviation or proportion of modal responses) following Jaso et al., 2022 criteria. We will conduct sensitivity analyses excluding low-variability responses or participants and report whether these checks affect the robustness of the results. We will also clarify in the Discussion that minimal EMA variance may reflect either true affective stability or reduced engagement, and discuss how this ambiguity may affect interpretation.

      Reviewer #2:

      We thank the reviewer for raising this fundamental conceptual concern. We agree that more research is needed to fully understand the processes captured by DQRT. In the revised manuscript, we will more clearly reference and summarize prior validation work from our lab providing strong support for a cognitive characterization of DQRT as a measure of cognitive processing speed, while also explicitly acknowledging potential confounds and limitations (Teckentrup et al., 2025). We will clarify that our DQRT computation followed those validated procedures, including exclusion of extreme values above the sample-specific median + 2 SD. In addition, consistent with Reviewer #1’s comment, we will expand the Discussion of how potential careless responding and non-cognitive factors may influence DQRT. We will further tone down language implying causal inference.

      References

      Jaso, B. A., Kraus, N. I., & Heller, A. S. (2022). Identification of careless responding in ecological momentary assessment research: From posthoc analyses to real-time data monitoring. Psychological Methods, 27(6), 958.

      Teckentrup, V., Rosická, A. M., Donegan, K. R., Gallagher, E., Hanlon, A. K., & Gillan, C. M. (2025). Digital questionnaire response time (DQRT): A ubiquitous and low-cost digital assay of cognitive processing speed. Behavior Research Methods, 57(7), 200.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews: 

      Reviewer #1 (Public review): 

      Petrovic et al. investigate CCR5 endocytosis via arrestin 2, with a particular focus on clathrin and AP2 contributions. The study is thorough and methodologically diverse. The NMR titration data clearly demonstrate chemical shift changes at the canonical clathrin-binding site (LIELD), present in both the 2S and 2L arrestin splice variants. 

      To assess the effect of arrestin activation on clathrin binding, the authors compare: truncated arrestin (1-393), full-length arrestin, and 1-393 incubated with CCR5 phosphopeptides. All three bind clathrin comparably, whereas controls show no binding. These findings are consistent with prior crystal structures showing peptide-like binding of the LIELD motif, with disordered flanking regions. The manuscript also evaluates a non-canonical clathrin binding site specific to the 2L splice variant. Though this region has been shown to enhance beta2-adrenergic receptor binding, it appears not to affect CCR5 internalization. 

      Similar analyses applied to AP2 show a different result. AP2 binding is activation-dependent and influenced by the presence and level of phosphorylation of CCR5-derived phosphopeptides. These findings are reinforced by cellular internalization assays. 

      In sum, the results highlight splice-variant-dependent effects and phosphorylation-sensitive arrestin-partner interactions. The data argue against a (rapidly disappearing) one-size-fitsall model for GPCR-arrestin signaling and instead support a nuanced, receptor-specific view, with one example summarized effectively in the mechanistic figure.

      We thank the referee for this positive assessment of our manuscript. Indeed, by stepping away from the common receptor models for understanding internalization (b2AR and V2R), we revealed the phosphorylation level of the receptor as a key factor in driving the sequestration of the receptor from the plasma membrane. We hope that the proposed mechanistic model will aid further studies to obtain an even more detailed understanding of forces driving receptor internalization.

      Weaknesses: 

      Figure 1 shows regions alphaFold model that are intrinsically disordered without making it clear that this is not an expected stable position. The authors NMR titration data are n=1. Many figure panels require that readers pinch and zoom to see the data.

      In the “Recommendations for the Authors” section, we addressed the reviewer’s stated weaknesses. In short, for the AlphaFold representation in Figure 1A, we added explicit labeling and revised the legend and main text to clearly state that the depicted loops are intrinsically disordered, absent from crystal structures due to flexibility, and shown only for visualization of their location. We also clarified that the NMR titration experiments inherently have n = 1 due to technical limitations, and that this is standard practice in the field, while ensuring individual data points remain visible. The supplementary NMR figures now have more vibrant coloring, allowing easier data assessment. However, we have not changed the zooming of the microscopy and NMR spectra. We believe that the presentation of microscopy data, which already show zoomed-in regions of interest, follow standard practices in the field. Furthermore, we strongly believe that we should display full NMR spectra in the supplementary figures to allow the reader to assess the overall quality and behavior. As indicated previously, the reader can zoom in to very high resolution, since the spectra are provided by vector graphics. Zoomed regions of the relevant details are provided in the main figures.

      Reviewer #2 (Public review): 

      Summary: 

      Based on extensive live cell assays, SEC, and NMR studies of reconstituted complexes, these authors explore the roles of clathrin and the AP2 protein in facilitating clathrin mediated endocytosis via activated arrestin-2. NMR, SEC, proteolysis, and live cell tracking confirm a strong interaction between AP2 and activated arrestin using a phosphorylated C-terminus of CCR5. At the same time a weak interaction between clathrin and arrestin-2 is observed, irrespective of activation. 

      These results contrast with previous observations of class A GPCRs and the more direct participation by clathrin. The results are discussed in terms of the importance of short and long phosphorylated bar codes in class A and class B endocytosis. 

      Strengths: 

      The 15N,1H and 13C,methyl TROSY NMR and assignments represent a monumental amount of work on arrestin-2, clathrin, and AP2. Weak NMR interactions between arrestin-2 and clathrin are observed irrespective of activation of arrestin. A second interface, proposed by crystallography, was suggested to be a possible crystal artifact. NMR establishes realistic information on the clathrin and AP2 affinities to activated arrestin with both kD and description of the interfaces.

      We sincerely thank the referee for this encouraging evaluation of our work and appreciate the recognition of the NMR efforts and insights into the arrestin–clathrin–AP2 interactions.

      Weaknesses: 

      This reviewer has identified only minor weaknesses with the study. 

      (1) I don't observe two overlapping spectra of Arrestin2 (1393) +/- CLTC NTD in Supp Figure 1

      We believe the referee is referring to Figure 1 – figure supplement 2. We have now made the colors of the spectra more vibrant and used different contouring to make the differences between the two spectra clearer. The spectra are provided as vector graphics, which allows zooming in to the very fine details.

      (2) Arrestin-2 1-418 resonances all but disappear with CCR5pp6 addition. Are they recovered with Ap2Beta2 addition and is this what is shown in Supp Fig 2D

      We believe the reviewer is referring to Figure 3 - figure supplement 1. In this figure, the panels E and F show resonances of arrestin2<sup>1-418</sup> (apo state shown with black outline) disappear upon the addition of CCR5pp6 (arrestin2<sup>1-418</sup>•CCR5pp6 complex spectrum in red). The panels C and D show resonances of arrestin2<sup>1-418</sup> (apo state shown with black outline), which remain unchanged upon addition of AP2b2 <sup>701-937</sup> (orange), indicating no complex formation. We also recorded a spectrum of the arrestin2<sup>1-418</sup>•CCR5pp6 complex under addition of AP2b2 <sup>701-937</sup> (not shown), but the arrestin2 resonances in the arrestin2<sup>1-418</sup> •CCR5pp6 complex were already too broad for further analysis. This had been already explained in the text.

      “In agreement with the AP2b2 NMR observations, no interaction was observed in the arrestin2 methyl and backbone NMR spectra upon addition of AP2b2 in the absence of phosphopeptide (Figure 3-figure supplement 1C, D). However, the significant line broadening of the arrestin2 resonances upon phosphopeptide addition (Figure 3-figure supplement 1E, F) precluded a meaningful assessment of the effect of the AP2b2 addition on arrestin2 in the presence of phosphopeptide”.

      (3) I don't understand how methyl TROSY spectra of arrestin2 with phosphopeptide could look so broadened unless there are sample stability problems?

      We thank the referee for this comment. We would like to clarify that in general a broadened spectrum beyond what is expected from the rotational correlation time does not necessarily correlate with sample stability problems. It is rather evidence of conformational intermediate exchange on the micro- to millisecond time scale.

      The displayed <sup>1</sup>H-<sup>15</sup>N spectra of apo arrestin2 already suffer from line broadening due to such intrinsic mobility of the protein. These spectra were recorded with acquisition times of 50 ms (<sup>15</sup>N) and 55 ms (<sup>1</sup>H) and resolution-enhanced by a 60˚-shifted sine-bell filter for <sup>15</sup>N and a 60˚-shifted squared sine-bell filter for <sup>1</sup>H, respectively, which leads to the observed resolution with still reasonable sensitivity. The <sup>1</sup>H-<sup>15</sup>N resonances in Fig. 1b (arrestin2<sup>1-393</sup>) look particularly narrow. However, this region contains a large number of flexible residues. The full spectrum, e.g. Figure 1-figure supplement 2, shows the entire situation with a clear variation of linewidths and intensities. The linewidth variation becomes stronger when omitting the resolution enhancement filters.

      The addition of the CCR5pp6 phosphopeptide does not change protein stability, which we assessed by measuring the melting temperature of arrestin2<sup>1-418</sup> and arrestin2<sup>1-418</sup>•CCR5pp6 complex (Tm = 57°C in both cases). We believe that the explanation for the increased broadening of the arrestin2 resonances is that addition of the CCR5pp6, possibly due to the release of the arrestin2 strand b20, amplifies the mentioned intermediate timescale protein dynamics. This results in the disappearance of arrestin2 resonances.

      We have now included the assessment of arrestin2<sup>1-418</sup> and arrestin2<sup>1-418</sup>•CCR5pp6 stability in the manuscript:

      “The observed line broadening of arrestin2 in the presence of phosphopeptide must be a result of increased protein motions and is not caused by a decrease in protein stability, since the melting temperature of arrestin2 in the absence and presence of phosphopeptide are identical (56.9 ± 0.1 °C)”.

      (4) At one point the authors added excess fully phosphorylated CCR5 phosphopeptide (CCR5pp6). Does the phosphopeptide rescue resolution of arrestin2 (NH or methyl) to the point where interaction dynamics with clathrin (CLTC NTD) are now more evident on the arrestin2 surface?

      Unfortunately, when we titrate arrestin2 with CCR5pp6 (please see Isaikina & Petrovic et. al, Mol. Cell, 2023 for more details), the arrestin2 resonances undergo fast-to-intermediate exchange upon binding. In the presence of phosphopeptide excess, very few resonances remain, the majority of which are in the disordered region, including resonances from the clathrin-binding loop. Due to the peak overlap, we could not unambiguously assign arrestin2 resonances in the bound state, which precluded our assessment of the arrestin2-clathrin interaction in the presence of phosphopeptide. We have made this now clearer in the paragraph ‘The arrestin2-clathrin interaction is independent of arrestin2 activation’

      “Due to significant line broadening and peak overlap of the arrestin2 resonances upon phosphopeptide addition, the influence of arrestin activation on the clathrin interaction could not be detected on either backbone or methyl resonances “.

      (5) Once phosphopeptide activates arrestin-2 and AP2 binds can phosphopeptide be exchanged off? In this case, would it be possible for the activated arrestin-2 AP2 complex to re-engage a new (phosphorylated) receptor?

      This would be an interesting mechanism. In principle, this should be possible as long as the other (phosphorylated) receptor outcompetes the initial phosphopeptide with higher affinity towards the binding site. However, we do not have experiments to assess this process directly. Therefore, we rather wish not to further speculate.

      (6) I'd be tempted to move the discussion of class A and class B GPCRs and their presumed differences to the intro and then motivate the paper with specific questions. 

      We appreciate the referee’s suggestion and had a similar idea previously. However, as we do not have data on other class-A or class-B receptors, we rather don’t want to motivate the entire manuscript by this question.

      (7) Did the authors ever try SEC measurements of arrestin-2 + AP2beta2+CCR5pp6 with and without PIP2, and with and without clathrin (CLTC NTD? The question becomes what the active complex is and how PIP2 modulates this cascade of complexation events in class B receptors.

      We thank the referee for this question. Indeed, we tested whether PIP2 can stabilize the arrestin2•CCR5pp6•AP2 complex by SEC experiments. Unfortunately, the addition of PIP2 increased the formation of arrestin2 dimers and higher oligomers, presumably due to the presence of additional charges. The resolution of SEC experiments was not sufficient to distinguish arrestin2 in oligomeric form or in arrestin2•CCR5pp6•AP2 complex. We now mention this in the text:

      “We also attempted to stabilize the arrestin2-AP2b2-phosphopetide complex through the addition of PIP2, which can stabilize arrestin complexes with the receptor (Janetzko et al., 2022). The addition of PIP2 increased the formation of arrestin2 dimers and higher oligomers, presumably due to the presence of additional charges. Unfortunately, the resolution of the SEC experiments was not sufficient to separate the arrestin2 oligomers from complexes with AP2b2”.

      Reviewer #3 (Public review): 

      Summary: 

      Overall, this is a well-done study, and the conclusions are largely supported by the data, which will be of interest to the field. 

      Strengths: 

      Strengths of this study include experiments with solution NMR that can resolve high-resolution interactions of the highly flexible C-terminal tail of arr2 with clathrin and AP2. Although mainly confirmatory in defining the arr2 CBL376LIELD380 as the clathrin binding site, the use of the NMR is of high interest (Fig. 1). The 15N-labeled CLTC-NTD experiment with arr2 titrations reveals a span from 39-108 that mediates an arr2 interaction, which corroborates previous crystal data, but does not reveal a second area in CLTC-NTD that in previous crystal structures was observed to interact with arr2. 

      SEC and NMR data suggest that full-length arr2 (1-418) binding with 2-adaptin subunit of AP2 is enhanced in the presence of CCR5 phospho-peptides (Fig. 3). The pp6 peptide shows the highest degree of arr2 activation, and 2-adaptin binding, compared to less phosphorylated peptide or not phosphorylated at all. It is interesting that the arr2 interaction with CLTC NTD and pp6 cannot be detected using the SEC approach, further suggesting that clathrin binding is not dependent on arrestin activation. Overall, the data suggest that receptor activation promotes arrestin binding to AP2, not clathrin, suggesting the

      AP2 interaction is necessary for CCR5 endocytosis. 

      To validate the solid biophysical data, the authors pursue validation experiments in a HeLa cell model by confocal microscopy. This requires transient transfection of tagged receptor (CCR5-Flag) and arr2 (arr2-YFP). CCR5 displays a "class B"-like behavior in that arr2 is rapidly recruited to the receptor at the plasma membrane upon agonist activation, which forms a stable complex that internalizes onto endosomes (Fig. 4). The data suggest that complex internalization is dependent on AP2 binding not clathrin (Fig. 5). 

      The addition of the antagonist experiment/data adds rigor to the study. 

      Overall, this is a solid study that will be of interest to the field.

      We thank the referee for the careful and encouraging evaluation of our work. We appreciate the recognition of the solidity of our data and the support for our conclusions regarding the distinct roles of AP2 and clathrin in arrestin-mediated receptor internalization.

      Recommendations for the authors: 

      Reviewer #1 (Recommendations for the authors): 

      I believe that the authors have made efforts to improve the accessibility to a broader audience. In a few cases, I believe that the authors response either did not truly address the concern or made the problem worse. I am grouping these as 'very strong opinions' and 'sticking point'. 

      Very strong opinion 1: 

      While data presentation is somewhat at the authors discretion, there were several figures where the presentation did not make the work approachable, including microscopy insets and NMR spectra. A suggestion to 'pinch and zoom' does not really address this. For the overlapping NMR spectra in supporting Figure 1, I actually -can- see this on zooming, but I did not recognize this on first pass because the colors are almost identical for the two spectra. This is an easy fix. Changing the presentation by coloring these distinctly would alleviate this. The Supplemental figure to Fig. 2 looks strange with pinch and zoom. But at the end of the day, data presentation where the reader is to infer that they must zoom in is not very approachable and may prevent readers from being able to independently assess the data. In this case, there doesn't seem to be a strong rationale to not make these panels easier to see at 100% size. 

      We appreciate the reviewer’s thoughtful comments regarding figure accessibility and agree that data presentation should be clear and interpretable without requiring readers to zoom in extensively. However, we must note that the presentation of the microscopy data follows standard practices in the field and that the panels already include zoomed-in regions, which enable easier access to key results and observations.

      Regarding the NMR data, we have revised Figure 1—figure supplement 2 and Figure 2— figure supplement 1 to match the presentation style of Figure 3—figure supplement 1, which the reviewer apparently found more accessible. We also made the colors of the spectra more vibrant, as the referee suggested. We would like to emphasize that it is absolutely necessary to display the full NMR spectra in order to allow independent assessment of signal assignment, data quality, and overall protein behavior. Zoomed regions of the relevant details are provided in the main figures.

      Very strong opinion 2: 

      The author's response to lack of individual data points and error bars is that this is an n=1 experiment. I do not believe this meets the minimum standard for best practices in the field.

      We respectfully disagree with the reviewer’s assessment. The Figure already displays individual data points, as shown already in the initial submission. Performing NMR titrations with isotopically labeled protein samples is inherently resource-intensive, and single-sample (n = 1) experiments are widely accepted and routinely reported in the field. Numerous studies have used the same approach, including Rosenzweig et al., Science (2013); Nikolaev et al., Nat. Methods (2019); and Hobbs et al., J. Biomol. NMR (2022), as well as our own recent work (Isaikina & Petrovic et al., Mol. Cell, 2023). These studies demonstrate that such NMR-based affinity measurements, even when performed on a single sample, are highly reproducible, precise, and consistent with orthogonal evidence and across different sample conditions.

      Sticking point:

      Figure 1A - the alphaFold model of arrestin2L depicts the disordered loops as ordered. The depiction is misleading at best, and inaccurate in truth. To use an analogy, what the authors depict is equivalent to publishing an LLM hallucination in the text. Unlike LLMs, alphaFold will actually flag its hallucination with the confidence (pLDDT) in the output. Both for LLMs and for alphaFold, we are spending much time teaching our students in class how to use computation appropriately - both to improve efficiency but also to ensure accuracy by removing hallucinations.

      The original review indicated that confidences needed to be shown and that this needed to be depicted in a way that clarifies that this is NOT a structural state of the loops. The newly added description ("The model was used to visualize the clathrin-binding loop and the 344-loop of the arrestin2 Cdomain, which are not detected in the available crystal structures...) worsens the concern because it even more strongly implies that a 0 confidence computational output is a likely structural state. It also indicates that these regions were 'not detected' in crystal structures. These regions of arrestin are intrinsically disordered. AlphaFold (by it's nature) must put out something in terms of coordinates, even if the pLDDT suggests that the region cannot be predicted or is not in a stable position, which is the case here. In crystal structures, these regions are not associated with interpretable electron density, meaning that coordinates are omitted in these regions because adding them would imply that under the conditions used, the protein adopts a low energy structural state in this region. This region is instead intrinsically disordered. 

      A good description of why showing disordered loops in a defined position is incorrect and how to instead depict disorder correctly is in Brotzakis et al. Nat communications 16, 1632 (2025) "AlphaFold prediction of structural ensembles of disordered proteins", where figures 3A, 4A, and 5A show one AlphaFold prediction colored by confidence and 3B, 4B and 5B are more accurate depictions of the structural ensemble. 

      Coming back to the original comment "The AlphaFold model could benefit from a more transparent discussion of prediction confidence and caveats. The younger crowd (part of the presumed intended readership) tends to be more certain that computational output is 'true'...." Right now, the authors are still showing in Fig 1A a depiction of arrestin with models for the loops that are untrue. They now added text indicating that these loops are visualized in an AlphaFold prediction and 'true' but 'not detected in crystal structures'. There is no indication in the text that these are intrinsically disordered. The lack of showing the pLDDT confidence and the lack of any indication that these are disordered regions is simply incorrect. 

      We appreciate the concern of the reviewer towards AlphaFold models. As NMR spectroscopists we are highly aware of intrinsic biomolecular motions. However, our AlphaFold2 model is used as a graphical representation to display the interaction sites of loops; it is not intended to depict the loops as fixed structural states. The flexibility of the loops had been clearly described in the main text before:

      “Arrestin2 consists of two consecutive (N- and C-terminal) β-sandwich domains (Figure 1A), followed by the disordered clathrin-binding loop (CBL, residues 353–386), strand b20 (residues 386–390), and a disordered C-terminal tail after residue 393”.

      and

      “Figure 1B depicts part of a 1H-15N TROSY spectrum (full spectrum in Figure 1-figure supplement 2A) of the truncated 15N-labeled arrestin2 construct arrestin21-393 (residues 1393), which encompasses the C-terminal strand β20, but lacks the disordered C-terminal tail. Due to intrinsic microsecond dynamics, the assignment of the arrestin21-393 1H-15N resonances by triple resonance methods is largely incomplete, but 16 residues (residues 367381, 385-386) within the mobile CBL could be assigned. This region of arrestin is typically not visible in either crystal or cryo-EM structures due to its high flexibility”.

      as well as in the legend to Figure 1:

      “The model was used to visualize the clathrin-binding loop and the 344-loop of the arrestin2 C-domain, which are not detected in the available crystal structures of apo arrestin2 [bovine: PDB 1G4M (Han et al., 2001), human: PDB 8AS4 (Isaikina et al., 2023)]. In the other structured regions, the model is virtually identical to the crystal structures”.

      We have now further added a label ‘AlphaFold2 model’ to Figure 1A and amended the respective Figure legend to

      “The model was used to visualize the clathrin-binding loop and the 344-loop of the arrestin2 C-domain, which are not detected in the available crystal structures of apo arrestin2 [bovine: PDB 1G4M (Han et al., 2001), human: PDB 8AS4 (Isaikina et al., 2023)] due to flexibility. In the other structured regions, the model is virtually identical to the crystal structures”.

      Reviewer #2 (Recommendations for the authors): 

      I appreciated the response by the authors to all of my questions. I have no further comments

      We thank the referee for the raised questions, which we believe have improved the quality of the manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Because the "source" and "target" tasks are merely parameter variations of the same paradigm, it is unclear whether EIDT achieves true crosstask transfer. The manuscript provides no measure of how consistent each participant's behaviour is across these variants (e.g., two- vs threestep MDP; easy vs difficult MNIST). Without this measure, the transfer results are hard to interpret. In fact, Figure 5 shows a notable drop in accuracy when transferring between the easy and difficult MNIST conditions, compared to transfers between accuracy-focused and speedfocused conditions. Does this discrepancy simply reflect larger withinparticipant behavioural differences between the easy and difficult settings? A direct analysis of intra-individual similarity for each task pair and how that similarity is related to EIDT's transfer performance is needed.

      Thank you for your insightful comment. We agree that the tasks used in our study are variations of the same paradigm. Accordingly, we have revised the manuscript to consistently frame our findings as demonstrating individuality transfer "across task conditions" rather than "across distinct tasks."

      In response to your suggestion, we have conducted a new analysis to directly investigate the relationship between individual behavioural patterns and transfer performance. As show in the new Figures 4, 11, S8, and S9, we found a clear relationship between the distance in the space of individual latent representation (called individuality index in the previous manuscript) and prediction performance. Specifically, prediction accuracy for a given individual's behaviour degrades as the latent representation of the model's source individual becomes more distant. This result directly demonstrates that our framework captures meaningful individual differences that are predictive of transfer performance across conditions.

      We have also expanded the Discussion (Lines 332--343) to address the potential for applying this framework to more structurally distinct tasks, hypothesizing that this would rely on shared underlying cognitive functions.

      Related to the previous comment, the individuality index is central to the framework, yet remains hard to interpret. It shows much greater within-participant variability in the MNIST experiment (Figure S1) than in the MDP experiment (Figure 3). Is such a difference meaningful? It is hard to know whether it reflects noisier data, greater behavioural flexibility, or limitations of the model.

      Thank you for raising this important point about interpretability. To enhance the interpretability of the individual latent representation, we have added a new analysis for the MDP task (see Figures 6 and S4). By applying our trained encoder to data from simulated Q-learning agents with known parameters, we demonstrate that the dimensions of the latent space systematically map onto the agents' underlying cognitive parameters (learning rate and inverse temperature). This analysis provides a clearer interpretation by linking our model's data-driven representation to established theoretical constructs.

      Regarding the greater within-participant variability observed in the MNIST task (visualized now in Figure S7), this could be attributed to several factors, such as greater behavioural flexibility in the perceptual task. However, disentangling these potential factors is complex and falls outside the primary scope of the current study, which prioritizes demonstrating robust prediction accuracy across different task conditions.

      The authors suggests that the model's ability to generalize to new participants "likely relies on the fact that individuality indices form clusters and individuals similar to new participants exist in the training participant pool". It would be helpful to directly test this hypothesis by quantifying the similarity (or distance) of each test participant's individuality index to the individuals or identified clusters within the training set, and assessing whether greater similarity (or closer proximity) to the clusters in the training set is associated with higher prediction accuracy for those individuals in the test set.

      Thank you for this excellent suggestion. We have performed the analysis you proposed to directly test this hypothesis. Our new results, presented in Figures 4, 11, S5, S8, and S9, quantify the distance between the latent representation of a test participant and that of the source participant used to generate the prediction model.

      The results show a significant negative correlation: prediction accuracy consistently decreases as the distance in the latent space increases. This confirms that generalization performance is directly tied to the similarity of behavioural patterns as captured by our latent representation, strongly supporting our hypothesis.

      Reviewer #2 (Public review):

      The MNIST SX baseline appears weak. RTNet isn't directly comparable in structure or training. A stronger baseline would involve training the GRU directly on the task without using the individuality index-e.g., by fixing the decoder head. This would provide a clearer picture of what the index contributes.

      We agree that a more direct baseline is crucial for evaluating the contribution of our transfer mechanism. For the Within-Condition Prediction scenario, the comparison with RTNet was intended only to validate that our task solver architecture could achieve average humanlevel task performance (Figure 7).

      For the critical Cross-Condition Transfer scenario, we have now implemented a stronger and more appropriate baseline, which we call ``task solver (source).'' This model has the same architecture as our EIDT task solver but is trained directly on the source task data of the specific test participant. As shown in revised Figure 9, our EIDT framework significantly outperforms this direct-training approach, clearly demonstrating the benefit of the individuality transfer mechanism.

      Although the focus is on prediction, the framework could offer more insight into how behaviour in one task generalizes to another. For example, simulating predicted behaviours while varying the individuality index might help reveal what behavioural traits it encodes.

      Thank you for this valuable suggestion. To provide more insight into the encoded behavioural traits, we have conducted a new analysis linking the individual latent representation to a theoretical cognitive model. As detailed in the revised manuscript (Figures 6 and S4), we applied our encoder to simulated data from Q-learning agents with varying parameters. The results show a systematic relationship between the latent space coordinates and the agents' learning rates and inverse temperatures, providing a clearer interpretation of what the representation captures.

      It's not clear whether the model can reproduce human behaviour when acting on-policy. Simulating behaviour using the trained task solver and comparing it with actual participant data would help assess how well the model captures individual decision tendencies.

      We have added the suggested on-policy evaluation (Lines 195--207). In the revised manuscript (Figure 5), we present results from simulations where the trained task solvers performed the MDP task. We compared their performance (total reward and rate of the highly-rewarding action selected) against their corresponding human participants. The strong correlations observed demonstrate that our model successfully captures and reproduces individual-specific behavioural tendencies in an onpolicy setting.

      Figures 3 and S1 aim to show that individuality indices from the same participant are closer together than those from different participants. However, this isn't fully convincing from the visualizations alone. Including a quantitative presentation would help support the claim.

      We agree that the original visualizations of inter- and intraparticipant distances was not sufficiently convincing. We have therefore removed that analysis. In its place, we have introduced a more direct and quantitative analysis that explicitly links the individual latent representation to prediction performance (see Figures 4, 11, S5, S8, and S9). This new analysis demonstrates that prediction error for an individual is a function of distance in the latent space, providing stronger evidence that the representation captures meaningful, individual-specific information.

      The transfer scenarios are often between very similar task conditions (e.g., different versions of MNIST or two-step vs three-step MDP). This limits the strength of the generalization claims. In particular, the effects in the MNIST experiment appear relatively modest, and the transfer is between experimental conditions within the same perceptual task. To better support the idea of generalizing behavioural traits across tasks, it would be valuable to include transfers across more structurally distinct tasks.

      We agree with this limitation and have revised the manuscript to be more precise. We now frame our contribution as "individuality transfer across task conditions" rather than "across tasks" to accurately reflect the scope of our experiments. We have also expanded the Discussion section (Line 332-343) to address the potential and challenges of applying this framework to more structurally distinct tasks, noting that it would likely depend on shared underlying cognitive functions.

      For both experiments, it would help to show basic summaries of participants' behavioural performance. For example, in the MDP task, first-stage choice proportions based on transition types are commonly reported. These kinds of benchmarks provide useful context.

      We have added behavioral performance summaries as requested. For the MDP task, Figure 5 now compares the total reward and rate of highlyrewarding action selected between humans and our model. For the MNIST task, Figure 7 shows the rate of correct responses for humans, RTNet, and our task solver across all conditions. These additions provide better context for the model's performance.

      For the MDP task, consider reporting the number or proportion of correct choices in addition to negative log-likelihood. This would make the results more interpretable.

      Thank you for the suggestion. To make the results more interpretable, we have added a new prediction performance metric: the rate for behaviour matched. This metric measures the proportion of trials where the model's predicted action matches the human's actual choice. This is now included alongside the negative log-likelihood in Figures 2, 3, 4, 8, 9, and 11.

      In Figure 5, what is the difference between the "% correct" and "% match to behaviour"? If so, it would help to clarify the distinction in the text or figure captions.

      We have clarified these terms in the revised manuscript. As defined in the Result section (Lines 116--122, 231), "%correct" (now "rate of correct responses") is a measure of task performance, whereas "%match to behaviour" (now "rate for behaviour matched") is a measure of prediction accuracy.

      For the cognitive model, it would be useful to report the fitted parameters (e.g., learning rate, inverse temperature) per individual. This can offer insight into what kinds of behavioural variability the individual latent representation might be capturing.

      We have added histograms of the fitted Q-learning parameters for the human participants in Supplementary Materials (Figure S1). This analysis revealed which parameters varied most across the population and directly informed the design of our subsequent simulation study with Q-learning agents (see response to Comment 2-2), where we linked these parameters to the individual latent representation (Lines 208--223).

      A few of the terms and labels in the paper could be made more intuitive. For example, the name "individuality index" might give the impression of a scalar value rather than a latent vector, and the labels "SX" and "SY" are somewhat arbitrary. You might consider whether clearer or more descriptive alternatives would help readers follow the paper more easily.

      We have adopted the suggested changes for clarity.

      "Individuality index" has been changed to "individual latent representation".

      "Situation SX" and "Situation SY" have been renamed to the more descriptive "Within-Condition Prediction" and "Cross-Condition Transfer", respectively.

      We have also added a table in Figure 7 to clarify the MNIST condition acronyms (EA/ES/DA/DS).

      Please consider including training and validation curves for your models. These would help readers assess convergence, overfitting, and general training stability, especially given the complexity of the encoder-decoder architecture.

      Training and validation curves for both the MDP and MNIST tasks have been added to Supplementary Materials (Figure S2 and S6) to show model convergence and stability.

      Reviewer #3 (Public review):

      To demonstrate the effectiveness of the approach, the authors compare a Q-learning cognitive model (for the MDP task) and RTNet (for the MNIST task) against the proposed framework. However, as I understand it, neither the cognitive model nor RTNet is designed to fit or account for individual variability. If that is the case, it is unclear why these models serve as appropriate baselines. Isn't it expected that a model explicitly fitted to individual data would outperform models that do not? If so, does the observed superiority of the proposed framework simply reflect the unsurprising benefit of fitting individual variability? I think the authors should either clarify why these models constitute fair control or validate the proposed approach against stronger and more appropriate baselines.

      Thank you for raising this critical point. We wish to clarify the nature of our baselines:

      For the MDP task, the cognitive model baseline was indeed designed to account for individual variability. We estimated its parameters (e.g., learning rate) from each individual's source task behaviour and then used those specific parameters to predict their behaviour in the target task. This makes it a direct, parameter-based transfer model and thus a fair and appropriate baseline for individuality transfer.

      For the MNIST task, we agree that the RTNet baseline was insufficient for evaluating individual-level transfer in the "Cross-Condition Transfer" scenario. We have now introduced a much stronger baseline, the "task solver (source)," which is trained specifically on the source task data of each test participant. Our results (Figure 9) show that the EIDT framework significantly outperforms this more appropriate, individualized baseline, highlighting the value of our transfer method over direct, within-condition fitting.

      It's not very clear in the results section what it means by having a shorter within-individual distance than between-individual distances. Related to the comment above, is there any control analysis performed for this? Also, this analysis appears to have nothing to do with predicting individual behavior. Is this evidence toward successfully parameterizing individual differences? Could this be task-dependent, especially since the transfer is evaluated on exceedingly similar tasks in both experiments? I think a bit more discussion of the motivation and implications of these results will help the reader in making sense of this analysis.

      We agree that the previous analysis on inter- and intra-participant distances was not sufficiently clear or directly linked to the model's predictive power. We have removed this analysis from the manuscript. In its place, we have introduced a new, more direct analysis (Figures 4, 11, S5, S8, and S9) that demonstrates a quantitative relationship between the distance in the latent space and prediction accuracy. This new analysis shows that prediction error for an individual increases as a function of this distance, providing much stronger and clearer evidence that our framework successfully parameterizes meaningful individual differences.

      The authors have to better define what exactly he meant by transferring across different "tasks" and testing the framework in "more distinctive tasks". All presented evidence, taken at face value, demonstrated transferring across different "conditions" of the same task within the same experiment. It is unclear to me how generalizable the framework will be when applied to different tasks.

      Conceptually, it is also unclear to me how plausible it is that the framework could generalize across tasks spanning multiple cognitive domains (if that's what is meant by more distinctive). For instance, how can an individual's task performance on a Posner task predict task performance on the Cambridge face memory test? Which part of the framework could have enabled such a cross-domain prediction of task performance? I think these have to be at least discussed to some extent, since without it the future direction is meaningless.

      We agree with your assessment and have corrected our terminology throughout the manuscript. We now consistently refer to the transfer as being "across task conditions" to accurately describe the scope of our findings.

      We have also expanded our Discussion (Line 332-343) to address the important conceptual point about cross-domain transfer. We hypothesize that such transfer would be possible if the tasks, even if structurally different, rely on partially shared underlying cognitive functions (e.g., working memory). In such a scenario, the individual latent representation would capture an individual's specific characteristics related to that shared function, enabling transfer. Conversely, we state that transfer between tasks with no shared cognitive basis would not be expected to succeed with our current framework.

      How is the negative log-likelihood, which seems to be the main metric for comparison, computed? Is this based on trial-by-trial response prediction or probability of responses, as what usually performed in cognitive modelling?

      The negative log-likelihood is computed on a trial-by-trial basis. It is based on the probability the model assigned to the specific action that the human participant actually took on that trial. This calculation is applied consistently across all models (cognitive models, RTNet, and EIDT). We have added sentences to the Results section to clarify this point (Lines 116--122).

      None of the presented evidence is cross-validated. The authors should consider performing K-fold cross-validation on the train, test, and evaluation split of subjects to ensure robustness of the findings.

      All prediction performance results reported in the revised manuscript are now based on a rigorous leave-one-participant-out cross-validation procedure to ensure the robustness of our findings. We have updated the

      Methods section to reflect this (Lines 127--129 and 229).

      For some purely illustrative visualizations (e.g., plotting the entire latent space in Figures S3 and S7), we used a model trained on all participants' data to provide a single, representative example and avoid clutter. We have explicitly noted this in the relevant figure captions.

      The authors excluded 25 subjects (20% of the data) for different reasons. This is a substantial proportion, especially by the standards of what is typically observed in behavioral experiments. The authors should provide a clear justification for these exclusion criteria and, if possible, cite relevant studies that support the use of such stringent thresholds.

      We acknowledge the concern regarding the exclusion rate. The previous criteria were indeed empirical. We have now implemented more systematic exclusion procedure based on the interquartile range of performance metrics, which is detailed in Section 4.2.2 (Lines 489--498). This revised, objective criterion resulted in the exclusion of 42 participants (34% of the initial sample). While this rate is high, we attribute it to the online nature of the data collection, where participant engagement can be more variable. We believe applying these strict criteria was necessary to ensure the quality and reliability of the behavioural data used for modeling.

      The authors should do a better job of creating the figures and writing the figure captions. It is unclear which specific claim the authors are addressing with the figure. For example, what is the key message of Figure 2C regarding transfer within and across participants? Why are the stats presentation different between the Cognitive model and the EIDT framework plots? In Figure 3, it's unclear what these dots and clusters represent and how they support the authors' claim that the same individual forms clusters. And isn't this experiment have 98 subjects after exclusion, this plot has way less than 98 dots as far as I can tell. Furthermore, I find Figure 5 particularly confusing, as the underlying claim it is meant to illustrate is unclear. Clearer figures and more informative captions are needed to guide the reader effectively.

      We agree that several figures and analyses in the original manuscript were unclear, and we have thoroughly revised our figures and their captions to improve clarity.

      The confusing analysis in the old Figures 2C and 5 (Original/Others comparison) have been completely removed. The unclear visualization of the latent space for the test pool (old Figure 3 showing representations only from test participants) has also been removed to avoid confusion. For visualization of the overall latent space, we now use models trained on all data (Figures S3 and S7) and have clarified this in the captions. In place of these removed analyses, we have introduced a new, more intuitive "cross-individual" analysis (presented in Figures 4, 11, S5, S8, and S9). As explained in the new, more detailed captions, this analysis directly plots prediction performance as a function of the distance in latent space, providing a much clearer demonstration of how the latent representation relates to predictive accuracy.

      I also find the writing somewhat difficult to follow. The subheadings are confusing, and it's often unclear which specific claim the authors are addressing. The presentation of results feels disorganized, making it hard to trace the evidence supporting each claim. Also, the excessive use of acronyms (e.g., SX, SY, CG, EA, ES, DA, DS) makes the text harder to parse. I recommend restructuring the results section to be clearer and significantly reducing the use of unnecessary acronyms.

      Thank you for this feedback. We have made significant revisions to improve the clarity and organization of the manuscript. We have renamed confusing acronyms: "Situation SX" is now "Within- Condition Prediction," and "Situation SY" is now "Cross-Condition Transfer." We also added a table to clarify the MNIST condition acronyms (EA/ES/DA/DS) in Figure 7.

      The Results section has been substantially restructured with clearer subheadings.

    1. Author response:

      Reviewer #1

      (1) Mechanistic insight into how Hsp70 but not Hsc70 increase PL-SF FL tau aggregation/pathology is missing. This is despite both chaperones binding to PL-SF FL tau. What species of tau does Hsp70 bind, and what cofactors are important in this process?

      We agree that explaining why Hsp70, but not Hsc70, promotes tau aggregation would strengthen the study. Although both chaperones bind tau, they diverge slightly in 1) protein sequence, 2) biochemical activity, and 3) co-chaperone engagement.

      Sequence: Hsp70 has an extra cysteine residue (Cys306) that is highly reactive to oxidation and a glycine residue that is critical for cysteine oxidation (Gly557). Both residues are specific to Hsp70 (not present in Hsc70) and may alter Hsp70 conformation or client handling (Hong et al., 2022).

      Biochemical activity: Prior studies indicate that Hsp70’s ATPase domain (NBD) is critical for tau interactions (Jinwal et al., 2009; Fontaine et al., 2015; Young et al., 2016) and can be disrupted with point mutations including K71E and E175S for ATPase and A406G/V438G for substrate binding (Fontaine et al., 2015).

      Co-chaperone engagement: Hsp70 recruits the co-chaperone and E3 ubiquitin ligase CHIP/Stub1 more strongly than Hsc70, suggesting co-chaperone engagement could lead to differences in tau processing (Jinwal et al., 2013).

      To directly test how the two closely related chaperones could differentially impact tau, we plan to perform the following experiments:

      (a) We will mutate residues responsible for cysteine reactivity in Hsp70 including the cysteine itself (Cys306) and the critical glycine that facilitates cysteine reactivity (Gly557). These residues will be deleted from Hsp70 or alternatively inserted into Hsc70 to determine whether cysteine reactivity is the reason for Hsp70’s ability to drive tau aggregation.

      (b) We will generate Hsp70 mutants lacking ATPase- or substrate-binding mutants to determine which Hsp70 domains are responsible for driving tau aggregation.

      (c) We will perform seeding assays in stable tau-expressing cell lines to determine whether Hsp70/Hsc70 overexpression or depletion alters seeded tau aggregation.

      (d) We will perform confocal microscopy to determine the extent of co-localization of Hsp70 or Hsc70 with phospho-tau, oligomeric tau, or Thioflavin-S (ThioS) to identify which tau species are engaged by Hsp70/Hsc70.

      (e) We will perform immunoprecipitation pull-downs followed by mass spectrometry to globally identify any relevant Hsp70/Hsc70 interacting factors that might account for the differences in tau aggregation.

      (2) The study relies heavily on densitometry of bands to draw conclusions; in several instances, the blots are overexposed to accurately quantify the signal.

      All immunoblots were acquired as 16-bit TIFFs with exposure settings chosen to prevent pixel saturation, and quantification was performed on raw, unsaturated images. Brightness and contrast adjustments were applied only for visualization and did not alter pixel values used for analysis. All quantified bands fell within the linear range of the detector, with one exception in Figure 7B, which we removed from quantification. We will add both low- and high-exposure versions of immunoblots to the revised figures to demonstrate signal linearity and dynamic range.

      Reviewer #2

      (1) Although the PL-SF model can accelerate tau aggregation, it is crucial to determine whether this aligns with the temporal progression and spatial distribution of tau pathology in the brains of patients with tauopathies.

      No single tauopathy model fully recapitulates the temporal and spatial progression of human tauopathies. The PL-SF system is not intended to model the disease course. Rather, it is an excellent model for mechanistic studies of mature tau aggregation, which is otherwise challenging to study. We note that prior studies showed that PL-SF tau expression in transgenic mice (Xia et al., 2022 and Smith et al., 2025) and rhesus monkeys (Beckman et al., 2021) led to prion-like tau seeding and aggregation in hippocampal and cortical regions. Indeed, the spatial and temporal tau aggregation patterns aligned with features of human tauopathies. So far, these findings all support PL-SF as a valid accelerated model of tauopathy than can be used to interrogate pathogenic mechanisms that impact tau processing, degradation, and/or aggregation.

      (2) The authors did not elucidate the specific molecular mechanism by which Hsp70 promotes tau aggregation.

      We agree that a deeper understanding of the molecular mechanism is needed. The revision experiments outlined above (Reviewer #1, point #1) will define how Hsp70 promotes tau aggregation by testing sequence contributions, dissecting ATPase and substrate-binding domain requirements, and mapping Hsp70/Hsc70 interactors to directly address this mechanistic question.

      (3) Some figures in this study show large error bars in the quantitative data (some statistical analysis figures, MEA recordings, etc.), indicating significant inter-sample variability. It is recommended to label individual data points in all quantitative figures and clearly indicate them in figure legends.

      We acknowledge the inter-sample variability in some of the quantitative datasets. This level of variability can occur in primary neuronal cultures (e.g., MEA recordings) that are sensitive to growth and surface adhesion conditions, leading to many technical considerations. To improve transparency and interpretation, we will revise all quantitative figures to display individual data points overlaid on summary statistics and will update figure legends to clearly indicate sample sizes and statistical tests used.

      References

      Hong Z, Gong W, Yang J, Li S, Liu Z, Perrett S, Zhang H. Exploration of the cysteine reactivity of human inducible Hsp70 and cognate Hsc70. J Biol Chem. 2023 Jan;299(1):102723. doi: 10.1016/j.jbc.2022.102723. Epub 2022 Nov 19. PMID: 36410435; PMCID: PMC9800336.

      Jinwal UK, Miyata Y, Koren J 3rd, Jones JR, Trotter JH, Chang L, O'Leary J, Morgan D, Lee DC, Shults CL, Rousaki A, Weeber EJ, Zuiderweg ER, Gestwicki JE, Dickey CA. Chemical manipulation of hsp70 ATPase activity regulates tau stability. J Neurosci. 2009 Sep 30;29(39):12079-88. doi: 10.1523/JNEUROSCI.3345-09.2009. PMID: 19793966; PMCID: PMC2775811.

      Fontaine SN, Rauch JN, Nordhues BA, Assimon VA, Stothert AR, Jinwal UK, Sabbagh JJ, Chang L, Stevens SM Jr, Zuiderweg ER, Gestwicki JE, Dickey CA. Isoform-selective Genetic Inhibition of Constitutive Cytosolic Hsp70 Activity Promotes Client Tau Degradation Using an Altered Co-chaperone Complement. J Biol Chem. 2015 May 22;290(21):13115-27. doi: 10.1074/jbc.M115.637595. Epub 2015 Apr 11. PMID: 25864199; PMCID: PMC4505567

      Young ZT, Rauch JN, Assimon VA, Jinwal UK, Ahn M, Li X, Dunyak BM, Ahmad A, Carlson G, Srinivasan SR, Zuiderweg ERP, Dickey CA, Gestwicki JE. Stabilizing the Hsp70‑Tau Complex Promotes Turnover in Models of Tauopathy. Cell Chem Biol. 2016 Aug 4;23(8):992–1001. doi:10.1016/j.chembiol.2016.04.014.

      Jinwal UK, Akoury E, Abisambra JF, O'Leary JC 3rd, Thompson AD, Blair LJ, Jin Y, Bacon J, Nordhues BA, Cockman M, Zhang J, Li P, Zhang B, Borysov S, Uversky VN, Biernat J, Mandelkow E, Gestwicki JE, Zweckstetter M, Dickey CA. Imbalance of Hsp70 family variants fosters tau accumulation. FASEB J. 2013 Apr;27(4):1450-9. doi: 10.1096/fj.12-220889. Epub 2012 Dec 27. PMID: 23271055; PMCID: PMC3606536.

      Xia, Y., Prokop, S., Bell, B.M. et al. Pathogenic tau recruits wild-type tau into brain inclusions and induces gut degeneration in transgenic SPAM mice. Commun Biol 5, 446 (2022). https://doi.org/10.1038/s42003-022-03373-1.

      Smith ED, Paterno G, Bell BM, Gorion KM, Prokop S, Giasson BI. Tau from SPAM Transgenic Mice Exhibit Potent Strain-Specific Prion-Like Seeding Properties Characteristic of Human Neurodegenerative Diseases. Neuromolecular Med. 2025 May 30;27(1):44. doi: 10.1007/s12017-025-08850-4. PMID: 40447946; PMCID: PMC12125038.

      Beckman D, Chakrabarty P, Ott S, Dao A, Zhou E, Janssen WG, Donis-Cox K, Muller S, Kordower JH, Morrison JH. A novel tau-based rhesus monkey model of Alzheimer's pathogenesis. Alzheimers Dement. 2021 Jun;17(6):933-945. doi: 10.1002/alz.12318. Epub 2021 Mar 18. PMID: 33734581; PMCID: PMC8252011.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review): 

      Summary: 

      This study presents convincing findings that oligodendrocytes play a regulatory role in spontaneous neural activity synchronisation during early postnatal development, with implications for adult brain function. Utilising targeted genetic approaches, the authors demonstrate how oligodendrocyte depletion impacts Purkinje cell activity and behaviours dependent on cerebellar function. Delayed myelination during critical developmental windows is linked to persistent alterations in neural circuit function, underscoring the lasting impact of oligodendrocyte activity. 

      Strengths: 

      (1) The research leverages the anatomically distinct olivocerebellar circuit, a well-characterized system with known developmental timelines and inputs, strengthening the link between oligodendrocyte function and neural synchronization. 

      (2) Functional assessments, supported by behavioral tests, validate the findings of in vivo calcium imaging, enhancing the study's credibility. 

      (3) Extending the study to assess the long-term effects of early-life myelination disruptions adds depth to the implications for both circuit function and behavior.

      We appreciate these positive evaluation.

      Weaknesses: 

      (1) The study would benefit from a closer analysis of myelination during the periods when synchrony is recorded. Direct correlations between myelination and synchronized activity would substantiate the mechanistic link and clarify if observed behavioral deficits stem from altered myelination timing. 

      We appreciate the reviewer’s thoughtful suggestion and have expanded the manuscript to clarify how oligodendrocyte maturation relates to the development of Purkinje-cell synchrony. The developmental trajectory of Purkinje-cell synchrony has already been comprehensively characterized by Good et al. (2017, Cell Reports 21: 2066–2073): synchrony drops from a high level at P3–P5 to adult-like values by P8. We found that the myelination in the cerebellum starts to appear from P5-P7 (Figure S1A, B), indicating that the timing of Purkinje cell desynchronization coincides with the initial appearance of oligodendrocytes and myelin in the cerebellum. To determine whether myelin growth could nevertheless modulate this process, we quantified ASPA-positive oligodendrocyte density and MBP-positive bundle thickness and area at P10, P14, P21 and adulthood (Fig. 1J, K, Fig. S1E). Both metrics increase monotonically and clearly lag behind the rapid drop in synchrony, indicating that myelination could be not the primary trigger for the desynchronization. When oligodendrocytes were ablated during the second postnatal week, the synchrony was reduced (new Fig. 2). Thus, once myelination is underway, oligodendrocytes become critical for maintaining the synchrony, acting not as the initiators but as the stabilizers and refiners of the mature network state.

      We have added the new subsection in discussion (lines 451–467) now in which we propose a two-phase model. Phase I (P3–P8): High early synchrony is generated by non-myelin mechanisms (e.g. transient gap junctions, shared climbing-fiber input). Phase II (P8-). As oligodendrocytes proliferate and ensheath axons, they fine-tune conduction velocity and stabilize the mature, low-synchrony network state.

      We believe these additions fully address the reviewer’s concerns.

      (2) Although the study focuses on Purkinje cells in the cerebellum, neural synchrony typically involves cross-regional interactions. Expanding the discussion on how localized Purkinje synchrony affects broader behaviors - such as anxiety, motor function, and sociality - would enhance the findings' functional significance.

      We appreciate the reviewer’s helpful suggestion and have expanded the Discussion (lines 543–564) to clarify how localized Purkinje-cell synchrony can influence broader behavioral domains. In the revised text we note that changes in PC synchrony propagate  into thalamic, prefrontal, limbic, and parietal targets, thereby impacting distributed networks involved in motor coordination, affect, and social interaction. Our optogenetic rescue experiments further support this framework, as transient resynchronization of PCs normalized sociability and motor coordination while leaving anxiety-like behavior impaired. This dissociation highlights that different behavioral domains rely to varying degrees on precise cerebellar synchrony and underscores how even localized perturbations in Purkinje timing can acquire system-level significance.

      (3) The authors discuss the possibility of oligodendrocyte-mediated synapse elimination as a possible mechanism behind their findings, drawing from relevant recent literature on oligodendrocyte precursor cells. However, there are no data presented supporting this assumption. The authors should explain why they think the mechanism behind their observation extends beyond the contribution of myelination or remove this point from the discussion entirely.

      We thank the reviewer for pointing out that our original discussion of oligodendrocyte-mediated synapse elimination was not directly supported by data in the present manuscript. Because we are actively analyzing this question in a separate, follow-up study, we have deleted the speculative passage to keep the current paper focused on the demonstrated, myelination-dependent effects. We believe this change sharpens the mechanistic narrative and fully addresses the reviewer’s concern.

      (4) It would be valuable to investigate the secondary effects of oligodendrocyte depletion on other glial cells, particularly astrocytes or microglia, which could influence long-term behavioral outcomes. Identifying whether the lasting effects stem from developmental oligodendrocyte function alone or also involve myelination could deepen the study's insights. 

      We thank the reviewer for raising this point and have performed the requested analyses. Using IBA1 immunostaining for microglia and S100b for Bergmann glia, we quantified cell density and these marker signal intensity at P14 and P21. Neither microglial or Bergmann-glial differed between control and oligodendrocyte-ablated mice at either time‐point (new Figure S2). These results indicate that the behavioral phenotypes we report are unlikely to arise from secondary activation or loss of other glial populations.

      We now added results (lines 275–286) and also discuss myelination and other oligodendrocyte function (lines 443–450). It remains difficult to disentangle conduction-related effects from myelination-independent trophic roles of oligodendrocytes. We therefore note explicitly that future work employing stage-specific genetic tools or acute metabolic manipulations will be required to parse these contributions more definitively.

      (5) The authors should explore the use of different methods to disturb myelin production for a longer time, in order to further determine if the observed effects are transient or if they could have longer-lasting effects.

      We agree that distinguishing transient from enduring effects is critical. Importantly, our original submission already included data demonstrating a persistent deficit of PC population synchrony (Fig. 4, previous Fig. 3): (i) at P14—the early age after oligodendrocyte ablation—population synchrony is reduced, and (ii) the same deficit is still present in adults (P60–P70) despite full recovery of ASPA-positive cell density and MBP-area and -thickness (Fig. 2H-K, Fig. S1E, and Fig. 4). We also performed the ablation of oligodendrocytes after the third postnatal week. Despite a similar acute drop in ASPA-positive cells, neither population synchrony nor anxiety-, motor-, or social behaviors differed from littermate controls. Thus, extending myelin disruption beyond the developmental window does not exacerbate or prolong the phenotype, whereas a short perturbation within that window leaves a permanent timing defect. These findings strengthen our conclusion that it is the developmental oligodendrocyte/myelination program itself—rather than ongoing adult myelin production—that is essential for establishing stable network synchrony. We now highlight this point explicitly in the revised Discussion (lines 507–522).

      (6) Throughout the paper, there are concerns about statistical analyses, particularly on the use of the Mann-Whitney test or using fields of view as biological replicates.

      We appreciate the reviewer’s guidance on appropriate statistical treatment. To address these concerns we have re-analyzed all datasets that contained multiple measurements per animal (e.g., fields of view, lobules, or trials) using nested statistics with animal as the higher-order unit. Specifically, we applied a two-level nested ANOVA when more than two groups were compared and a nested t-test when two conditions were present. The re-analysis confirmed all original conclusions. Because the nested models yielded comparable effect sizes to the Mann–Whitney tests, we have retained the mean ± SEM for ease of comparison with prior literature but now also report all values for each mouse in Table 1. In cases where a single measurement per mouse was compared between two groups, we used the Mann–Whitney test and present the results in the graphs as median values.

      Major

      (1) The authors present compelling evidence that early loss of myelination disrupts synchronous firing prematurely. However, synchronous neuronal firing does not equate to circuit synchronization. It is improbable that myelination directly generates synchronous firing in Purkinje cells (PCs). For instance, Foran et al. (1992) identified that cerebellar myelination begins around postnatal day 6 (P6), while Good et al. (2017) recorded a developmental decline in PC activity correlation from P5-P11. To clarify myelin's role, we recommend detailed myelin imaging through light microscopy (MBP staining at higher magnification) to assess the extent of myelin removal accurately. Myelin sheaths, as shown by Snaidero et al. (2020), can persist after oligodendrocyte (OL) death, particularly following DTA induction (Pohl et al. 2011). Quantification of MBP+ area, rather than mean MBP intensity, is necessary to accurately measure myelin coverage.

      We appreciate the reviewer’s concern that residual sheaths might remain after oligodendrocyte ablation and have therefore re-examined myelin at higher spatial resolution. Then, two independent metrics were extracted: MBP⁺ area fraction in the white matter and MBP⁺ bundle thickness (new Figure 1J, K, and Fig. S1E). We confirm a robust, transient loss of myelin at P10 and P14 as shown by the reduction of MBP⁺ area and MBP⁺ bundle thickness. Both parameters recovered to control values by P21 and adulthood, indicating effective remyelination. These data demonstrate that, in our paradigm, oligodendrocyte ablation is accompanied by substantial sheath loss rather than the persistent myelin reported after acute toxin exposure. We have added them in Result (lines 266–271).

      The results reinforce the view that myelin removal and/or loss of trophic support during a narrow developmental window drive the long-term hyposynchrony and behavioral phenotypes we report. We have added the new subsection in discussion (lines 443–450) now in which we propose a two-phase model. Phase I (P3–P8): High early synchrony is generated by non-myelin mechanisms (e.g. transient gap junctions, shared climbing-fiber input). Phase II (P8-). As oligodendrocytes proliferate and ensheath axons, they fine-tune conduction velocity and stabilize the mature, low-synchrony network state. We believe these additions fully address the reviewer’s concerns.

      (2) Surprisingly, the authors speculate about oligodendrocyte-mediated synaptic pruning without supportive data, shifting the focus away from the potential impact of myelination. Even if OLs perform synaptic pruning, OL depletion would likely maintain synchrony, yet the opposite was observed. Further characterisation of the model and the potential source of the effect is needed. 

      We thank the reviewer for pointing out that our original discussion of oligodendrocyte-mediated synapse elimination was not directly supported by data in the present manuscript. Because we are actively analyzing this question in a separate, follow-up study, we have deleted the speculative passage to keep the current paper focused on the demonstrated, myelination-dependent effects. We believe this change sharpens the mechanistic narrative and fully addresses the reviewer’s concern.

      (3) Improved characterization of the DTA model would add clarity. Although almost all infected cells are reported as OLs, quantification of infected OL-lineage cells (e.g., via Olig2 staining) would verify this. It remains possible that observed activity changes are driven by OL-independent demyelination effects. We suggest cross-staining with Iba1 and GFAP to rule out inflammation or gliosis. 

      We thank the reviewer for this important suggestion and have expanded our histological characterization accordingly. First, to verify that DTA expression is confined to mature oligodendrocytes, we co-stained cerebellar sections collected 7 days after AAV-hMAG-mCherry injection with Olig2 (pan-OL lineage) and ASPA (mature OL marker) as shown in Figure S1C-D. Quantitative analysis revealed that 100 % of mCherry⁺ cells were Olig2⁺/ASPA⁺, whereas mCherry signal was virtually absent in Olig2⁺/ASPA⁻ immature oligodendrocytes. These data confirm that our DTA manipulation targets mature myelinating OLs rather than earlier lineage stages. We have added them in Result (lines 260–262).

      Second, to examine indirect effects mediated by other glia, we performed cross-staining with IBA1 (microglia) and S100β (Bergmann). Cell density and fluorescence intensity for each marker were indistinguishable between control and DTA groups at P14 and P21 (Figure S2A-H). Thus, neither inflammation nor astro-/microgliosis accompanies OL ablation. We have added them in Result (lines 275–286).

      Collectively, these results demonstrate that the observed desynchronization and behavioral phenotypes arise from specific loss of mature oligodendrocytes and their myelin, rather than from off-target viral expression or secondary glial responses.

      (4) The use of an independent model of myelin loss, such as the inducible Myrf knockout mouse with a MAG promoter, to assess if oligodendrocyte loss causes temporary or sustained impacts, employing an extended knockout model like Myrf cKO with MAG-Cre viral methods would be advantageous.

      We agree that distinguishing transient from enduring effects is critical. Importantly, our original submission already included data demonstrating a persistent deficit of PC population synchrony (Fig. 4, previous Fig. 3): (i) at P13-15—the early age after oligodendrocyte ablation—population synchrony is reduced, and (ii) the same deficit is still present in adults (P60–P70) despite full recovery of ASPA-positive cell density and MBP-area and -thickness (Fig. 2H-K, Fig. S1E, and Fig. 4). We also performed the ablation of oligodendrocytes after the third postnatal week. Despite a similar acute drop in ASPA-positive cells, neither population synchrony nor anxiety-, motor-, or social behaviors differed from littermate controls. Thus, extending myelin disruption beyond the developmental window does not exacerbate or prolong the phenotype, whereas a short perturbation within that window leaves a permanent timing defect. These findings strengthen our conclusion that it is the developmental oligodendrocyte/myelination program itself—rather than ongoing adult myelin production—that is essential for establishing stable network synchrony. We now highlight this point explicitly in the revised Discussion (lines 507–522).

      (5) For statistical robustness, the use of non-parametric tests (Mann-Whitney) necessitates reporting the median instead of the mean as the authors do. Furthermore, as repeated measurements within the same animal are not independent, the authors should ideally use nested ANOVA (or nested t-test comparing two conditions) to validate their findings (Aarts et al., Nat. Neuroscience 2014). Alternatively use one-way ANOVA with each animal as a biological replicate, although this means that the distribution in the data sets per animal is lost.

      We appreciate the reviewer’s guidance on appropriate statistical treatment. To address these concerns we have re-analyzed all datasets that contained multiple measurements per animal (e.g., fields of view, lobules, or trials) using nested statistics with animal as the higher-order unit. Specifically, we applied a two-level nested ANOVA when more than two groups were compared and a nested t-test when two conditions were present. The re-analysis confirmed all original conclusions. Because the nested models yielded comparable effect sizes to the Mann–Whitney tests, we have retained the mean ± SEM for ease of comparison with prior literature but now also report all values for each mouse in Table 1. In cases where a single measurement per mouse was compared between two groups, we used the Mann–Whitney test and present the results in the graphs as median values.

      Minor Points 

      (1) In all figures, please specify the ages at which each procedure was conducted, as demonstrated in Figure 2A.

      All main and supplementary figures now specify the exact postnatal age.

      (2) Clarify the selection criteria for regions of interest (ROI) in calcium imaging, and provide representative ROIs.

      We appreciate the reviewer’s guidance. We have clarified that our ROI detection followed the protocol reported by our previous paper (Tanigawa et al., 2024, Communications Biology) (lines 177-178) and representative Purkinje cell ROIs are now shown in Fig. 2B.

      (3) Include data on the proportion of climbing fiber or inferior olive neurons expressing Kir and the total number of neurons transfected, which would help contextualize the observed effects on PC synchronization and its broader implications for cerebellar circuit function.

      We appreciate the reviewer’s guidance. New Fig. 7C summarizes the efficiency of AAV-GFP and AAV-Kir2.1-GFP injections into the inferior olive. Across 4 mice PCs with GFP-labeled CFs was detected in 19.3 ± 11.9 (mean ± S.D.) % for control and 26.2 ± 11.8 (mean ± S.D.) % for Kir2.1 of PCs. These numbers are reported in the Results (lines 373–375).

      (4) Higher magnification images in Figures 1 and S3 would improve visual clarity. 

      We have addressed the request for higher-magnification images in two ways. First, all panels in Figure S3 were placed on a larger canvas. Second, in Figure 1 we adjusted panel sizes to emphasize fine structure: panel 1C already represents an enlargement of the RFP positive cells shown in 1B, and panel 1H and 1J now occupies a wider span so that every ASPA-positive cell body can be distinguished. Should the reviewer still require an even closer view, we have additional ready for upload.

      (5) Consider language editing to enhance overall clarity and readability.

      The entire manuscript was edited to improve flow, consistency, and readability.

      (6) Refine the discussion to align with the presented data.

      We have refined the discussion.

      Thank you once again for your constructive suggestions and comments. We believe these changes have improved the clarity and readability of our manuscript.

      Reviewer #2 (Public review):

      We appreciate Reviewer #2’s positive evaluation of our work and thank him/her for the constructive suggestions and comments. We followed these suggestions and comments and have conducted additional experiments. We have rewritten the manuscript and revised the figures according to the points Reviewer #1 mentioned. Our point-by-point responses to the comments are as follows.

      Summary:

      In this manuscript, the authors use genetic tools to ablate oligodendrocytes in the cerebellum during postnatal development. They show that the oligodendrocyte numbers return to normal post-weaning. Yet, the loss of oligodendrocytes during development seems to result in decreased synchrony of calcium transients in Purkinje neurons across the cerebellum. Further, there were deficits in social behaviors and motor coordination. Finally, they suppress activity in a subset of climbing fibers to show that it results in similar phenotypes in the calcium signaling and behavioral assays. They conclude that the behavioral deficits in the oligodendrocyte ablation experiments must result from loss of synchrony. 

      Strengths:

      Use of genetic tools to induce perturbations in a spatiotemporally specific manner.

      We appreciate these positive evaluation.

      Weaknesses: 

      The main weakness in this manuscript is the lack of a cohesive causal connection between the experimental manipulation performed and the phenotypes observed. Though they have taken great care to induce oligodendrocyte loss specifically in the cerebellum and at specific time windows, the subsequent experiments do not address specific questions regarding the effect of this manipulation.

      Calcium transients in Purkinje neurons are caused to a large extent by climbing fibers, but there is evidence for simple spikes to also underlie the dF/F signatures (Ramirez and Stell, Cell Reports, 2016).

      We thank the reviewer for drawing attention to the work of Ramirez & Stell (2016), which showed that simple-spike bursts can elicit Ca²⁺ rises, but only in the soma and proximal dendrites of adult Purkinje cells. In our study, Regions of Interest were restricted to the dendritic arbor, where SS-evoked signals are essentially undetectable (Ramirez & Stell, 2016), whereas climbing-fiber complex spikes generate large, all-or-none transients (Good et al., 2017). Accordingly, even if a rare SS-driven event reached threshold it would likely fall outside our ROIs.

      In addition, we directly imaged CF population activity by expressing GCaMP7f in inferior-olive neurons. Correlation analysis of CF boutons revealed that DTA ablation lowers CF–CF synchrony at P14 (new Fig. 3A–D). Because CF synchrony is a principal driver of Purkinje-cell co-activation, this reduction provides a mechanistic link between oligodendrocyte loss and the hyposynchrony we observe among Purkinje cells. Consistent with this interpretation, electrophysiological recordings showed that parallel-fiber EPSCs and inhibitory synaptic inputs onto Purkinje cells were unchanged by DTA treatment (Fig. 3E-H) , which makes it less likely that the reduced synchrony simply reflects changes in other excitatory or inhibitory synaptic drive.

      That said, SS-dependent somatic Ca²⁺ signals could still influence downstream plasticity and long-term cerebellar function. In future work we therefore plan to combine somatic imaging with stage-specific oligodendrocyte manipulations to test whether SS-evoked Ca²⁺ dynamics are themselves modulated by oligodendrocyte support. We have added these descriptions in the Results (lines 288–294) and Discussion (lines 423–434).

      Also, it is erroneous to categorize these calcium signals as signatures of "spontaneous activity" of Purkinje neurons as they can have dual origins.

      Thank you for pointing out the potential ambiguity. In the revised manuscript we have clarified how we use the term “spontaneous activity” in the context of our measurements (lines 289-290). Our calcium imaging was restricted to the dendritic arbor of Purkinje cells, where calcium transients are dominated by climbing-fiber (CF) inputs (Ramirez & Stell, 2016; Good et al., 2017). Thus, the synchrony values reported here primarily reflect CF-driven complex spikes rather than mixed signals of dual origin. We have revised the Results section accordingly (lines 289–293) to make this measurement-specific limitation explicit.

      Further, the effect of developmental oligodendrocyte ablation on the cerebellum has been previously reported by Mathis et al., Development, 2003. They report very severe effects such as the loss of molecular layer interneurons, stunted Purkinje neuron dendritic arbors, abnormal foliations, etc. In this context, it is hardly surprising that one would observe a reduction of synchrony in Purkinje neurons (perhaps due to loss of synaptic contacts, not only from CFs but also from granule cells).

      We appreciate the reviewer’s comparison to Mathis et al. (2003). Mathis et al. used MBP–HSV-TK transgenic mice in which systemic FIAU treatment eliminates oligodendrocytes. When ablation began at P1, they observed severe dysmorphology—loss of molecular-layer interneurons, Purkinje-cell (PC) dendritic stunting, and abnormal foliation. Crucially, however, the same study reports that starting the ablation later (FIAU from P6-P20) left cerebellar cyto-architecture entirely normal.

      Our AAV MAG-DTA paradigm resembles this later window. Our temporally restricted DTA protocol produces the same ‘late-onset’ profile—robust yet reversible hypomyelination with no loss of Purkinje cells, interneurons, dendritic length, or synaptic input (new Fig. S1–S2, Fig. 3E-H). The enduring hyposynchrony we report therefore cannot be attributed to the dramatic anatomical defects seen after prenatal ablation, but instead reveals a specific requirement for early-postnatal myelin in stabilizing PC synchrony, especially affecting CF-CF synchrony.

      This clarification shows that we have carefully considered the Mathis model and that our findings not only replicate, but also extend the earlier work. We have added these description in Result (lines 273-286)

      The last experiment with the expression of Kir2.1 in the inferior olive is hardly convincing.

      We appreciate the reviewer’s concern and have reinforced the causal link between Purkinje-cell synchrony and behavior. To test whether restoring PC synchrony is sufficient to rescue behavior, we introduced a red-shifted opsin (AAV-L7-rsChrimine) into PCs of DTA mice raised to adulthood. During testing we delivered 590-nm light pulses (10 ms, 1 Hz) to the vermis, driving brief, population-wide spiking (new Fig. 8). This periodic re-synchronization left anxiety measures unchanged (open-field center time remained low) but rescued both motor coordination (rotarod latency normalized to control levels) and sociability (time spent with a novel mouse restored). The dissociation implies that distinct behavioral domains differ in their sensitivity to PC timing precision and confirms that reduced synchrony—not cell loss or gross circuit damage (Fig. S1F, S2)—is the primary driver of the motor and social deficits. Together, the optogenetic rescue establishes a bidirectional, mechanistic link between PC synchrony and behavior, addressing the reviewer’s reservations about the original experiment. We have added these descriptions in Result (lines 394-415)

      In summary, while the authors used a specific tool to probe the role of developmental oligodendrocytes in cerebellar physiology and function, they failed to answer specific questions regarding this role, which they could have done with more fine-grained experimental analysis.

      Thank you once again for your constructive suggestions and comments. We believe these changes have improved the clarity and readability of our manuscript.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) Show that ODC loss is specific to the cerebellum.

      We thank the reviewer for requesting additional evidence. To verify that oligodendrocyte ablation was confined to the cerebellum, we injected an AAV carrying mCherry under the human MAG promoter (AAV-hMAG-mCherry) into the cerebellum, and screened the whole brain one week later. As shown in the new Figure 1E–G, mCherry positive cells were present throughout the injected cerebellar cortex (Fig. 1E), but no fluorescent cells were detected in extracerebellar regions—including cerebral cortex, medulla, pons, midbrain. These data demonstrate that our viral approach are specific to the cerebellum, ruling out off-target demyelination elsewhere in the CNS as a contributor to the behavioral and synchrony phenotypes. We have added these descriptions in Result (lines 262-264)

      (2) Characterize the gross morphology of the cerebellum at different developmental stages. Are major cell types all present? Major pathways preserved? 

      We thank the reviewer for requesting additional evidence. To ensure that the developmental loss of oligodendrocytes did not globally disturb cerebellar architecture, we performed a comprehensive histological and electrophysiological survey during development. New data are presented (new Fig. S1–S2, Fig. 3E-H).

      (1) Overall morphology. Low-magnification parvalbumin counterstaining revealed similar cerebellar area in DTA versus control mice at every age (Fig. S1F, G).

      (2) Major neuronal classes. Quantification of parvalbumin-positive Purkinje cells and interneurons showed no differences in density between control and DTA (Fig. S2E, H, M, N, P). Purkinje dendritic arbors were not different between control and DTA (Fig. S2G, O).

      (3) Excitatory and inhibitory synapse inputs. Miniature IPSCs and Parallel-fiber-EPSCs onto Purkinje cells were quantified; neither was differed between groups (Fig. 3E-G).

      (4) Glial populations. IBA1-positive microglia and S100β-positive astrocytes exhibited normal density and marker intensity (Fig. S2).

      Taken together, these analyses show that all major cell types are present at normal density, synaptic inputs from excitatory and inhibitory neurons are preserved, and gross cerebellar morphology is intact after DTA-mediated oligodendrocyte ablation.

      (3) Recording of PNs to see whether the lack of synchrony is due to CFs or simple spikes.

      We thank the reviewer for drawing attention to the work of Ramirez & Stell (2016), which showed that simple-spike bursts can elicit Ca<sup>2+</sup> rises, but only in the soma and proximal dendrites of adult Purkinje cells. In our study, Regions of Interest were restricted to the dendritic arbor, where SS-evoked signals are essentially undetectable (Ramirez & Stell, 2016), whereas climbing-fiber complex spikes generate large, all-or-none transients (Good et al., 2017). Accordingly, even if a rare SS-driven event reached threshold it would likely fall outside our ROIs.

      In addition, we directly imaged CF population activity by expressing GCaMP7f in inferior-olive neurons. Correlation analysis of CF boutons revealed that DTA ablation lowers CF–CF synchrony at P14 (new Fig. 3A–D). Because CF synchrony is a principal driver of Purkinje-cell co-activation, this reduction provides a mechanistic link between oligodendrocyte loss and the hyposynchrony we observe among Purkinje cells. Consistent with this interpretation, electrophysiological recordings showed that parallel-fiber EPSCs and inhibitory synaptic inputs onto Purkinje cells were unchanged by DTA treatment (Fig. 3E-H) , which makes it less likely that the reduced synchrony simply reflects changes in other excitatory or inhibitory synaptic drive.

      That said, SS-dependent somatic Ca<sup>2+</sup> signals could still influence downstream plasticity and long-term cerebellar function. In future work we therefore plan to combine somatic imaging with stage-specific oligodendrocyte manipulations to test whether SS-evoked Ca²⁺ dynamics are themselves modulated by oligodendrocyte support. We have added these descriptions in the Results (lines 301–312) and Discussion (lines 423–434).

      (4) Is CF synapse elimination altered? Test using evoked EPSCs or staining methods.

      We agree that directly testing whether oligodendrocyte loss disturbs climbing-fiber synapse elimination would provide a full mechanistic picture. We are already quantifying climbing fiber terminal number with vGluT2 immunostaining and recording evoked CF-EPSCs in the same DTA model; these data, together with an analysis of how population synchrony is involved in synapse elimination, will form the basis of a separate manuscript now in preparation. To keep the present paper focused on the phenomena we have rigorously documented—transient oligodendrocyte loss and the resulting long-lasting hyposynchrony and abnormal behaviors—we have removed the speculative sentence on oligodendrocyte-mediated synapse elimination. We believe this revision meets the reviewer’s request without over-extending the current dataset.

      Thank you once again for your constructive suggestions and comments. We believe these changes have improved the clarity and readability of our manuscript.

    1. Author response:

      Reviewer #1

      (1) The main weakness is that the study is wholly in vitro, using cultured hippocampal neurons.

      We appreciate this reviewer's concern about the limitation of cultured hippocampal neurons in extracting disease-related spine phenotypes. While we fully recognize this limitation, we consider that this in vitro system has several advantages that contribute to translational research on mental disorders.

      First, our culture system has been shown to support the development of spine morphology similar to that of the hippocampal CA1 excitatory synapse in vivo. High-resolution imaging techniques confirmed that the in vitro spine structure was highly preserved compared with in vivo preparations (Kashiwagi et al., Nature Communications, 2019). The present study used the same culture system and SIM imaging. Therefore, the difference we detected in samples derived from disease models is likely to reflect impairment of molecular mechanisms underlying native structural development in vivo.

      Second, super-resolution imaging of thousands of spines in tissue preparations under precisely controlled conditions cannot be practically applied using currently available techniques. The advantage of our imaging and analytical pipeline is its reproducibility, which enabled us to compare the spine population data from eight different mouse models without normalization.

      Third, a reduced culture system can demonstrate the direct effects of gene mutations on synapse phenotypes, independent of environmental influences. This property is highly advantageous for screening chemical compounds that rescue spine phenotypes. Neuronal firing patterns and receptor functions can also be easily controlled in a culture system. The difference in spine structure between ASD and schizophrenia mouse models is valuable information to establish a drug screening system.

      Fourth, establishing an in vitro system for evaluating synapse phenotypes could reduce the need for animal experiments. Researchers should be aware of the 3Rs principles. In the future, combined with differentiation techniques for human iPS cells, our in vitro approach will enable the evaluation of disease-related spine phenotypes without the need for animal experiments. The effort to establish a reliable culture system should not be eliminated.

      (2) Another weakness is that CaMKIIαK42R/K42R mutant mice are presented as a schizophrenia model.

      We agree with this reviewer that CAMK2A mutations in humans are linked to multiple mental disorders, including developmental disorders, ASD, and schizophrenia. Association of gene mutations with the categories of mental disorders is not straightforward, as the symptoms of these disorders also overlap with each other. For the CaMKIIα K42R/K42R mutant, we considered the following points in its characterization as a model of mental disorder. Analysis of CaMKIIα +/- mice in Dr. Tsuyoshi Miyakawa's lab has provided evidence for the reduced CaMKIIα in schizophrenia-related phenotypes (Yamasaki et al., Mol Brain 2008; Frankland et al., Mol Brain Editorial 2008). It is also known that the CaMKIIα R8H mutation in the kinase domain is linked to schizophrenia (Brown et al., 2021). Both CaMKIIα R8H and CaMKIIα K42R mutations are located in the N-terminal domain and eliminate kinase activity. On the other hand, the representative CaMKIIα E183V mutation identified in ASD patients exhibits unique characteristics, including reduced kinase activity, decreased protein stability and expression levels, and disrupted interactions with ASD-associated proteins such as Shank3 (Stephenson et al., 2017). Importantly, reduced dendritic spines in neurons expressing CaMKIIα E183V is a property opposite to that of the CaMKIIα K42R/K42R mutant, which showed increased spine density (Koeberle et al. 2017).

      Different CAMK2A mutations likely cause distinct phenotypes observed in the broad spectrum of mental disorders. In the revised manuscript, we will include a discussion of the relevant literature to categorize this mouse model appropriately.

      References related to this discussion.

      (1) Yamasaki et al., Mol Brain. 2008 DOI: 10.1186/1756-6606-1-6

      (2) Frankland et al. Mol Brain. 2008 DOI: 10.1186/1756-6606-1-5

      (3) Stephenson et al., J Neurosci. 2017 DOI: 10.1523/JNEUROSCI.2068-16.2017

      (4) Koeberle et al. Sci Rep. 2017 DOI: 10.1038/s41598-017-13728-y

      (5) Brown et al., iScience. 2021 DOI: 10.1016/j.isci.2021.103184

      Reviewer #2

      We recognize the reviewer's comments as important for improving our manuscript. We outline our general approach to addressing major concerns. Detailed responses to each point, along with additional data, will be provided in a formal revised manuscript.

      (1) Demonstrating the robustness of statistical analyses

      We appreciate this reviewer's concern about our strategies for the quantitative analysis of the large spine population. For the PCA analysis (Point 2), our preliminary results indicated that including all parameters or the selected five parameters did not make a significant difference in the relative placement of spines with specific morphologies in the feature space defined by the principal components. This point will be discussed in the revised manuscript. The potential problem of selecting a particular region within a feature space for spine shape analysis (Point 1) can be addressed by using alternative simulation-based approaches, such as bootstrap or permutation tests. These analyses will be included in the revised manuscript. The use of sample numbers in statistical analyses should align with the analysis's purpose (Point 3). When analyzing the distribution of samples in the feature space, it is necessary to use spine numbers for statistical assessment. We will recheck the statistical methods and apply the appropriate method for each analysis. The spine population data in Figures 2 and 8 cannot be directly compared, as the spine visualization methods differ (Figure 2 with membrane DiI labeling; Figure 8 with cytoplasmic GFP labeling) (Point 9). Spine populations of the same size are inevitably plotted in different feature spaces. This point will be discussed more clearly in the revised manuscript.

      (2) Clarification of experimental conditions and data reliability

      Per this reviewer's suggestion, we will provide more information on the genetic background of mice and the differences in spine structure from DIV 18-22 (Points 4 and 5). We will also provide additional validation data for the functional analyses using knockdown and overexpression methods, for which we already have preliminary data (Point 7). Concerns about the interpretation of data obtained from in vitro culture (Point 12), raised by this reviewer, are also noted by reviewer #1. As explained in the response to reviewer #1, we intentionally selected an in vitro culture system to analyze multiple samples derived from mouse models of mental disorders for several reasons. Nevertheless, we will revise the discussion and incorporate the points this reviewer raised regarding the disadvantages of in vitro systems.

      (3) Validation of biological mechanisms and interpretation

      In the computational modeling (Point 6), we started from the data of spine turnover (excluding the data of spine volume increase/decrease), fitted the model with the data, and found that the best-fit model showed three features: fast spine turnover, lower spine density, and smaller size of transient spines in schizophrenia mouse models. As the reviewer noted, information about spine turnover is already present in the input data. However, the other two properties are generated independently of the input data, indicating the value of this model. We plan to add additional confirmatory analyses to this model in the revised manuscript.

      In response to Point 8, we will provide supporting data on the functional role of Ecgr4 in synapse regulation. We will also refine our discussion on the ASD and Schizophrenia phenotypes based on the suggested literature (Points 10 and 11). Quantification of the initial growth of spines is technically demanding, as it requires higher imaging frequency and longer time-lapse recordings to capture rare events. It is difficult to conclude which of the two possibilities, slow spine growth or initial size differences, is correct, based on our available data. This point will be discussed in the revised manuscript (Point 13).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary

      This is a strong paper that presents a clear advance in multi-animal tracking. The authors introduce an updated version of idtracker.ai that reframes identity assignment as a contrastive learning problem rather than a classification task requiring global fragments. This change leads to gains in speed and accuracy. The method eliminates a known bottleneck in the original system, and the benchmarking across species is comprehensive and well executed. I think the results are convincing and the work is significant.

      Strengths

      The main strengths are the conceptual shift from classification to representation learning, the clear performance gains, and the fact that the new version is more robust. Removing the need for global fragments makes the software more flexible in practice, and the accuracy and speed improvements are well demonstrated. The software appears thoughtfully implemented, with GUI updates and integration with pose estimators.

      Weaknesses

      I don't have any major criticisms, but I have identified a few points that should be addressed to improve the clarity and accuracy of the claims made in the paper.

      (1) The title begins with "New idtracker.ai," which may not age well and sounds more promotional than scientific. The strength of the work is the conceptual shift to contrastive representation learning, and it might be more helpful to emphasize that in the title rather than branding it as "new."

      We considered using “Contrastive idtracker.ai”. However, we thought that readers could then think that we believe they could use both the old idtracker.ai or this contrastive version. But we want to say that the new version is the one to use as it is better in both accuracy and tracking times. We think “New idtracker.ai” communicates better that this version is the version we recommend.

      (2) Several technical points regarding the comparison between TRex (a system evaluated in the paper) and idtracker.ai should be addressed to ensure the evaluation is fair and readers are fully informed.

      (2.1) Lines 158-160: The description of TRex as based on "Protocol 2 of idtracker.ai" overlooks several key additions in TRex, such as posture image normalization, tracklet subsampling, and the use of uniqueness feedback during training. These features are not acknowledged, and it's unclear whether TRex was properly configured - particularly regarding posture estimation, which appears to have been omitted but isn't discussed. Without knowing the actual parameters used to make comparisons, it's difficult to dassess how the method was evaluated.

      We added the information about the key additions of TRex in the section “The new idtracker.ai uses representation learning”, lines 153-157. Posture estimation in TRex was not explicitly used but neither disabled during the benchmark; we clarified this in the last paragraph of “Benchmark of accuracy and tracking time”, lines 492-495.

      (2.2) Lines 162-163: The paper implies that TRex gains speed by avoiding Protocol 3, but in practice, idtracker.ai also typically avoids using Protocol 3 due to its extremely long runtime. This part of the framing feels more like a rhetorical contrast than an informative one.

      We removed this, see new lines 153-157.

      (2.3) Lines 277-280: The contrastive loss function is written using the label l, but since it refers to a pair of images, it would be clearer and more precise to write it as l_{I,J}. This would help readers unfamiliar with contrastive learning understand the formulation more easily.

      We added this change in lines 613-620.

      (2.4) Lines 333-334: The manuscript states that TRex can fail to track certain videos, but this may be inaccurate depending on how the authors classify failures. TRex may return low uniqueness scores if training does not converge well, but this isn't equivalent to tracking failure. Moreover, the metric reported by TRex is uniqueness, not accuracy. Equating the two could mislead readers. If the authors did compare outputs to human-validated data, that should be stated more explicitly.

      We observed TRex crashing without outputting any trajectories on some occasions (Appendix 1—figure 1), and this is what we labeled as “failure”. These failures happened in the most difficult videos of our benchmark, that’s why we treated them the same way as idtracker.ai going to P3. We clarified this in new lines 464-469.

      The accuracy measured in our benchmark is not estimated but it is human-validated (see section Computation of tracking accuracy in Appendix 1). Both softwares report some quality estimators at the end of a tracking (“estimated accuracy” for idtracker.ai and "uniqueness” for TRex) but these were not used in the benchmark.

      (2.5) Lines 339-341: The evaluation approach defines a "successful run" and then sums the runtime across all attempts up to that point. If success is defined as simply producing any output, this may not reflect how experienced users actually interact with the software, where parameters are iteratively refined to improve quality.

      Yes, our benchmark was designed to be agnostic to the different experiences of the user. Also, our benchmark was designed for users that do not inspect the trajectories to choose parameters again not to leave room for potential subjectivity.

      (2.6) Lines 344-346: The simulation process involves sampling tracking parameters 10,000 times and selecting the first "successful" run. If parameter tuning is randomized rather than informed by expert knowledge, this could skew the results in favor of tools that require fewer or simpler adjustments. TRex relies on more tunable behavior, such as longer fragments improving training time, which this approach may not capture.

      We precisely used the TRex parameter track_max_speed to elongate fragments for optimal tracking. Rather than randomized parameter tuning, we defined the “valid range” for this parameter so that all values in it would produce a decent fragment structure. We used this procedure to avoid worsening those methods that use more parameters.

      (2.7) Line 354 onward: TRex was evaluated using two varying parameters (threshold and track_max_speed), while idtracker.ai used only one (intensity_threshold). With a fixed number of samples, this asymmetry could bias results against TRex. In addition, users typically set these parameters based on domain knowledge rather than random exploration.

      idtracker.ai and TRex have several parameters. Some of them have a single correct value (e.g. number of animals) or the default value that the system computes is already good (e.g. minimum blob size). For a second type of parameters, the system finds a value that is in general not as good, so users need to modify them. In general, users find that for this second type of parameter there is a valid interval of possible values, from which they need to choose a single value to run the system. idtracker.ai has intensity_threshold as the only parameter of this second type and TRex has two: threshold and track_max_speed. For these parameters, choosing one value or another within the valid interval can give different tracking results. Therefore, when we model a user that wants to run the system once except if it goes to P3 (idtracker.ai) or except if it crashes (TRex), it is these parameters we sample from within the valid interval to get a different value for each run of the system. We clarify this in lines 452-469 of the section “Benchmark of accuracy and tracking time”.

      Note that if we chose to simply run old idtracker.ai (v4 or v5) or TRex a single time, this would benefit the new idtracker.ai (v6). This is because old idtracker.ai can enter the very slow protocol 3 and TRex can fail to track. So running old idtracker.ai or TRex up to 5 times until old idtracker.ai does not use Protocol 3 and TRex does not fail is to make them as good as they can be with respect to the new idtracker.ai

      (2.8) Figure 2-figure supplement 3: The memory usage comparison lacks detail. It's unclear whether RAM or VRAM was measured, whether shared or compressed memory was included, or how memory was sampled. Since both tools dynamically adjust to system resources, the relevance of this comparison is questionable without more technical detail.

      We modified the text in the caption (new Figure 1-figure supplement 2) adding the kind of memory we measured (RAM) and how we measured it. We already have a disclaimer for this plot saying that memory management depends on the machine's available resources. We agree that this is a simple analysis of the usage of computer resources.

      (3) While the authors cite several key papers on contrastive learning, they do not use the introduction or discussion to effectively situate their approach within related fields where similar strategies have been widely adopted. For example, contrastive embedding methods form the backbone of modern facial recognition and other image similarity systems, where the goal is to map images into a latent space that separates identities or classes through clustering. This connection would help emphasize the conceptual strength of the approach and align the work with well-established applications. Similarly, there is a growing literature on animal re-identification (ReID), which often involves learning identity-preserving representations across time or appearance changes. Referencing these bodies of work would help readers connect the proposed method with adjacent areas using similar ideas, and show that the authors are aware of and building on this wider context.

      We have now added a new section in Appendix 3, “Differences with previous work in contrastive/metric learning” (lines 792-841) to include references to previous work and a description of what we do differently.

      (4) Some sections of the Results text (e.g., lines 48-74) read more like extended figure captions than part of the main narrative. They include detailed explanations of figure elements, sorting procedures, and video naming conventions that may be better placed in the actual figure captions or moved to supplementary notes. Streamlining this section in the main text would improve readability and help the central ideas stand out more clear

      Thank you for pointing this out. We have rewritten the Results, for example streamlining the old lines 48-74 (new lines 42-48)  by moving the comments about names, files and order of videos to the caption of Figure 1.

      Overall, though, this is a high-quality paper. The improvements to idtracker.ai are well justified and practically significant. Addressing the above comments will strengthen the work, particularly by clarifying the evaluation and comparisons.

      We thank the reviewer for the detailed suggestions. We believe we have taken all of them into consideration to improve the ms.

      Reviewer #2 (Public review):

      Summary:

      This work introduces a new version of the state-of-the-art idtracker.ai software for tracking multiple unmarked animals. The authors aimed to solve a critical limitation of their previous software, which relied on the existence of "global fragments" (video segments where all animals are simultaneously visible) to train an identification classifier network, in addition to addressing concerns with runtime speed. To do this, the authors have both re-implemented the backend of their software in PyTorch (in addition to numerous other performance optimizations) as well as moving from a supervised classification framework to a self-supervised, contrastive representation learning approach that no longer requires global fragments to function. By defining positive training pairs as different images from the same fragment and negative pairs as images from any two co-existing fragments, the system cleverly takes advantage of partial (but high-confidence) tracklets to learn a powerful representation of animal identity without direct human supervision. Their formulation of contrastive learning is carefully thought out and comprises a series of empirically validated design choices that are both creative and technically sound. This methodological advance is significant and directly leads to the software's major strengths, including exceptional performance improvements in speed and accuracy and a newfound robustness to occlusion (even in severe cases where no global fragments can be detected). Benchmark comparisons show the new software is, on average, 44 times faster (up to 440 times faster on difficult videos) while also achieving higher accuracy across a range of species and group sizes. This new version of idtracker.ai is shown to consistently outperform the closely related TRex software (Walter & Couzin, 2021\), which, together with the engineering innovations and usability enhancements (e.g., outputs convenient for downstream pose estimation), positions this tool as an advancement on the state-of-the-art for multi-animal tracking, especially for collective behavior studies.

      Despite these advances, we note a number of weaknesses and limitations that are not well addressed in the present version of this paper:

      Weaknesses

      (1) The contrastive representation learning formulation. Contrastive representation learning using deep neural networks has long been used for problems in the multi-object tracking domain, popularized through ReID approaches like DML (Yi et al., 2014\) and DeepReID (Li et al., 2014). More recently, contrastive learning has become more popular as an approach for scalable self-supervised representation learning for open-ended vision tasks, as exemplified by approaches like SimCLR (Chen et al., 2020), SimSiam (Chen et al., 2020\), and MAE (He et al., 2021\) and instantiated in foundation models for image embedding like DINOv2 (Oquab et al., 2023). Given their prevalence, it is useful to contrast the formulation of contrastive learning described here relative to these widely adopted approaches (and why this reviewer feels it is appropriate):

      (1.1) No rotations or other image augmentations are performed to generate positive examples. These are not necessary with this approach since the pairs are sampled from heuristically tracked fragments (which produces sufficient training data, though see weaknesses discussed below) and the crops are pre-aligned egocentrically (mitigating the need for rotational invariance).

      (1.2) There is no projection head in the architecture, like in SimCLR. Since classification/clustering is the only task that the system is intended to solve, the more general "nuisance" image features that this architectural detail normally affords are not necessary here.

      (1.3) There is no stop gradient operator like in BYOL (Grill et al., 2020\) or SimSiam. Since the heuristic tracking implicitly produces plenty of negative pairs from the fragments, there is no need to prevent representational collapse due to class asymmetry. Some care is still needed, but the authors address this well through a pair sampling strategy (discussed below).

      (1.4) Euclidean distance is used as the distance metric in the loss rather than cosine similarity as in most contrastive learning works. While cosine similarity coupled with L2-normalized unit hypersphere embeddings has proven to be a successful recipe to deal with the curse of dimensionality (with the added benefit of bounded distance limits), the authors address this through a cleverly constructed loss function that essentially allows direct control over the intra- and inter-cluster distance (D\_pos and D\_neg). This is a clever formulation that aligns well with the use of K-means for the downstream assignment step.

      No concerns here, just clarifications for readers who dig into the review. Referencing the above literature would enhance the presentation of the paper to align with the broader computer vision literature.

      Thank you for this detailed comparison. We have now added a new section in Appendix 3, “Differences with previous work in contrastive/metric learning” (lines 792-841) to include references to previous work and a description of what we do differently, including the points raised by the reviewer.

      (2) Network architecture for image feature extraction backbone. As most of the computations that drive up processing time happen in the network backbone, the authors explored a variety of architectures to assess speed, accuracy, and memory requirements. They land on ResNet18 due to its empirically determined performance. While the experiments that support this choice are solid, the rationale behind the architecture selection is somewhat weak. The authors state that: "We tested 23 networks from 8 different families of state-of-the-art convolutional neural network architectures, selected for their compatibility with consumer-grade GPUs and ability to handle small input images (20 × 20 to 100 × 100 pixels) typical in collective animal behavior videos."

      (2.1) Most modern architectures have variants that are compatible with consumer-grade GPUs. This is true of, for example, HRNet (Wang et al., 2019), ViT (Dosovitskiy et al., 2020), SwinT (Liu et al., 2021), or ConvNeXt (Liu et al., 2022), all of which report single GPU training and fast runtime speeds through lightweight configuration or subsequent variants, e.g., MobileViT (Mehta et al., 2021). The authors may consider revising that statement or providing additional support for that claim (e.g., empirical experiments) given that these have been reported to outperform ResNet18 across tasks.

      Following the recommendation of the reviewer, we tested the architectures SwinT, ConvNeXt and ViT. We found out that none of them outperformed ResNet18 since they all showed a slower learning curve. This would result in higher tracking times. These tests are now included in the section “Network architecture” (lines 550-611).

      (2.2) The compatibility of different architectures with small image sizes is configurable. Most convolutional architectures can be readily adapted to work with smaller image sizes, including 20x20 crops. With their default configuration, they lose feature map resolution through repeated pooling and downsampling steps, but this can be readily mitigated by swapping out standard convolutions with dilated convolutions and/or by setting the stride of pooling layers to 1, preserving feature map resolution across blocks. While these are fairly straightforward modifications (and are even compatible with using pretrained weights), an even more trivial approach is to pad and/or resize the crops to the default image size, which is likely to improve accuracy at a possibly minimal memory and runtime cost. These techniques may even improve the performance with the architectures that the authors did test out.

      The only two tested architectures that require a minimum image size are AlexNet and DenseNet. DenseNet proved to underperform ResNet18 in the videos where the images are sufficiently large. We have tested AlexNet with padded images to see that it also performs worse than ResNet18 (see Appendix 3—figure 1).

      We also tested the initialization of ResNet18 with pre-trained weights from ImageNet (in Appendix 3—figure 2) and it proved to bring no benefit to the training speed (added in lines 591-592).

      (2.3) The authors do not report whether the architecture experiments were done with pretrained or randomly initialized weights.

      We adapted the text to make it clear that the networks are always randomly initialized (lines 591-592, lines 608-609 and the captions of Appendix 3—figure 1 and 2).

      (2.4) The authors do not report some details about their ResNet18 design, specifically whether a global pooling layer is used and whether the output fully connected layer has any activation function. Additionally, they do not report the version of ResNet18 employed here, namely, whether the BatchNorm and ReLU are applied after (v1) or before (v2) the conv layers in the residual path.

      We use ResNet18 v1 with no activation function nor bias in its last layer (this has been clarified in the lines 606-608). Also, by design, ResNet has a global average pool right before the last fully connected layer which we did not remove. In response to the reviewer, Resnet18 v2 was tested and its performance is the same as that of v1 (see Appendix 3—figure 1 and lines 590-591).

      (3) Pair sampling strategy. The authors devised a clever approach for sampling positive and negative pairs that is tailored to the nature of the formulation. First, since the positive and negative labels are derived from the co-existence of pretracked fragments, selection has to be done at the level of fragments rather than individual images. This would not be the case if one of the newer approaches for contrastive learning were employed, but it serves as a strength here (assuming that fragment generation/first pass heuristic tracking is achievable and reliable in the dataset). Second, a clever weighted sampling scheme assigns sampling weights to the fragments that are designed to balance "exploration and exploitation". They weigh samples both by fragment length and by the loss associated with that fragment to bias towards different and more difficult examples.

      (3.1) The formulation described here resembles and uses elements of online hard example mining (Shrivastava et al., 2016), hard negative sampling (Robinson et al., 2020\), and curriculum learning more broadly. The authors may consider referencing this literature (particularly Robinson et al., 2020\) for inspiration and to inform the interpretation of the current empirical results on positive/negative balancing.

      Following this recommendation, we added references of hard negative mining in the new section “Differences with previous work in contrastive/metric learning”, lines 792-841. Regarding curriculum learning, even though in spirit it might have parallels with our sampling method in the sense that there is a guided training of the network, we believe the approach is more similar to an exploration-exploitation paradigm.

      (4) Speed and accuracy improvements. The authors report considerable improvements in speed and accuracy of the new idTracker (v6) over the original idTracker (v4?) and TRex. It's a bit unclear, however, which of these are attributable to the engineering optimizations (v5?) versus the representation learning formulation.

      (4.1) Why is there an improvement in accuracy in idTracker v5 (L77-81)? This is described as a port to PyTorch and improvements largely related to the memory and data loading efficiency. This is particularly notable given that the progression went from 97.52% (v4; original) to 99.58% (v5; engineering enhancements) to 99.92% (v6; representation learning), i.e., most of the new improvement in accuracy owes to the "optimizations" which are not the central emphasis of the systematic evaluations reported in this paper.

      V5 was a two year-effort designed to improve time efficiency of v4. It was also a surprise to us that accuracy was higher, but that likely comes from the fact that the substituted code from v4 contained some small bug/s. The improvements in v5 are retained in v6 (contrastive learning) and v6 has higher accuracy and shorter tracking times. The difference in v6 for this extra accuracy and shorter tracking times is contrastive learning.

      (4.2) What about the speed improvements? Relative to the original (v4), the authors report average speed-ups of 13.6x in v5 and 44x in v6. Presumably, the drastic speed-up in v6 comes from a lower Protocol 2 failure rate, but v6 is not evaluated in Figure 2 - figure supplement 2.

      Idtracker.ai v5 runs an optimized Protocol 2 and, sometimes, the Protocol 3. But v6 doesn’t run either of them. While P2 is still present in v6 as a fallback protocol when contrastive fails, in our v6 benchmark P2 was never needed. So the v6 speedup comes from replacing both P2 and P3 with the contrastive algorithm.

      (5) Robustness to occlusion. A major innovation enabled by the contrastive representation learning approach is the ability to tolerate the absence of a global fragment (contiguous frames where all animals are visible) by requiring only co-existing pairs of fragments owing to the paired sampling formulation. While this removes a major limitation of the previous versions of idtracker.ai, its evaluation could be strengthened. The authors describe an ablation experiment where an arc of the arena is masked out to assess the accuracy under artificially difficult conditions. They find that the v6 works robustly up to significant proportions of occlusions, even when doing so eliminates global fragments.

      (5.1) The experiment setup needs to be more carefully described.

      (5.1.1) What does the masking procedure entail? Are the pixels masked out in the original video or are detections removed after segmentation and first pass tracking is done?

      The mask is defined as a region of interest in the software. This means that it is applied at the segmentation step where the video frame is converted to a foreground-background binary image. The region of interest is applied here, converting to background all pixels not inside of it. We clarified this in the newly added section Occlusion tests, lines 240-244.

      (5.1.2) What happens at the boundary of the mask? (Partial segmentation masks would throw off the centroids, and doing it after original segmentation does not realistically model the conditions of entering an occlusion area.)

      Animals at the boundaries of the mask are partially detected. This can change the location of their detected centroid. That’s why, when computing the ground-truth accuracy for these videos, only the groundtruth centroids that were at minimum 15 pixels further from the mask were considered. We clarified this in the newly added section Occlusion tests, lines 248-251.

      (5.1.3) Are fragments still linked for animals that enter and then exit the mask area?

      No artificial fragment linking was added in these videos. Detected fragments are linked the usual way. If one animal hides into the mask, the animal disappears so the fragment breaks.  We clarified this in the newly added section Occlusion tests, lines 245-247.

      (5.1.4) How is the evaluation done? Is it computed with or without the masked region detections?

      The groundtruth used to validate these videos contains the positions of all animals at all times. But only the positions outside the mask at each frame were considered to compute the tracking accuracy. We clarified this in the newly added section Occlusion tests, lines 248-251.

      (5.2) The circular masking is perhaps not the most appropriate for the mouse data, which is collected in a rectangular arena.

      We wanted to show the same proof of concept in different videos. For that reason, we used to cover the arena parametrized by an angle. In the rectangular arena the circular masking uses an external circle, so it is covering the rectangle parametrized by an angle.

      (5.3) The number of co-existing fragments, which seems to be the main determinant of performance that the authors derive from this experiment, should be reported for these experiments. In particular, a "number of co-existing fragments" vs accuracy plot would support the use of the 0.25(N-1) heuristic and would be especially informative for users seeking to optimize experimental and cage design. Additionally, the number of co-existing fragments can be artificially reduced in other ways other than a fixed occlusion, including random dropout, which would disambiguate it from potential allocentric positional confounds (particularly relevant in arenas where egocentric pose is correlated with allocentric position).

      We included the requested analysis about the fragment connectivity in Figure 3-figure supplement 1. We agree that there can be additional ways of reducing co-existing fragments, but we think the occlusion tests have the additional value that there are many real experiments similar to this test.

      (6) Robustness to imaging conditions. The authors state that "the new idtracker.ai can work well with lower resolutions, blur and video compression, and with inhomogeneous light (Figure 2 - figure supplement 4)." (L156). Despite this claim, there are no speed or accuracy results reported for the artificially corrupted data, only examples of these image manipulations in the supplementary figure.

      We added this information in the same image, new Figure 1 - figure supplement 3.

      (7) Robustness across longitudinal or multi-session experiments. The authors reference idmatcher.ai as a compatible tool for this use case (matching identities across sessions or long-term monitoring across chunked videos), however, no performance data is presented to support its usage. This is relevant as the innovations described here may interact with this setting. While deep metric learning and contrastive learning for ReID were originally motivated by these types of problems (especially individuals leaving and entering the FOV), it is not clear that the current formulation is ideally suited for this use case. Namely, the design decisions described in point 1 of this review are at times at odds with the idea of learning generalizable representations owing to the feature extractor backbone (less scalable), low-dimensional embedding size (less representational capacity), and Euclidean distance metric without hypersphere embedding (possible sensitivity to drift). It's possible that data to support point 6 can mitigate these concerns through empirical results on variations in illumination, but a stronger experiment would be to artificially split up a longer video into shorter segments and evaluate how generalizable and stable the representations learned in one segment are across contiguous ("longitudinal") or discontiguous ("multi-session") segments.

      We have now added a test to prove the reliability of idmatcher.ai in v6. In this test, 14 videos are taken from the benchmark and split in two non-overlapping parts (with a 200 frames gap in between). idmatcher.ai is run between the two parts presenting a 100% accuracy identity matching across all of them (see section “Validity of idmatcher.ai in the new idtracker.ai”, lines 969-1008).

      We thank the reviewer for the detailed suggestions. We believe we have taken all of them into consideration to improve the ms.

      Reviewer #3 (Public review):

      Summary

      The authors propose a new version of idTracker.ai for animal tracking. Specifically, they apply contrastive learning to embed cropped images of animals into a feature space where clusters correspond to individual animal identities.

      Strengths

      By doing this, the new software alleviates the requirement for so-called global fragments - segments of the video, in which all entities are visible/detected at the same time - which was necessary in the previous version of the method. In general, the new method reduces the tracking time compared to the previous versions, while also increasing the average accuracy of assigning the identity labels.

      Weaknesses

      The general impression of the paper is that, in its current form, it is difficult to disentangle the old from the new method and understand the method in detail. The manuscript would benefit from a major reorganization and rewriting of its parts. There are also certain concerns about the accuracy metric and reducing the computational time.

      We have made the following modifications in the presentation:

      (1) We have added section tiles to the main text so it is clearer what tracking system we are referring to. For example, we now have sections “Limitation of the original idtracker.ai”, “Optimizing idtracker.ai without changes in the learning method” and “The new idtracker.ai uses representation learning”.

      (2) We have completely rewritten all the text of the ms until we start with contrastive learning. Old L20-89 is now L20-L66, much shorter and easier to read.

      (3) We have rewritten the first 3 paragraphs in the section “The new idtracker.ai uses representation learning” (lines 68-92).

      (4) We now expanded Appendix 3 to discuss the details of our approach  (lines 539-897).  It discusses in detail the steps of the algorithm, the network architecture, the loss function, the sampling strategy, the clustering and identity assignment, and the stopping criteria in training

      (5) To cite previous work in detail and explain what we do differently, we have now added in Appendix 3 the new section “Differences with previous work in contrastive/metric learning” (lines 792-841).

      Regarding accuracy metrics, we have replaced our accuracy metric with the standard metric IDF1. IDF1 is the standard metric that is applied to systems in which the goal is to maintain consistent identities across time. See also the section in Appendix 1 "Computation of tracking accuracy” (lines 414-436) explaining IDF1 and why this is an appropriate metric for our goal.

      Using IDF1 we obtain slightly higher accuracies for the idtracker.ai systems. This is the comparison of mean accuracy over all our benchmark for our previous accuracy score and the new one for the full trajectories:

      v4:   97.42% -> 98.24%

      v5:   99.41% -> 99.49%

      v6:   99.74% -> 99.82%

      trex: 97.89% -> 97.89%

      We thank the reviewer for the suggestions about presentation and about the use of more standard metrics.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) Figure 1a: A graphical legend inset would make it more readable since there are multiple colors, line styles, and connecting lines to parse out.

      Following this recommendation, we added a graphical legend in the old Figure 1 (new Figure 2).

      (2) L46: "have images" → "has images".

      We applied this correction. Line 35.

      (3) L52: "videos start with a letter for the species (z,**f**,m)", but "d" is used for fly videos.

      We applied this correction in the caption of Figure 1.

      (4) L62: "with Protocol 3 a two-step process" → "with Protocol 3 being a two-step process".

      We rewrote this paragraph without mentioning Protocol 3, lines 37-41.

      (5) L82-89: This is the main statement of the problems that are being addressed here (speed and relaxing the need for global fragments). This could be moved up, emphasized, and made clearer without the long preamble and results on the engineering optimizations in v5. This lack of linearity in the narrative is also evident in the fact that after Figure 1a is cited, inline citations skip to Figure 2 before returning to Figure 1 once the contrastive learning is introduced.

      We have rewritten all the text until the contrastive learning, (old lines 20-89 are now lines 20-66). The text is shorter, more linear and easier to read.

      (6) L114: "pairs until the distance D_{pos}" → "pairs until the distance approximates D_{pos}".

      We rewrote as “ pairs until the distance 𝐷pos (or 𝐷neg) is reached” in line 107.

      (7) L570: Missing a right parenthesis in the equation.

      We no longer have this equation in the ms.

      (8) L705: "In order to identify fragments we, not only need" → "In order to identify fragments, we not only need".

      We applied this correction, Line 775.

      (9) L819: "probably distribution" → "probability distribution".

      We applied this correction, Line 776.

      (10) L833: "produced the best decrease the time required" → "produced the best decrease of the time required".

      We applied this correction, Line 746.

      Reviewer #3 (Recommendations for the authors):

      (1) We recommend rewriting and restructuring the manuscript. The paper includes a detailed explanation of the previous approaches (idTracker and idTracker.ai) and their limitations. In contrast, the description of the proposed method is short and unstructured, which makes it difficult to distinguish between the old and new methods as well as to understand the proposed method in general. Here are a few examples illustrating the problem. 

      (1.1) Only in line 90 do the authors start to describe the work done in this manuscript. The previous 3 pages list limitations of the original method.

      We have now divided the main text into sections, so it is clearer what is the previous method (“Limitation of the original idtracker.ai”, lines 28-51), the new optimization we did of this method (“Optimizing idtracker.ai without changes in the learning method”, lines 52-66) and the new contrastive approach that also includes the optimizations (“The new idtracker.ai uses representation learning”, lines 66-164). Also, the new text has now been streamlined until the contrastive section, following your suggestion. You can see that in the new writing the three sections are 25 , 15 and 99 lines. The more detailed section is the new system, the other two are needed as reference, to describe which problem we are solving and the extra new optimizations.  

      (1.2) The new method does not have a distinct name, and it is hard to follow which idtracker.ai is a specific part of the text referring to. Not naming the new method makes it difficult to understand.

      We use the name new idtracker.ai (v6) so it becomes the current default version. v5 is now obsolete, as well as v4. And from the point of view of the end user, no new name is needed since v6 is just an evolution of the same software they have been using. Also, we added sections in the main text to clarify the ideas in there and indicate the version of idtracker.ai we are referring to.

      (1.3) There are "Protocol 2" and "Protocol 3" mixed with various versions of the software scattered throughout the text, which makes it hard to follow. There should be some systematic naming of approaches and a listing of results introduced.

      Following this recommendation we no longer talk about the specific protocols of the old version of idtracker.ai in the main text. We rewritten the explanation of these versions in a more clear and straightforward way, lines 29-36.

      (2) To this end, the authors leave some important concepts either underexplained or only referenced indirectly via prior work. For example, the explanation of how the fragments are created (line 15) is only explained by the "video structure" and the algorithm that is responsible for resolving the identities during crossings is not detailed (see lines 46-47, 149-150). Including summaries of these elements would improve the paper's clarity and accessibility.

      We listed the specific sections from our previous publication where the reader can find information about the entire tracking pipeline (lines 539-549). This way, we keep the ms clear and focused on the new identification algorithm while indicating where to find such information.

      (3) Accuracy metrics are not clear. In line 319, the authors define it as based on "proportion of errors in the trajectory". This proportion is not explained. How is the error calculated if a trajectory is lost or there are identity swaps? Multi-object tracking has a range of accuracy metrics that account for such events but none of those are used by the authors. Estimating metrics that are common for MOT literature, for example, IDF1, MOTA, and MOTP, would allow for better method performance understanding and comparison.

      In the new ms, we replaced our accuracy metric with the standard metric IDF1. IDF1 is the standard metric that is applied to systems in which the goal is to maintain consistent identities across time. See also the section in Appendix 1 "Computation of tracking accuracy” explaining why IDF1 and not MOTA or MOTP is the adequate metric for a system that wants to give correct tracking by identification in time. See lines 416-436.

      Using IDF1 we obtain slightly higher accuracies for the idtracker.ai systems. This is the comparison of mean accuracy four our previous accuracy and the new one for the full trajectories:

      v4:   97.42% -> 98.24%

      v5:   99.41% -> 99.49%

      v6:   99.74% -> 99.82%

      trex: 97.89% -> 97.89%

      (4) Additionally, the authors distinguish between tracking with and without crossings, but do not provide statistics on the frequency of crossings per video. It is also unclear how the crossings are considered for the final output. Including information such as the frame rate of the videos would help to better understand the temporal resolution and the differences between consecutive frames of the videos.

      We added this information in the Appendix 1 “Benchmark of accuracy and tracking time”, lines 445-451. The framerate in our benchmark videos goes from 25 to 60 fps (average of 37 fps). On average 2.6% of the blobs are crossings (1.1% for zebrafish 0.7% for drosophila 9.4% for mice).

      (5) In the description of the dataset used for evaluation (lines 349-365), the authors describe the random sampling of parameter values for each tracking run. However, it is unclear whether the same values were used across methods. Without this clarification, comparisons between the proposed method, older versions, and TRex might be biased due to lucky parameter combinations. In addition, the ranges from which the values were randomly sampled were also not described.

      Only one parameter is shared between idtracker.ai and TRex: intensity_threshold (in idtracker.ai) and threshold (in TRex). Both are conceptually equivalent but differ in their numerical values since they affect different algorithms. V4, v5, and TRex each required the same process of independent expert visual inspection of the segmentation to select the valid value range. Since versions 5 and 6 use exactly the same segmentation algorithm, they share the same parameter ranges.

      All the ranges of valid values used in our benchmark are public here https://drive.google.com/drive/folders/1tFxdtFUudl02ICS99vYKrZLeF28TiYpZ as stated in the section “Data availability”, lines 227-228.

      (6) Lines 122-123, Figure 1c. "batches" - is an imprecise metric of training time as there is no information about the batch size.

      We clarified the Figure caption, new Figure 2c.

      (7) Line 145 - "we run some steps... For example..." leaves the method description somewhat unclear. It would help if you could provide more details about how the assignments are carried out and which metrics are being used.

      Following this recommendation, we listed the specific sections from our previous publication where the reader can find information about the entire tracking pipeline (lines 539-549). This way, we keep the ms clear and focused on the new identification algorithm while indicating where to find such information.

      (8) Figure 3. How is tracking accuracy assessed with occlusions? Are the individuals correctly recognized when they reappear from the occluded area?

      The groundtruth for this video contains the positions of all animals at all times. Only the groundtruth points inside the region of interest are taken into account when computing the accuracy. When the tracking reaches high accuracy, it means that animals are successfully relabeled every time they enter the non-masked region. Note that this software works all the time by identification of animals, so crossings and occlusion are treated the same way. What is new here is that the occlusions are so large that there are no global fragments. We clarified this in the new section “Occlusion tests” in Methods, lines 239-251.

      (9) Lines 185-187 this part of the sentence is not clear.

      We rewrote this part in a clearer way, lines 180-182.

      (10) The authors also highlight the improved runtime performance. However, they do not provide a detailed breakdown of the time spent on each component of the tracking/training pipeline. A timing breakdown would help to compare the training duration with the other components. For example, the calculation of the Silhouette Score alone can be time-consuming and could be a bottleneck in the training process. Including this information would provide a clearer picture of the overall efficiency of the method.

      We measured that the training of ResNet takes on average in our benchmark 47% of the tracking time (we added this information line 551 section “Network Architecture”). In this training stage the bottleneck becomes the network forward and backward pass, limited by the GPU performance. All other processes happening during training have been deeply optimized and parallelized when needed so their contribution to the training time is minimal. Apart from the training, we also measured 24.4% of the total tracking time spent in reading and segmenting the video files and 11.1% in processing the identification images and detecting crossings.

      (11) An important part of the computational cost is related to model training. It would be interesting to test whether a model trained on one video of a specific animal type (e.g., zebrafish_5) generalizes to another video of the same type (e.g., zebrafish_7). This would assess the model's generalizability across different videos of the same species and spare a lot of compute. Alternatively, instead of training a model from scratch for each video, the authors could also consider training a base model on a superset of images from different videos and then fine-tuning it with a lower learning rate for each specific video. This could potentially save time and resources while still achieving good performance.

      Already before v6, there was the possibility for the user to start training the identification network by copying the final weights from another tracking session. This knowledge transfer feature is still present in v6 and it still decreases the training times significatively. This information has been added in Appendix 4, lines 906-909.

      We have already begun working on the interesting idea of a general base model but it brings some complex challenges. It could be a very useful new feature for future idtracker.ai releases.

      We thank the reviewer for the many suggestions. We have implemented all of them.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #2 (Public review):

      (1) Vglut2 isn't a very selective promoter for the STN. Did the authors verify every injection across brain slices to ensure the para-subthalamic nucleus, thalamus, lateral hypothalamus, and other Vglut2-positive structures were never infected?

      The STN is anatomically well-confined, with its borders and the overlying zona incerta (composed of GABAergic neurons) providing protection against off-target expression in most neighboring forebrain regions. All viral injections were histologically verified and did not into extend into thalamic or hypothalamic areas. As described in the Methods, we employed an app we developed (Brain Atlas Analyzer, available on OriginLab) that aligns serial histological sections with the Allen Brain Atlas to precisely assess viral spread and confirm targeting accuracy. The experiments included in the revised manuscript now focus on optogenetic inhibition and irreversible lesion approaches—three complementary methods that consistently targeted the STN and yielded similar behavioral effects.

      (2) The authors say in the methods that the high vs low power laser activation for optogenetic experiments was defined by the behavioral output. This is misleading, and the high vs low power should be objectively stated and the behavioral results divided according to the power used, not according to the behavioral outcome.

      Optogenetic excitation is no longer part of the study.

      (3) In the fiber photometry experiments exposing mice to the range of tones, it is impossible to separate the STN response to the tone from the STN response to the movement evoked by the tone. The authors should expose the mouse to the tones in a condition that prevents movement, such as anesthetized or restrained, to separate out the two components.

      The new mixed-effects modeling approach clearly differentiates sensory (auditory) from motor contributions during tone-evoked STN activation. In prior work (see Hormigo et al, 2023, eLife), we explored experimental methods such as head restraint or anesthesia to reduce movement, but we concluded that these approaches are unsuitable for addressing this question. Mice exhibit substantial residual movement even when head-fixed, and anesthesia profoundly alters neural excitability and behavioral state, introducing major confounds. To fully eliminate movement would require paralysis and artificial ventilation, which would again disrupt physiological network dynamics and raise ethical concerns. Therefore, the current modeling approach—incorporating window-specific covariates for movement—is the most appropriate and rigorous way to dissociate tone-evoked sensory activity from motor activity in behaving animals.

      (4) The claim 'STN activation is ideally suited to drive active avoids' needs more explanation. This claim comes after the fiber photometry experiments during active avoidance tasks, so there has been no causality established yet.

      Text adjusted. 

      (5) The statistical comparisons in Figure 7E need some justification and/or clarification. The 9 neuron types are originally categorized based on their response during avoids, then statistics are run showing that they respond differently during avoids. It is no surprise that they would have significantly different responses, since that is how they were classified in the first place. The authors must explain this further and show that this is not a case of circular reasoning.

      Statistically verifying the clustering is useful to ensure that the selected number of clusters reflects distinct classes. It is also necessary when different measurements are used to classify (movement time series classified the avoids) and to compare neuronal types within each avoid mode/class (know called “mode”). Moreover, the new modeling approach goes beyond the prior statistical limitations related to considering movement and neuronal variables separately. 

      (6) The authors show that neurons that have strong responses to orientation show reduced activity during avoidance. What are the implications of this? The author should explain why this is interesting and important.

      The new modeling approach goes beyond the prior analysis limitations. For instance, it shows that most of the prior orienting related activations closely reflect the orienting movement, and only in a few cases (noted and discussed in the results) orienting activations are related to the behavioral contingencies or behavioral outcomes in the task. 

      (8) The experiments in Figure 10 are used to say that STN stimulation is not aversive, but they only show that STN stimulation cannot be used as punishment in place of a shock. This doesn't mean that it is not aversive; it just means it is not as aversive as a shock. The authors should do a simpler aversion test, such as conditioned or real-time place preference, to claim that STN stimulation is not aversive. This is particularly surprising as previous work (Serra et al., 2023) does show that STN stimulation is aversive.

      Optogenetic excitation is no longer part of the study. 

      (7) It is not clear which conditions each mouse experienced in which order. This is critical to the interpretation of Figure 9 and the reduction of passive avoids during STN stimulation. Did these mice have the CS1+STN stimulation pairing or the STN+US pairing prior to this experiment? If they did, the stimulation of the STN could be strongly associated with either punishment or with the CS1 that predicts punishment. If that is the case, stimulating the STN during CS2 could be like presenting CS1+CS2 at the same time and could be confusing.

      Optogenetic excitation is no longer part of the study. 

      (8) The experiments in Figure 10 are used to say that STN stimulation is not aversive, but they only show that STN stimulation cannot be used as punishment in place of a shock. This doesn't mean that it is not aversive; it just means it is not as aversive as a shock. The authors should do a simpler aversion test, such as conditioned or real-time place preference, to claim that STN stimulation is not aversive. This is particularly surprising as previous work (Serra et al., 2023) does show that STN stimulation is aversive.

      Optogenetic excitation is no longer part of the study.

      (9) In the discussion, the idea that the STN encodes 'moving away' from contralateral space is pretty vague and unsupported. It is puzzling that the STN activates more strongly to contraversive turns, but when stimulated, it evokes ipsiversive turns; however, it seems a stretch to speculate that this is related to avoidance. In the last experiments of the paper, the axons from the STN to the GPe and to the midbrain are selectively stimulated. Do these evoke ipsiversive turns similarly?

      Optogenetic excitation is no longer part of the study. 

      (10) In the discussion, the authors claim that the STN is essential for modulating action timing in response to demands, but their data really only show this in one direction. The STN stimulation reliably increases the speed of response in all conditions (except maximum speed conditions such as escapes). It seems to be over-interpreting the data to say this is an inability to modulate the speed of the task, especially as clear learning and speed modulation do occur under STN lesion conditions, as shown in Figure 12B. The mice learn to avoid and increase their latency in AA2 vs AA1, though the overall avoids and latency are different from controls. The more parsimonious conclusion would be that STN stimulation biases movement speed (increasing it) and that this is true in many different conditions.

      Optogenetic excitation is no longer part of the study.

      (11)  In the discussion, the authors claim that the STN projections to the midbrain tegmentum directly affect the active avoidance behavior, while the STN projections to the SNr do not affect it. This seems counter to their results, which show STN projections to either area can alter active avoidance behavior. What is the laser power used in these terminal experiments? If it is high (3mW), the authors may be causing antidromic action potentials in the STN somas, resulting in glutamate release in many brain areas, even when terminals are only stimulated in one area. The authors could use low (0.25mW) laser power in the terminals to reduce the chance of antidromic activation and spatially restrict the optical stimulation.

      Optogenetic excitation is no longer part of the study. 

      (12) Was normality tested for data prior to statistical testing?

      Yes, although now we use mixed models

      (13) Why are there no error bars on Figure 5B, black circles and orange triangles?

      When error bars are not visible, they are smaller than the trace thickness or bar line—for example, in Figure 5B, the black circles and orange triangles include error bars, but they are smaller than the symbol size.

      Reviewer #3 (Public review):

      (1) I really don't understand or accept this idea that delayed movement is necessarily indicative of cautious movements. Is the distribution of responses multi-modal in a way that might support this idea, or do the authors simply take a normal distribution and assert that the slower responses represent 'caution'? Even if responses are multi-modal and clearly distinguished by 'type', why should readers think this that delayed responses imply cautious responding instead of say: habituation or sensitization to cue/shock, variability in attention, motivation, or stress; or merely uncertainty which seems plausible given what I understand of the task design where the same mice are repeatedly tested in changing conditions. This relates to a major claim (i.e., in the work's title).

      In our study, “caution” is defined operationally as the tendency to delay initiation of an avoidance response in demanding situations (e.g., taking more time or care before crossing a busy street). The increase in avoidance latency with task difficulty is highly robust, as we have shown previously through detailed analyses of timing distributions and direct comparisons with appetitive behaviors (e.g., Zhou et al., 2022 JNeurosci). Moreover, we used the tracked movement time series to statistically classify responses into cautious modes, which is likely novel. This definition can dissociate cautious responding from broader constructs listed by a reviewer, such as attention, motivation, or stress, which must be explicitly defined to be rigorously considered in this context, including the likelihood that they covary with caution without being equivalent to it. 

      Cue-evoked orienting responses at CS onset are directly measured, and their habituation and sensitization have been characterized in our prior work (e.g., Zhou et al., 2023 JNeurosci). US-evoked escapes are also measured in the present study and directly compared with avoidance responses. Together, these analyses provide a rigorous and consistent framework for defining and quantifying caution within our behavioral procedures.

      Importantly, mice exhibit cautious responding as defined here across different tasks, making it more informative to classify avoidance responses by behavioral mode rather than by task alone. Accordingly, in the miniscope, single-neuron, and mixed-effects model analyses, we classified active avoids into distinct modes reflecting varying levels of caution. Although these modes covary with task contingencies, their explicit classification improves model predictability and interpretability with respect to cautious responding.

      (2) Related to the last, I'm struggling to understand the rationale for dividing cells into 'types' based the their physiological responses in some experiments (e.g., Figure 7).

      This section has now been expanded into 3 figures (Fig. 7-9) with new modeling approaches that should make the rationale more straight forward.

      By emphasizing the mixed-effects modeling results and integrating these analyses directly into the figures, the revised manuscript now more clearly delineates what is encoded at the population and single-neuron levels. Including movement and baseline covariates allowed us to dissociate motor-related modulation from other neural signals, substantially clarifying the distinction between movement encoding and other task-related variables, which we focus on in the paper. These analyses confirm the strong role of the STN in representing movement while revealing additional signals related to aversive stimulation and cautious responding that persist after accounting for motor effects. These signals arise from distinct neuronal populations that can be differentiated by their movement sensitivity and activation patterns across avoidance modes, reflecting varying levels of caution. At the same time, several effects that initially reflected orienting-related activity at CS-onset (note that our movement tracking captures both head position and orientation as a directional vector) dissipated once movement and baseline covariates were included in the models, emphasizing the utility of the analytical improvements in the revision.

      (3)The description and discussion of orienting head movements were not well supported, but were much discussed in the avoidance datasets. The initial speed peaks to cue seem to be the supporting data upon which these claims rest, but nothing here suggests head movement or orientation responses.

      As described in the methods (and noted above), we track the head and decompose the movement into rotational and translational components. With the new approach, several effects that initially reflected orienting-related activity at CS-onset (note that our movement tracking captures both head position and orientation as a directional vector) dissipated once movement and baseline covariates were included in the models, emphasizing the utility of the analytical improvements in the revision.

      (4) Similar to the last, the authors note in several places, including abstract, the importance of STN in response timing, i.e., particularly when there must be careful or precise timing, but I don't think their data or task design provides a strong basis for this claim.

      The avoidance modes and the measured latencies directly support the relation to action timing, but now the portion of the previous paper about optogenetic excitation and apparently the main source of criticism is no longer in the present study. 

      (5) I think that other reports show that STN calcium activity is recruited by inescapable foot shock as well. What do these authors see? Is shock, independent of movement, contributing to sharp signals during escapes?

      The question, “Is shock, independent of movement, contributing to sharp signals during escapes?” is now directly addressed in the revised analyses. By incorporating movement and baseline covariates into the mixed-effects models, we dissociate STN activity related to aversive stimulation from that associated with motor output. The results show that shock-evoked STN activation persists even after controlling for movement within defined neuronal populations, supporting a specific nociceptive contribution independent of motor dynamics—a dissociation that appears to be new in this field.

      (6) In particular, and related to the last point, the following work is very relevant and should be cited:  Note that the focus of this other paper is on a subset of VGLUT2+ Tac1 neurons in paraSTN, but using VGLUT2-Cre to target STN will target both STN and paraSTN.

      We appreciate the reviewer’s reference to the recent preprint highlighting the role of the para-subthalamic nucleus in avoidance learning. However, our study focused specifically on performance in well-trained mice rather than on learning processes. Behavioral learning is inherently more variable and can be disrupted by less specific manipulations, whereas our experiments targeted the stable execution of learned avoidance behaviors. Future work will extend these findings to the learning phase and examine potential contributions of subthalamic subdivisions, which our current Vglut2-based manipulations do not dissociate. We will consider this and related work more closely in those studies.

      (7) In multiple other instances, claims that were more tangential to the main claims were made without clearly supporting data or statistics. E.g., claim that STN activation is related to translational more than rotational movement; claim that GCaMP and movement responses to auditory cues were small; claims that 'some animals' responded differently without showing individual data.

      We have adjusted the text accordingly.

      (8) In several figures, the number of subjects used was not described. This is necessary. Also necessary is some assessment of the variability across subjects. The only measure of error shown in many figures relates to trial-to-trial or event variability, which is minimal because, in many cases, it appears that hundreds of trials may have been averaged per animal, but this doesn't provide a strong view of biological variability. When bar/line plots are used to display data, I recommend showing individual animals where feasible.

      All experiments report number of mice and sessions. Wherever feasible, we display individual data points (e.g., Figures 1 and 2) to convey variability directly. However, in cases where figures depict hundreds of paired (repeated-measures) data points, showing all points without connecting them would not be appropriate, while linking them would make the figures visually cluttered and uninterpretable. All plots and traces include measures of variability (SEM), and the raw data will be shared on Dryad. When error bars are not visible, they are smaller than the trace thickness or bar line—for example, in Figure 5B, the black circles and orange triangles include error bars, but they are smaller than the symbol size.

      Also, to minimize visual clutter, only a subset of relevant comparisons is highlighted with asterisks, whereas all relevant statistical results, comparisons, and mouse/session numbers are fully reported in the Results section, with statistical analyses accounting for the clustering of data within subjects and sessions.

      (9) Can the authors consider the extent to which calcium imaging may be better suited to identify increases compared to decreases and how this may affect the results, particularly related to the GRIN data when similar numbers of cells show responses in both directions (e.g., Figure 3)?

      This is an interesting issue related to a widely used technique beyond the scope of our study.

      (10) Raw example traces are not provided.

      We do not think raw traces are useful here. All figures contain average traces to reflect the activity of the estimated population.

      (11) The timeline of the spontaneous movement and avoidance sessions was not clear, nor was the number of events or sessions per animal nor how this was set. It is not clear if there was pre-training or habituation, if many or variable sessions were combined per animal, or what the time gaps between sessions were, or if or how any of these parameters might influence interpretation of the results.

      We have enhanced the description of the sessions, including the number of animals and sessions, which are daily and always equal per animals in each group of experiments. As noted, the sessions are part of the random effects in the model.

      (12) It is not clear if or how the spread of expression outside of the target STN was evaluated, and if or how many mice were excluded due to spread or fiber placements.

      The STN is anatomically well-confined, with its borders and the overlying zona incerta (composed of GABAergic neurons) providing protection against off-target expression in most neighboring forebrain regions. All viral injections were histologically verified and did not into extend into thalamic or hypothalamic areas. As described in the Methods, we employed an app we developed (Brain Atlas Analyzer, available on OriginLab) that aligns serial histological sections with the Allen Brain Atlas to precisely assess viral spread and confirm targeting accuracy. The experiments included in the revised manuscript now focus on optogenetic inhibition and irreversible lesion approaches—three complementary methods that consistently targeted the STN and yielded similar behavioral effects.

      Recommendations for the authors:

      Reviewing Editor Comments:

      The primary feedback agreed upon by all the reviewers was that the manuscript requires significant streamlining as it is currently overly long and convoluted.

      We thank the reviewers and editors for their thoughtful and constructive feedback. In response to the primary comment that “the manuscript requires significant streamlining as it is currently overly long and convoluted,” we have substantially revised and refocused the paper. Specifically, we streamlined the included data and enhanced the analyses to emphasize the central findings: the encoding of movement, cautious responding, and punishment in the STN during avoidance behavior. We also focused the causal component of the study by including only the loss-of-function experiments—both optogenetic inhibition and irreversible viral/electrolytic lesions—that establish the critical role of STN circuits in generating active avoidance. Together, these revisions enhance clarity, tighten the narrative focus, and align the manuscript more closely with the reviewers’ recommendations.

      Major revisions include the addition of mixed-effects modeling to dissociate the contributions of movement from other STN-encoded signals related to caution and punishment. This modeling approach allowed us to reveal that these components are statistically separable, demonstrating that movement, cautious responding, and aversive input are encoded by neuronal subsets. To streamline the manuscript and address reviewer concerns, we removed the optogenetic excitation experiments. As revised, the paper presents a more concise and cohesive narrative showing that STN neurons differentially encode movement, caution, and aversive stimuli, and that this circuitry is essential for generating active avoidance behavior.

      Many of the specific points raised by reviewers now fall outside the scope of the revised manuscript. This is primarily because the revised version omits data and analyses related to optogenetic excitation and associated control experiments. By removing these components, the paper now presents a streamlined and internally consistent dataset focused on how the STN encodes movement, cautious responding, and aversive outcomes during avoidance behavior, as well as on loss-of-function experiments demonstrating its necessity for generating active avoidance. Below, we address the points that remain relevant across reviews.

      Following extensive revisions, the current manuscript differs in several important ways from what the assessment describes:

      The description that the study “uses fiber photometry, implantable lenses, and optogenetics” is more accurately represented as using both fiber photometry and singleneuron calcium imaging with miniscopes, combined with optogenetic and irreversible lesion approaches.

      The phrase stating that “active but not passive avoidance depends in part on STN projections to substantia nigra” is better characterized as “STN projections to the midbrain,” since our data show that optogenetic inhibition of STN terminals in both the mesencephalic reticular tegmentum (MRT) and substantia nigra pars reticulata (SNr) produce equivalent effects, and thus these sites are combined in the study. 

      Finally, the original concern that evidence for STN involvement in cautious responding or avoidance speed was incomplete no longer applies. The revised focus on encoding, through the inclusion of mixed-effects modeling, now dissociates movement-related, cautious, and aversive components of STN activity. By removing the optogenetic excitation data, we no longer claim that the STN controls caution but rather that it encodes cautious responding, alongside movement and punishment signals. Furthermore, loss-of-function experiments demonstrate that silencing STN output abolishes active avoidance entirely, supporting an essential role for the STN in generating goal-directed avoidance behavior—a behavioral domain that, unlike appetitive responding, is fundamentally defined by caution and the need to balance action timing under threat.

      Reviewer #2 (Recommendations for the authors):

      (1) Show individual data points on bar plots.

      Wherever feasible, we display individual data points (e.g., Figures 1 and 2) to convey variability directly. However, in cases where figures depict hundreds of paired (repeatedmeasures) data points, showing all points without connecting them would not be appropriate, while linking them would make the figures visually cluttered and uninterpretable. All plots and traces include measures of variability (SEM), and the raw data will be shared on Dryad. When error bars are not visible, they are smaller than the trace thickness or bar line—for example, in Figure 5B, the black circles and orange triangles include error bars, but they are smaller than the symbol size.

      Also, to minimize visual clutter, only a subset of relevant comparisons is highlighted with asterisks, whereas all relevant statistical results, comparisons, and mouse/session numbers are fully reported in the Results section, with statistical analyses accounting for the clustering of data within subjects and sessions.

      (2) The active avoidance experiments are confusing when they are introduced in the results section. More explanation of what paradigms were used and what each CS means at the time these are introduced would add clarity. For example, AA1, AA2, etc, are explained only with references to other papers, but a brief description of each protocol and a schematic figure would really help.

      The avoidance protocols (AA1–4) are now described briefly but clearly in the Results section (second paragraph of “STN neurons activate during goal-directed avoidance contingencies”) and in greater detail in the Methods section. As stated, these tasks were conducted sequentially, and mice underwent the same number of sessions per procedure, which are indicated. All relevant procedural information has been included in these sections. Mice underwent daily sessions and learnt these tasks within 1-2 sessions, progressing sequentially across tasks with an equal number of sessions per task (7 per task), and the resulting data were combined and clustered by mouse/session in the statistical models.

      (3) How do the Class 1, 2, 3 avoids relate to Class 1, 2, 3 neural types established in Figure 3? It seems like they are not related, and if that is the case, they should be named something different from each other to avoid confusion. (4) Similarly, having 3 different cell types (a,b,c) in the active avoidance seems unrelated to the original classification of cell types (1,2,3), and these are different for each class of avoid. This is very confusing, and it is unclear how any of these types relate to each other. Presumably, the same mouse has all three classes of avoids, so there are recordings from each cell during each type of avoid.

      The terms class, mode, and type are now clearly distinguished throughout the manuscript. Modes refer to distinct patterns of avoidance behavior that differ in the level of cautious responding (Mode 3 is most cautious). Within each mode, types denote subgroups of neurons identified based on their ΔF/F activity profiles. In contrast, classes categorize neurons according to their relationship to movement, determined by cross-correlation analyses between ΔF/F and head speed (Class1-4; Fig. 7 is a new analysis) or head turns (ClassA-C, renamed from 1-3). This updated terminology clarifies the analytic structure, highlighting distinct neuronal populations within each analysis. For example, during avoidance behaviors, these classifications distinguish neurons encoding movement-, caution-, and outcome-related signals. Comparisons are conducted within each analytical set, within classes (A-C or 1-4 separately), within avoidance modes, or within modespecific neuronal types.

      …So the authors could compare one cell during each avoid and determine whether it relates to movement or sound, or something else. It is interesting that types a,b, and c have the exact same proportions in each class of avoid, and makes it important to investigate if these are the exact same cells or not.

      That previous table with the a,b,c % in the three figure panels was a placeholder, which was not updated in the included figure. It has now been correctly updated. They do not have the same proportions as shown in Fig. 9, although they are similar.

      Also, these mice could be recorded during the open field, so the original neural classification (class 1, 2,3) could be applied to these same cells, and then the authors can see whether each cell type defined in the open field has a different response to the different avoid types. As it stands, the paper simply finds that during movement and during avoidance behaviors, different cells in the STN do different things.

      We included a new analysis in Fig. 7 that classifies neurons based on the cross-correlation with movement. The inclusion of the models now clearly assigns variance to movement versus the other factors, and this analysis leads to the classification based on avoid modes. 

      (5) The use of the same colors to mean two different things in Figure 9 is confusing. AA1 vs AA2 shouldn't be the same colors as light-naïve vs light signaling CS.

      Optogenetic excitation is no longer part of the study.

      (6) The exact timeline of the optogenetics experiments should be presented as a schematic for understanding. It is not clear which conditions each mouse experienced in which order. This is critical to the interpretation of Figure 9 and the reduction of passive avoids during STN stimulation. Did these mice have the CS1+STN stimulation pairing or the STN+US pairing prior to this experiment? If they did, the stimulation of the STN could be strongly associated with either punishment or with the CS1that predicts punishment. If that is the case, stimulating the STN during CS2 could be like presentingCS1+CS2 at the same time and could be confusing. The authors should make it clear whether the mice were naïve during this passive avoid experiment or whether they had experienced STN stimulation paired with anything prior to this experiment.

      Optogenetic excitation is no longer part of the study.

      (20) Similarly, the duration of the STN stimulation should be made clear on the plots that show behavior over time (e.g., Figure 9E).

      Optogenetic excitation is no longer part of the study.

      (21) There is just so much data and so many conditions for each experiment here. The paper is dense and difficult to read. It would really benefit readability if the authors put only the key experiments and key figure panels in the main text and moved much of the repetitive figure panels to supplemental figures. The addition of schematic drawings for behavioral experiment timing and for the different AA1, AA2, and AA3 conditions would also really improve clarity.

      By focusing the study, we believe it has substantially improved clarity and readability. 

      Reviewer #3 (Recommendations for the authors):

      (1) Minor error in results 'Cre-AAV in the STN of Vglut2-Cre' Fixed.

      (2) In some Figure 2 panels, the peaks appear to be cut off, and blue traces are obscured by red.

      In Fig. 2, the peaks of movement (speed) traces are intentionally truncated to emphasize the rising phase of the turn, which would otherwise be obscured if the full y-axis range were displayed (peaks and other measures are statistically compared). This adjustment enhances clarity without omitting essential detail and is now noted in the legend.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Artiushin et al. establish a comprehensive 3D atlas of the brain of the orb-web building spider Uloborus diversus. First, they use immunohistochemistry detection of synapsin to mark and reconstruct the neuropils of the brain of six specimens and they generate a standard brain by averaging these brains. Onto this standard 3D brain, they plot immunohistochemical stainings of major transmitters to detect cholinergic, serotonergic, octopaminergic/taryminergic and GABAergic neurons, respectively. Further, they add information on the expression of a number of neuropeptides (Proctolin, AllatostatinA, CCAP, and FMRFamide). Based on this data and 3D reconstructions, they extensively describe the morphology of the entire synganglion, the discernible neuropils, and their neurotransmitter/neuromodulator content.

      Strengths:

      While 3D reconstruction of spider brains and the detection of some neuroactive substances have been published before, this seems to be the most comprehensive analysis so far, both in terms of the number of substances tested and the ambition to analyze the entire synganglion. Interestingly, besides the previously described neuropils, they detect a novel brain structure, which they call the tonsillar neuropil.<br /> Immunohistochemistry, imaging, and 3D reconstruction are convincingly done, and the data are extensively visualized in figures, schemes, and very useful films, which allow the reader to work with the data. Due to its comprehensiveness, this dataset will be a valuable reference for researchers working on spider brains or on the evolution of arthropod brains.

      Weaknesses:

      As expected for such a descriptive groundwork, new insights or hypotheses are limited, apart from the first description of the tonsillar neuropil. A more comprehensive labeling in the panels of the mentioned structures would help to follow the descriptions. The reconstruction of the main tracts of the brain would be a very valuable complementary piece of data.

      Reviewer #2 (Public review):

      Summary

      Artiushin et al. created the first three-dimensional atlas of a synganglion in the hackled orb-weaver spider, which is becoming a popular model for web-building behavior. Immunohistochemical analysis with an impressive array of antisera reveals subcompartments of neuroanatomical structures described in other spider species as well as two previously undescribed arachnid structures, the protocerebral bridge, hagstone, and paired tonsillar neuropils. The authors describe the spider's neuroanatomy in detail and discuss similarities and differences from other spider species. The final section of the discussion examines the homology between onychophoran and chelicerate arcuate bodies and mandibulate central bodies.

      Strengths

      The authors set out to create a detailed 3D atlas and accomplished this goal.

      Exceptional tissue clearing and imaging of the nervous system reveal the three-dimensional relationships between neuropils and some connectivity that would not be apparent in sectioned brains.

      A detailed anatomical description makes it easy to reference structures described between the text and figures.

      The authors used a large palette of antisera which may be investigated in future studies for function in the spider nervous system and may be compared across species.

      Weaknesses

      It would be useful for non-specialists if the authors would introduce each neuropil with some orientation about its function or what kind of input/output it receives, if this is known for other species. Especially those structures that are not described in other arthropods, like the opisthosomal neuropil. Are there implications for neuroanatomical findings in this paper on the understanding of how web-building behaviors are mediated by the brain?

      Likewise, where possible, it would be helpful to have some discussion of the implications of certain neurotransmitters/neuropeptides being enriched in different areas. For example, GABA would signal areas of inhibitory connections, such as inhibitory input to mushroom bodies, as described in other arthropods. In the discussion section on relationships between spider and insect midline neuropils, are there similarities in expression patterns between those described here and in insects?

      Reviewer #3 (Public review):

      Summary:

      This is an impressive paper that offers a much-needed 3D standardized brain atlas for the hackled-orb weaving spider Uloborus diversus, an emerging organism of study in neuroethology. The authors used a detailed immunohistological whole-mount staining method that allowed them to localize a wide range of common neurotransmitters and neuropeptides and map them on a common brain atlas. Through this approach, they discovered groups of cells that may form parts of neuropils that had not previously been described, such as the 'tonsillar neuropil', which might be part of a larger insect-like central complex. Further, this work provides unique insights into the previously underappreciated complexity of higher-order neuropils in spiders, particularly the arcuate body, and hints at a potentially important role for the mushroom bodies in vibratory processing for web-building spiders.

      Strengths:

      To understand brain function, data from many experiments on brain structure must be compiled to serve as a reference and foundation for future work. As demonstrated by the overwhelming success in genetically tractable laboratory animals, 3D standardized brain atlases are invaluable tools - especially as increasing amounts of data are obtained at the gross morphological, synaptic, and genetic levels, and as functional data from electrophysiology and imaging are integrated. Among 'non-model' organisms, such approaches have included global silver staining and confocal microscopy, MRI, and, more recently, micro-computed tomography (X-ray) scans used to image multiple brains and average them into a composite reference. In this study, the authors used synapsin immunoreactivity to generate an averaged spider brain as a scaffold for mapping immunoreactivity to other neuromodulators. Using this framework, they describe many previously known spider brain structures and also identify some previously undescribed regions. They argue that the arcuate body - a midline neuropil thought to have diverged evolutionarily from the insect central complex - shows structural similarities that may support its role in path integration and navigation.

      Having diverged from insects such as the fruit fly Drosophila melanogaster over 400 million years ago, spiders are an important group for study - particularly due to their elegant web-building behavior, which is thought to have contributed to their remarkable evolutionary success. How such exquisitely complex behavior is supported by a relatively small brain remains unclear. A rich tradition of spider neuroanatomy emerged in the previous century through the work of comparative zoologists, who used reduced silver and Golgi stains to reveal remarkable detail about gross neuroanatomy. Yet, these techniques cannot uncover the brain's neurochemical landscape, highlighting the need for more modern approaches-such as those employed in the present study.

      A key insight from this study involves two prominent higher-order neuropils of the protocerebrum: the arcuate body and the mushroom bodies. The authors show that the arcuate body has a more complex structure and lamination than previously recognized, suggesting it is insect central complex-like and may support functions such as path integration and navigation, which are critical during web building. They also report strong synapsin immunoreactivity in the mushroom bodies and speculate that these structures contribute to vibratory processing during sensory feedback, particularly in the context of web building and prey localization. These findings align with prior work that noted the complex architecture of both neuropils in spiders and their resemblance (and in some cases greater complexity) compared to their insect counterparts. Additionally, the authors describe previously unrecognized neuropils, such as the 'tonsillar neuropil,' whose function remains unknown but may belong to a larger central complex. The diverse patterns of neuromodulator immunoreactivity further suggest that plasticity plays a substantial role in central circuits.

      Weaknesses:

      My major concern, however, is that some of the authors' neuroanatomical descriptions rely too heavily on inference rather than what is currently resolvable from their immunohistochemistry stains alone.

      We would like to thank the reviewers for their time and effort in carefully reading our manuscript and providing helpful feedback, and particularly for their appreciation and realistic understanding of the scope of this study and its context within the existing spider neuroanatomical literature.

      Regarding the limitations and potential additions to this study, we believe these to be well-reasoned and are in agreement. We plan to address some of these shortcomings in future publications.

      As multiple reviewers remarked, a mapping of the major tracts of the brain would be a welcome addition to understanding the neuroanatomy of U. diversus. This is something which we are actively working on and hope to provide in a forthcoming publication. Given the length of this paper as is, we considered that a treatment of the tracts would be better served as an additional paper. Likewise, mapping of the immunoreactive somata of the currently investigated targets is a component which we would like to describe as part of a separate paper, keeping the focus of the current one on neuropils, in order to leverage our aligned volumes to describe co-expression patterns, which is not as useful for the more widely dispersed somata. Furthermore, while we often see somata through immunostaining, the presence and intensity of the signal is variable among immunoreactive populations. We are finding that these populations are more consistently and comprehensively revealed thru fluorescent in situ hybridization.

      We appreciate the desire of the reviewers for further information regarding the connectivity and function of the described neuropils, and where possible we have added additional statements and references. That being said, where this context remains sparse is largely a reflection of the lack of information in the literature. This is particularly the case for functional roles for spider neuropils, especially higher order ones of the protocerebrum, which are essentially unexamined. As summarized in the quite recent update to Foelix’s Spider Neuroanatomy, a functional understanding for protocerebral neuropil is really only available for the visual pathway. Consequently, it is therefore also difficult to speak of the implications for presence or absence of particular signaling elements in these neuropils, if no further information about the circuitry or behavioral correlates are available. Finally, multiple reviewers suggested that it might be worthwhile to explore a comparison of the arcuate body layer innervation to that of the central bodies of insects, of which there is a richer literature. This is an idea which we were also initially attracted to, and have now added some lines to the discussion section. Our position on this is a cautious one, as a series of more recent comparative studies spanning many insect species using the same antibody, reveals a considerable amount of variation in central body layering even within this clade, which has given us pause in interpreting how substantive similarities and differences to the far more distant spiders would be. Still, this is an interesting avenue which merits an eventual comprehensive analysis, one which would certainly benefit from having additional examples from more spider species, in order to not overstate conclusions based on the currently limited neuroanatomical representation.

      Given our framing for the impetus to advance neuroanatomical knowledge in orb-web builders, the question of whether the present findings inform the circuitry controlling web-building is one that naturally follows. While we are unable with this dataset alone to define which brain areas mediate web-building - something which would likely be beyond any anatomical dataset lacking complementary functional data – the process of assembling the atlas has revealed structures and defined innervation patterns in previously ambiguous sectors of the spider brain, particularly in the protocerebrum. A simplistic proposal is that such regions, which are more conspicuous by our techniques and in this model species, would be good candidates for further inquiries into web-building circuitry, as their absence or oversight in past work could be attributable to the different behavioral styles of those model species. Regardless, granted that such a hypothesis cannot be readily refuted by the existing neuroanatomical literature, underscores the need to have more finely refined models of the spider brain, to which we hope that we have positively contributed to and are gratified by the reviewer’s enthusiasm for the strengths of this study.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Brenneis 2022 has done a very nice and comprehensive study focused on the visual system - this might be worth including.

      Thank you, we have included this reference on Line 34.

      (2) L 29: When talking about "connectivity maps", the emerging connectomes based on EM data could be mentioned.

      Additional references have been added, thank you. Line 35.

      (3) L 99: Please mention that you are going to describe the brain from ventral to dorsal.

      Thank you, we have added a comment to Line 99.

      (4) L 13: is found at the posterior.

      Thank you, revised.

      (5) L 168: How did you pick those two proctolin+ somata, given that there is a lot of additional punctate signal?

      Although not visible in this image, if you scroll through the stack there is a neurite which extends from these neurons directly to this area of pronounced immunoreactivity.

      (6) Figure 1: Please add the names of the neuropils you go through afterwards.

      We have added labels for neuropils which are recognizable externally.

      (7) Figure 1 and Figure 5: Please mark the esophagus.

      Label has now been added to Figure 1. In Figure 5, the esophagus should not really be visible because these planes are just ventral to its closure.

      (8) Figure 5A: I did not see any CCAP signal where the arrow points to; same for 5B (ChAT).

      In hindsight, the CCAP point is probably too minor to be worth mentioning, so we have removed it.

      The ChAT signal pattern in 5B has been reinforced by adding a dashed circle to show its location as well.

      (9) L 249: Could the circular spot also be a tract (many tracts lack synapsin - at least in insects)?

      Yes, thank you for pointing this out – the sentence is revised (L274). We are currently further analyzing anti-tubulin volumes and it seem that indeed there are tracts which occupy these synapsin-negative spaces, although interestingly they do not tend to account for the entire space.

      (10) L 302: Help me see the "conspicuous" thing.

      Brace added to Fig. 8B, note in caption.

      (11) L 315: Please first introduce the number of the eyes and how these relate to 1{degree sign} and 2{degree sign} pathway. Are these separate pathways from separate eyes or two relay stations of one visual pathway?

      We have expanded the introduction to this section (L336). Yes, these are considered as two separate visual pathways, with a typical segregation of which eyes contribute to which pathway – although there is evidence for species-specific differences in these contributions. In the context of this atlas, we are not currently able to follow which eyes are innervating which pathway.

      (12) L 343: It seems that the tonsillar neuropil could be midline spanning (at least this is how I interpret the signal across the midline). Would it make sense to re-formulate from a paired structure to midline-spanning? Would that make it another option for being a central complex homolog?

      In the spectrum from totally midline spanning and unpaired (e.g., arcuate body (at least in adults)) to almost fully distinct and paired (e.g., mushroom bodies (although even here there is a midline spanning ‘bridge’)), we view the tonsillar to be more paired due to the oval components, although it does have a midline spanning section, particularly unambiguous just posterior to the oval sections.

      Regarding central complex homology, if the suggestion is that the tonsillar with its midline spanning component could represent the entire central complex, then this is a possibility, but it would neglect the highly innervated and layered arcuate body, which we think represent a stronger contender – at least as a component of the central complex. For this reason, we would still be partial to the possibility that the tonsillar is a part of the central complex, but not the entire complex.

      (13) L 407: ...and dorsal (..) lobe...

      Added the word ‘lobe’ to this sentence (L429).

      (14) L 620ff: Maybe mention the role of MBs in learning and memory.

      A reference has been added at L661.

      (15) L 644: In the context of arcuate body homology with the central body, I was missing a discussion of the neurotransmitters expressed in the respective parts in insects. Would that provide additional arguments?

      This is an interesting comparison to explore, and is one that we initially considered making as well. There are certainly commonalities that one could point to, particularly in trying to build the case of whether particular lobes of the arcuate body are similar to the fan-shaped or ellipsoid bodies in insects. Nevertheless, something which has given us pause is studying the more recent comparative works between insect species (Timm et al., 2021, J Comp Neuro, Homberg et al., 2023, J Comp Neuro), which also reveal a fair degree of heterogeneity in expression patterns between species – and this is despite the fact that the neuropils are unambiguously homologous. When comparing to a much more evolutionarily distant organism such as the spider, it becomes less clear which extant species should serve as the best point of comparison, and therefore we fear making specious arguments by focusing on similarities when there are also many differences. We have added some of these comments to the discussion (L699-725).

      Throughout the text, I frequently had difficulties in finding the panels right away in the structures mentioned in the text. It would help to number the panels (e.g., 6Ai, Aii, Aii,i etc) and refer to those in the text. Further, all structures mentioned in the text should be labelled with arrows/arrowheads unless they are unequivocally identified in the panel

      Thank you for the suggestion. We have adopted the additional numbering scheme for panels, and added additional markers where suggested.

      Reviewer #2 (Recommendations for the authors):

      (1) L 18: "neurotransmitter" should be pluralized.

      Thank you, revised (L18).

      (2) L 55: Missing the word "the" before "U. diversus".

      Thank you, revised (L57).

      (3) L 179: Change synaptic dense to "synapse-dense".

      Thank you, revised (L189).

      (4) L 570: "present in" would be clearer than "presented on in".

      Our intention here was to say that Loesel et al did not show slices from the subesophageal mass for CCAP, so it was ambiguous as to whether it had immunoreactivity there but they simply did not present it, or if it indeed doesn’t show signal in the subesophageal. But agreed, this is awkward phrasing which has been revised (L606-608), thank you.

      (5) L 641: It would be worth noting that the upper and lower central bodies are referred to as the fan-shaped and ellipsoid bodies in many insects.

      Thank you, this has been added in L694.

      (6) L 642: Although cited here regarding insect central body layers, Strausfeld et al. 2006 mainly describe the onychophoran brain and the evolutionary relationship between the onychophoran and chelicerate arcuate bodies. The phylogenetic relationships described here would strengthen the discussion in the section titled "A spider central complex?"

      The phylogenetic relationship of onychophorans and chelicerates remains controversial and therefore we find it tricky to use this point to advance the argument in that discussion section, as one could make opposing arguments. The homology of the arcuate body (between chelicerates, onychophorans, and mandibulates) has likewise been argued over, with this Strausfeld et al paper offering one perspective, while others are more permissive (good summary at end of Doeffinger et al., 2010). Our thought was simply to draw attention to grossly similar protocerebral neuropils in examples from distantly related arthropods, without taking a stance, as our data doesn’t really deeply advance one view over the other.

      (7) L 701- Noduli have been described in stomatopods (Thoen et al., Front. Behav. Neurosci., 2017).

      This is an important addition, thank you – it has been incorporated and cited (L766).

      (8) Antisera against DC0 (PKA-C alpha) may distinguish globuli cells from other soma surrounding the mushroom bodies, but this may be accomplished in future studies.

      Agreed, this is something we have been interested in, but have not yet acquired the antibody.

      Reviewer #3 (Recommendations for the authors):

      Overall, this paper is both timely and important. However, it may face some resistance from classically trained arthropod neuroanatomists due to the authors' reliance on immunohistochemistry alone. A method to visualize fiber tracts and neuropil morphology would have been a valuable and grounding complement to the dataset and can be added in future publications. Tract-tracing methods (e.g., dextran injections) would strengthen certain claims about connectivity - particularly those concerning the mushroom bodies. For delineating putative cell populations across regions, fluorescence in situ hybridization for key transcripts would offer convincing evidence, especially in the context of the arcuate body, the tonsillar neuropil, and proposed homologies to the insect central complex.

      That said, the dataset remains rich and valuable. Outlined below are a number of issues the authors may wish to address. Most are relatively minor, but a few require further clarification.

      (1) Abstract

      (a) L 12-14: The authors should frame their work as a novel contribution to our understanding of the spider brain, rather than solely as a tool or stepping stone for future studies. The opening sentences currently undersell the significance of the study.

      Thank you for your encourament! We have revised the abstract.

      (b) Rather than touting "first of its kind" in the abstract, state what was learned from this.

      Thank you, we have revised the abstract.

      (c) The abstract does not mention the major results of the study. It should state which brain regions were found. It should list all of the peptides and transmitters that were tested so that they can be discoverable in searches.

      Thank you, revised.

      (2) Introduction

      (a) L 38: There's a more updated reference for Long (2016): Long, S. M. (2021). Variations on a theme: Morphological variation in the secondary eye visual pathway across the order of Araneae. Journal of Comparative Neurology, 529(2), 259-280.

      Thank you, this has been updated (L41 and elsewhere).

      (b) L 47: While whole-mount imaging offers some benefits, a downside is the need for complete brain dissection from the cuticle, which in spiders likely damages superficial structures (such as the secondary eye pathways).

      True – we have added this caveat to the section (L48-51).

      (c) L 49-52: If making this claim, more explicit comparisons with non-web building C. saeli in terms of neuropil presence, volume, or density later in the paper would be useful.

      We do not have the data on hand to make measured comparisons of C. salei structures, and the neuropils identified in this study are not clearly identifiable in the slices provided in the literature, so would likely require new sample preparations. We’ve removed the reference to proportionality and softened this sentence slightly – we are not trying to make a strong claim, but simply state that this is a possibility.

      (3) Results

      (a) The authors should state how they accounted for autofluorescence.

      While we did not explicitly test for autofluorescence, the long process of establishing a working whole-mount immuno protocol and testing antibodies produced many examples of treated brains which did not show any substantial signal.  We have added a note to the methods section (L866).

      (b) L 69: There is some controversy in delineating the subesophageal and supraesophageal mass as the two major divisions despite its ubiquity in the literature. It might be safer to delineate the protocerebrum, deutocerebrum, and fused postoral ganglia (including the pedipalp ganglion) instead.

      Thank you for this insight, we have modified the section, section headings and Figure 1 to account for this delineation as well. We have chosen to include both ways of describing the synganglion, in order to maintain a parallel with the past literature, and to be further accessible to non-specialist readers. L73-77

      (c) L 90: It might be useful to include a justification for the use of these particular neuropeptides.

      Thank you, revised. L97-99.

      (d) L 106 - 108: It is stated that the innervation pattern of the leg neuropils is generally consistent, but from Figure 2, it seems that there are differences. The density of 5HT, Proctolin, ChAT, and FMRFamide seems to be higher in the posterior legs. AstA seems to have a broader distribution in L1 and is absent in L4.

      We would still stand by the generalization that the innervation pattern is fairly similar for each leg. The L1 neuropils tend to be bigger than the posterior legs, which might explain the difference in density. Another important aspect to keep in mind is that not all of the leg neuropils appear at the exact same imaging plane as we move from ventral to dorsal. If you scroll through the synapsin stack (ventral to dorsal), you will see that L2 and L3 appear first, followed shortly by L1, and then L4, and at the dorsal end of the subesophageal they disappear in the opposite order. The observations listed here are true for the single z-plane in Figure 2, but the fact that they don’t appear at the same time seems to mainly account for these differences. For example, if you scroll further ventrally in the AstA volume, you will see a very similar innervation appear in L4 as well, even though it is absent in the Fig. 2 plane. We plan to have these individual volumes available from a repository so that they can be individually examined to better see the signal at all levels. At the moment, the entire repository can be accessed here: https://doi.org/10.35077/ace-moo-far.

      (e) Figure 1 and elsewhere: The axes for the posterior and lateral views show Lateral and Medial. It would be more accurate to label them Left and Right. because it does not define the medial-to-lateral axis. The medial direction is correct for only one hemiganglion, and it's the opposite for the contralateral side.

      Thank you, revised.

      (f) In Figures that show particular sections, it might be helpful to include a plane in the standard brain to illustrate where that section is.

      Yes, we agree and it was our original intention. It is something we can attempt to do, but there is not much room in the corners of many of the synapsin panels, making it harder to make the 3D representation big enough to be clear.

      (g) Figure 2, 3: Presenting the z-section stack separately in B and C is awkward because it makes it seem that they are unrelated. I think it would be better to display the z160-190 directly above its corresponding z230-260 for each of the exemplars in B and C. Since there's no left-right asymmetry, a hemibrain could be shown for all examples as was done for TH in D. It's not clear why TH was presented differently.

      Thank you for this suggestion. We rearranged the figure as described, but ultimately still found the original layout to be preferrable, in part because the labelling becomes too cramped. We hope that the potential confusion of the continuity of the B and C sections will be mitigated by focusing on the z plane labels and overall shape – which should suggest that the planes are not far from each other. We trust that the form of the leg neuropils is recognizable in both B and C synapsin images, and so readers will make the connection.

      Regarding TH, this panel is apart from the rest because we were unable to register the TH volume to the standard brain because the variant of the protocol which produced good anti-TH staining conflicted with synapsin, and we could not simultaneously have adequate penetration of the synapsin signal. We did not want to align the TH panel with the others to avoid potential confusion that this was a view from the same z-plane of a registered volume, as the others are. We have added a note to the figure caption.

      (h) The locations of the labels should be consistent. The antisera are below the images in Figure 2, above in Figure 3, and to the bottom left in Figure 5. The slices are shown above in Figure 2 and below in Figure 3.

      Thank you, this has been revised for better consistency.

      (i) It is surprising to me that there is no mention of the neuronal somata visible in Figure 2 and Figure 3. A typical mapping of the brain would map the locations of the neurons, not just the neuropils.

      Our first arrangement of this paper described each immunostain individually from ventral to dorsal, including locations of the immunoreactive somata which could be observed. To aid the flow of the paper and leverage the aligned volumes to emphasize co-expression in the function divisions of the brain, we re-formulated to this current layout which is organized around neuropils. Somata locations are tricky to incorporate in this format of the paper which focuses on key z-planes or tight max projections, because the relevant immunoreactive somata are more dispersed throughout the synganglion, not always overlapping in neighboring z-planes. Further, since only a minority of the antisera we used can reveal traceable projections from the supplying somata in the whole-mount preparation, we would be quite limited in the degree to which we could integrate the specific somata mapping with expression patterns in the neuropil.  Finally, compared to immuno, which can be variable in staining intensity between somata for the same target, we find that FISH reveals these locations more clearly and comprehensively – so while we agree that this mapping would also be useful for the atlas, we would like to better provide this information in a future publication using whole-mount FISH.

      (j) L 139: There is a reference to a "brace" in Figure 3B, which does not seem to exist. There's one in Figure 3C.

      There is a smaller brace near the bottom of the TDC2 panel in Fig. 3B.

      (k) L 151 should be "3D".

      Thank you, revised (L160).

      (l) Figure 4C: It is not mentioned in the legend that the bottom inset is Proctolin without synapsin.

      Thank you, revised (L1213).

      (m) L 199: Are the authors sure this subdivision is solely on the anterior-posterior axis? Could it also be dorsal ventral? (i.e., could this be an artifact of the protocerebrum and deutocerebrum?)

      Yes, this division can be appreciated to extend somewhat in the dorsal-ventral axis and it is possible that this is the protocerebrum emerging after the deutocerebrum, although this area is largely dorsal to the obvious part of the deutocerebrum. In the horizontal planes there appears to be a boundary line which we use for this subdivision in order to assist in better describing features within this generally ventral part of the protocerebrum – referred to as “stalk” because it is thinner before the protocerebrum expands in size, dorsally. Our intention was more organizational, and as stated in the text, this area is likely heterogenous and we are not suggesting that it has a unified function, so being a visual artifact would not be excluded.

      (n) L 249: Could it also indicate large tracts projecting elsewhere?

      Yes, definitely, we have evidence that part of the space is occupied by tracts. Revised, thank you (L262).

      (o) L 281: Several investigators, including Long (2021,) noted very large and robust mushroom bodies of Nephila.

      Thank you – the point is well taken that there are examples of orb-web builders that do have appreciable mushroom bodies. We have added a note in this section (L295), giving the examples of Deinopis spinosa and Argiope trifasciata (Figure 4.20 and 4.22 in Long, 2016).

      It looks like these species make the point better than Nephila, as Long lists the mushroom body percentage of total protocerebral volume for D. spinosa as 4.18%, for A. trifasciata as 2.38%, but doesn’t give a percentage for Nephila clavipes (Figure 4.24) and only labels the mushroom bodies structures as “possible” in the figure.

      In Long (2021), Nephilidae is described as follows: “In Nephilidae, I found what could be greatly reduced medullae at the caudal end of the laminae, as well as a structure that has many physical hallmarks of reduced mushroom bodies”

      (p) L 324: If the authors were able to stain for histamine or supplement this work with a different dissection technique for the dorsal structures, the visual pathways might have been apparent, which seems like a very important set of neuropils to include in a complete brain atlas.

      Yes, for this reason histamine has been an interesting target which we have attempted to visualize, but unfortunately have not yet been able to successfully stain for in U. diversus. An additional complication is that the antibodies we have seen call for glutaraldehyde fixation, which may make them incompatible with our approach to producing robust synapsin staining throughout the brain. 

      We agree that the lack of the complete visual pathway is a substantial weakness of our preparation, and should be amended in future work, but this will likely require developing a modified approach in order to preserve these delicate structures in U. diversus.

      (q) L 331: Is this bulbous shape neuropil, or just the remains of neuropil that were not fully torn away during dissection?

      This certainly is a severed part of the primary pathway, although it seems more likely that the bulbous shape is indicative of a neuropil form, rather than just being a happenstance shape that occurred during the breakage. We have examples where the same bulbous shape appears on both sides, and in different brains. It is possible that this may be the principal eye lamina – although we did not see co-staining with expected markers in examples where it did appear, so cannot be sure.

      (r) L 354: Is tyraminergic co-staining with the protocerebral bridge enough evidence to speculate that inputs are being supplied?

      We agree that this is not compelling, and have removed the statement.

      (s) L 372: This whole structure appears to be a previously described structure in spiders, the 'protocerebral commissure'.

      We are reasonably sure that what we are calling the PCB is a distinct structure from the protocerebral bridge (PCC). In Babu and Barth’s (1984) horizontal slice (Fig. 11b), you can see the protocerebral commissure immediately adjacent to the mushroom body bridge. It is found similarly located in other species, as can be seen in the supplementary 3D files provided by Steinhoff et al., (2024).

      While not visible with synapsin in U. diversus, we likewise can make out a commissure in this area in close proximity to the mushroom body bridge using tubulin staining. What we are calling the protocerebral bridge is a structure which is much more dorsal to the protocerebral commissure, not appearing in the same planes as the MB bridge.

      (t) L 377: Do you have an intuition why the tonsillar neuropil and the protocerebral bridge would show limited immunoreactivity, while the arcuate body's is quite extensive?

      This is an interesting question. Given the degree of interconnection and the fact that multiple classes of neurons in insects will innervate both central body as well as PCB or noduli, perhaps it would be expected that expression in tonsillar and protocerebral bridge should be commensurate to the innervation by that particular neurotransmitter expressing population in the arcuate body. Apart from the fact that the arcuate body is just bigger, perhaps this points to a great role of the arcuate body for integration, whereas the tonsillar and PCB may engage in more particular processing, or be limited to certain sensory modalities.

      Interestingly, it seems that this pattern of more limited immunoreactivity in the PCB and noduli compared with the central bodies (fan-shaped/ellipsoid) also appears in insects (Kahsai et al., 2010, J Comp Neuro, Timm et al., 2021, J Comp Neuro, Homberg et al., 2023, J Comp Neuro) – particularly, with almost every target having at least some layering in the fan-shaped body (Kahsai et al., 2010, J Comp Neuro).  For example, serotoninergic innervation is fairly consistently seen in the upper and lower central bodies across insects, but its presence in the PCB or noduli is more variable – appearing in one or the other in a species-dependent manner (Homberg et al., 2023, J Comp Neuro).

      (4) Discussion

      (a) L 556: But if confocal images from slices are aligned, is the 3D shape not preserved?

      Yes, fair enough – the point we wanted to make was that there is still a limitation in z resolution depending on the thickness of the slices used, which could obscure structures, but perhaps this is too minor of a comment.

      (b) L 597: This is a very interesting result. I agree it's likely to do with the processing of mechanosensory information relevant to web activities, and the mushroom body seems like the perfect candidate for this.

      (c) L 638: Worth noting that neuropil volume vs density of synapses might play a role in this, as the literature is currently a bit ambiguous with regards to the former.

      Thank you, noted (L689).

      (d) L 651: The latter seems far more plausible.

      Agreed, though the presence of mushroom bodies appears to be variable in spiders, so we didn’t want to take a strong stance, here.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Review #1 (Public review):

      Figures 1 through 4 contain data that largely recapitulate published findings (Fulton et al., 2015; Lee et al., 2024; Swee et al., 2016; Dong et al., 2021); it is noted that there is value in confirming phenotypic differences between naive CD5lo and CD5hi CD8 T cells in the NOD background. It is important to contextualize the data while being wary of making parallels with results obtained from CD5lo and CD5hi CD4 T cells. There should also be additional attention paid to the wording in the text describing the data (e.g., the authors assert that, in Figure 4C, the “CD5hi group exhibited higher percentages of CD8+ T cells producing TNF-α, IFN-γ and IL-2” though there is no difference in IL-2 nor consistent differences in TNF-α between the CD5lo and CD5hi population<sup>hi</sup> CD8<sup>+</sup> and CD5<sup>lo</sup>CD8<sup>+</sup> T cells have been previously characterized in other genetic backgrounds. In our study, we aimed to confirm and extend these observations specifically in the autoimmune-prone NOD background, which had not been systematically addressed. Additionally, we carefully reviewed the text describing Figure 4C and revised the wording to accurately reflect the observed data (line 263-264). Specifically, we now state that the CD5<sup>hi</sup> group exhibited higher levels of IFN-γ and a trend toward increased TNF-α, while IL-2 production did not show a significant difference.

      The comparison of CD5 across thymocyte populations is cautioned due to variation in developmental stages, particularly in transgenic models. The reported differences may reflect maturation stages rather than self-reactivity.

      We appreciate the reviewer’s important point regarding the interpretation of CD5 levels across thymocyte subsets. In our revised manuscript (lines 455–471), we have added clarification that CD5 expression in DN and DP subsets reflects pre-TCR and TCR signaling events during thymic development. We also acknowledge that differences in maturation stages, especially in the NOD8.3 transgenic model, may influence CD5 expression. We now discuss this caveat and interpret our results with caution, particularly emphasizing that our data support but do not sufficiently define their differential self-reactivity.

      The conclusion that PTPN22 overexpression does not inhibit the diabetogenic potential of CD5<sup>hi</sup>CD8<sup>+</sup> T cells is potentially confounded by differences between polyclonal and TCR transgenic systems.

      We thank the reviewer for raising this concern. We acknowledge that this system introduces confounders due to differences in precursor frequencies and clonal expansion compared to polyclonal repertoires. These differences may affect the responsiveness to phosphatase-mediated attenuation of signaling. Therefore, while our results support that high-affinity autoreactive CD8<sup>+</sup> T cells may be less sensitive to PTPN22 overexpression, we do not claim that this finding generalizes to all autoreactive CD8<sup>+</sup> T cells. Rather, it highlights a potential inability of peripheral tolerance in T cells with strong intrinsic self-reactivity.

      TCR sequencing data shows variability; is this representative of the overall repertoire?

      We appreciate the reviewer’s comment. We acknowledge that data from bulk TCR sequencing has potential limitations, including variability across experiments and limited resolution at the clonotype level. To improve representativeness and reduce sampling bias, we performed TCR repertoire analysis in two independent experiments. In each experiment, naïve CD5<sup>hi</sup> CD8<sup>+</sup> and CD5<sup>lo</sup>CD8<sup>+</sup> T cells were sorted from pooled peripheral lymph nodes of at least 20 individual NOD mice per group. This approach allowed us to capture a broader range of clonotypes and ensured that the resulting repertoire profiles reflect the characteristics of the overall CD5<sup>hi</sup> and CD5<sup>lo</sup> populations, rather than isolated outliers. Despite some variability, we observed consistent trends in key features, such as shorter CDR3β length, altered TRAV/TRBV usage and reduced diversity in the CD5<sup>hi</sup> subset across both experiments. To enhance resolution and directly assess clonotype-specific reactivity, we plan to perform single-cell RNA and TCR sequencing in future studies, as noted in the revised Discussion (lines 466–471).

      Clarifications are requested regarding naive gating, controls, gMFI reporting, and missing methods.

      We thank the reviewer for these specific suggestions. We have revised figure legends to better describe gating strategies and included appropriate controls in Figures or Supplementary Figures. Regarding gMFI reporting, we have now shown in the figure legends whether values are reported as gMFI. Additionally, we have added the missing methods for cytokine staining, EdU incorporation, overlapped count matrix construction and TCR repertoire diversity metrics.

      Review #2 (Public review):

      Summary Comment:

      The study is nicely performed, but the definition of naive T cells using only CD44 and CD62L may be oversimplified. CD5hi naive T cells express higher CD44 than CD5lo cells.

      We thank the reviewer for the critical evaluation and thoughtful comment. As noted, we defined naïve CD8<sup>+</sup> T cells using a well-established gating strategy based on CD44<sup>lo</sup> and CD62L<sup>hi</sup> expression, consistent with previous studies (Immunity. 2010; 32(2):214–26; Nat Immunol. 2015; 16(1):107–17). We acknowledge that CD44 is expressed along a continuum, and indeed, within the naïve gate, CD5<sup>hi</sup> CD8<sup>+</sup> T cells exhibited slightly higher CD44 levels compared to their CD5<sup>lo</sup> counterparts. However, both subsets remained well below the CD44 expression observed in conventional effector/memory CD8<sup>+</sup> T cells, supporting their classification as naïve. To further validate this, we assessed additional markers associated with activation and memory differentiation, including CD69, PD-1, KLRG1 and CD25. These analyses confirmed that the sorted CD5<sup>hi</sup> and CD5<sup>lo</sup> populations retained a phenotypically naïve profile while exhibiting meaningful differences in baseline activation readiness (Figure 1F).

      Review #3 (Public review):

      CD5 can be regulated by peripheral signals. Therefore, it cannot be concluded that predisposition to effector/memory differentiation is solely programmed in the thymus.

      We thank the reviewer for this important point. We agree that CD5 expression can be dynamically regulated in the periphery by tonic TCR signals and antigen encounter, as also reflected in our own data that cells with high CD5 level display elevated activation potential upon encountering antigen (e.g., Figure 3L). To minimize the confounding effects of pre-existing peripheral activation, we performed an adoptive T cell transfer experiment (Figure 4). In this experiment, naïve CD5<sup>hi</sup>CD<sup>+</sup>and CD5<sup>lo</sup>CD8<sup>+</sup>T cells were sorted from the peripheral lymph nodes of young (6–8-week-old) prediabetic NOD mice and transferred into NOD Rag1<sup>–/–</sup> recipients. After 4 weeks, we compared the disease phenotypes and functional profiles of CD8<sup>+</sup> T cells from these two groups. This approach allowed us to evaluate the stability and differentiation capacity of CD5<sup>hi</sup> versus CD5<sup>lo</sup> cells in a lymphopenic environment, while excluding the possibility that the observed differences were due to already activated CD8<sup>+</sup>T cells at the time of isolation. We have revised the Discussion (lines 440–450) to acknowledge these experimental limitations and clarify that, while our findings demonstrate functional differences between CD5<sup>hi</sup>CD8<sup>+</sup> and CD5<sup>lo</sup>CD8<sup>+</sup>T cells, we cannot fully exclude contributions from peripheral influences.

      Experiments do not explain why PTPN22 overexpression protects in polyclonal T cells but not in NOD8.3 mice.

      We appreciate this critical comment. Our findings support that autoreactive T cells with high-affinity TCRs as in NOD8.3 mice receive strong signaling that even PTPN22 overexpression is insufficient to attenuate their activation and effector function. We acknowledge that further mechanistic studies are needed to fully elucidate the differential effects of PTPN22 in polyclonal versus TCR-transgenic settings.

      Evidence that PTPN22 does not regulate TCR signaling in NOD8.3 T cells is weak.

      We thank the reviewer for this critical comment. Our data show that NOD8.3 T cells with an intrinsic high CD5-associated self-reactivity are more resistant to transgenic Pep-mediated change in the phosphorylation status of TCR signaling molecules CD3ζ and Erk and CD5 expression (Figure 6, B-D). However, we agree that additional functional assays would strengthen this conclusion.

      TCR sequencing does not conclusively link CD5hi cells with autoreactivity; single-cell analysis is needed.

      We agree with this critical comment. Bulk TCR sequencing revealed repertoire features associated with autoreactivity, but cannot definitively link specific TCRs to function. We have acknowledged this in the discussion (lines 466–471) and highlighted plans to perform single-cell analysis.

      CD5hi cells in the PLNs may reflect antigen exposure rather than basal signaling.

      We thank the reviewer for this insightful comment. As also noted in Figure 3L, CD5 expression can be influenced by peripheral tonic TCR signals and recent antigen exposure. To minimize the contribution of peripheral activation, we particularly characterized naïve CD8<sup>+</sup>T cells isolated from the peripheral lymph nodes of young (6–8-week-old) prediabetic NOD mice before the onset of overt autoimmunity. Furthermore, we performed an adoptive transfer experiment (Figure 4) using sorted naïve CD5<sup>hi</sup>CD8<sup>+</sup> and CD5<sup>lo</sup>CD8<sup>+</sup>T cells from these mice and characterized their disease phenotype after 4 weeks in lymphopenic NOD Rag1<sup>–/–</sup> recipients and evaluated the effector function of CD8<sup>+</sup>T cells. This approach allowed us to compare the differentiation potential of these subsets in a controlled setting, independent of their activation status at the time of isolation. We have revised the Discussion (lines 440–450) to emphasize that, while our data support functional differences between CD5<sup>hi</sup>CD8<sup>+</sup> and CD5<sup>lo</sup>CD8<sup>+</sup>T cells, we cannot fully exclude the role of peripheral cues in shaping CD5 expression.

      Provide proper gating controls and representative flow plots.

      We thank the reviewer for this comment. We have revised figure legends to better describe gating strategies and included representative flow cytometry plots and appropriate gating controls in Figures or Supplementary Figures.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The authors):

      (1) The figure presentation is inconsistent and the labels/font are often too small to read easily.

      As Reviewer suggested, the figure presentation has been revised for consistency. Labels and fonts have been adjusted for improved readability. Specific figures that were difficult to read have been reformatted with larger fonts and clearer legends.

      (2) A careful review of the text to ensure clarity of the content is suggested (e.g., “gratitude” at line 91, “were generally lied” at line 123).

      Thanks for Reviewer’s comments. The text has been carefully reviewed for clarity and grammatical accuracy. Corrections have been made, including changing “gratitude” to “magnitude” (line 47) and “were generally lied” to “fell between” (line 79).

      Reviewer #2 (Recommendations For The Authors):

      (1) The definition of naïve T cells based solely on CD44low and CD62Lhigh staining may be oversimplistic. Indeed, even within this definition, naïve CD5high CD8 T cells express much higher levels of CD44 than CD5low CD8 T cells.

      Thanks for Reviewer’s comments. We used a literature-supported gating strategy (Immunity. 2010; 32(2):214–26; Nat Immunol. 2015; 16(1):107–17) to define naïve T cells based on CD44<sup>low</sup> and CD62L<sup>high</sup> expression. It is important to note that CD44 expression exists along a continuum. While we were initially surprised to observe that CD5<sup>lo</sup>CD8<sup>+</sup>T cells expressed relatively higher levels of CD44 than CD5<sup>lo</sup>CD8<sup>+</sup>T cells within the naïve gate, both populations still exhibited significantly lower CD44 expression compared to conventional effector/memory CD8<sup>+</sup>T cells. To further validate the distinction between CD5<sup>hi</sup> and CD5 subsets, we also examined additional markers such as CD69, PD1, KLRG1 and CD25, which supported their phenotypic differences within the naïve compartment (Figure 1F).

      (2) Figure 1G should show the proportion of IGRP-tetramer+ in the three groups of CD8 T cells. Additionally, it would be useful to assess reactivity against a pool of other islet autoantigens using a similar strategy.

      As suggested by the reviewer, the revised manuscript now includes additional data showing the proportion of IGRP-tetramer+ cells (Supplementary Figure 1D), as well as reactivity against another islet autoantigen, insulin-1/insulin-2 (Insulin B15–23) (Supplementary Figure 1E). The description of these results, including the proportions of IGRP-tetramer<sup>+</sup> and Insulin B15–23<sup>+</sup> CD8<sup>+</sup>Tcells, has been added to lines 126–129 of the revised manuscript.

      (3) The resolution of Figure 2 is suboptimal and at places poorly visible. Figure 2D is stated to show “two significant pathways stand out.” In fact, the data are barely significant, and the authors may want to correct their statement.

      The resolution of Figure 2 has been improved. As Reviewer suggested, the text has been revised to state “two potential pathways stand out” (line 187) instead of “two significant pathways stand out”.

      (4) Figure 3C-F and 3H, showing fold change over baseline values would be much easier for the reader to grasp the data.

      As Reviewer suggested, data in Figures 3C-F and 3H now are shown in fold change over baseline values for clarity. Baseline gMFI is the mean of each group (total CD<sup>+</sup> , CD5<sup>hi</sup>CD8<sup>+</sup> and CD5<sup>lo</sup>CD8<sup>+</sup>) at 0 μg/ml anti-CD3, with fold changes calculated for stimulation conditions (0.625-10 μg/ml anti-CD3). The figure legend has been updated accordingly.

      (5) Figure 4A, it would be much more valuable to show the diabetes frequency upon transfer of CD25- CD4 T cells alone and upon transfer of CD5high CD8 T cells alone. The word “spontaneous” in the Figure 4A legend seems inappropriate.

      Thanks for the Reviewer’s comment. We apologize for not including the data for the CD25 CD4<sup>+</sup> T cell transfer group in the original manuscript. While this group was part of our initial experimental design, we had considered it a control group and unintentionally omitted it from the figure. The revised manuscript now includes this group in Figure 4A. In addition, the term “spontaneous” has been replaced with “diabetes incidence” in the Figure 4A legend and manuscript (line 248). Regarding the suggestion to assess CD5<sup>hi</sup>CD8<sup>+</sup>T cells transfer alone, we appreciate the Reviewer’s point. However, previous studies have shown that CD8<sup>+</sup> T cells alone are not effective and sufficient to induce diabetes in adoptive transfer models, and that effective β-cell destruction typically requires both CD4<sup>+</sup> and CD8<sup>+</sup> T cell subsets. For instance, Christianson et al. (1993) demonstrated that enriched CD8<sup>+</sup> T cells from NOD mice fail to transfer diabetes on their own, while CD4<sup>+</sup> T cells—particularly from diabetic donors—can induce disease only under specific conditions and are significantly potentiated by co-transfer of CD8<sup>+</sup>cells. These findings have contributed to the widely available standard of co-transferring both subsets when studying diabetogenic potential in NOD models (Diabetes. 1993;42(1):44–55).

      (6) Line 257-258, please remove “indicating superior in vivo proliferation by the CD5hi subset.” Indeed, several other possibilities may explain the phenotype, including survival, migration, etc.

      As Reviewer suggested, the phrase “indicating superior in vivo proliferation by the CD5<sup>hi</sup> subset” has been replaced with “implying increased expansion and activation/effector potential” (line 261).

      (7) Figure 5A, it is unclear to this referee what is the significance of CD5 and pCD3zeta expression on DN thymocytes. Do these cells express rearranged alpha/beta TCR? Is it signaling through pre-TCRalpha/TCRbeta pairs?

      Thanks a lot for this important question. In the revised manuscript, we have expanded the discussion (line 455–471) to address the developmental significance of CD5 and pCD3ζ expression on DN thymocytes. CD5 expression at this stage reflects pre-TCR signaling strength during early selection, which occurs following successful TCRβ rearrangement. The associated phosphorylation of CD3ζ indicates activation of downstream signaling through the pre-TCRα/TCRβ complex. As discussed in the revised text, these early signals play a critical role in determining lineage progression and self-reactivity tuning. We now acknowledge that signaling at the DN stage occurs through the pre-TCRα/TCRβ heterodimer, not a fully rearranged αβ TCR, and that CD5 expression serves as a marker of the strength of these initial pre-selection signals (Sci Signal. 2022;15(736):eabj9842.). These developmental checkpoints are essential for calibrating TCR sensitivity and ensuring proper thymocyte maturation. This has been clarified in the revised discussion (line 455–471).

      (8) Figure 5F, could the DP TCRbeta- CD69- thymocytes from 8.3-TCR NOD mice already express low levels of the self-reactive TCR at this stage to explain their high expression of CD5? Addressing the question experimentally would be useful.

      Thanks a lot for this useful comment. According to a review by Huseby et al. (2022), expression of a functional TCRβ chain begins at the DN3 stage, initiating progression through the β-selection checkpoint. This is followed by TRAV locus recombination, resulting in the generation of αβ TCR-expressing double-positive 1 (DP-1) thymocytes. At the DP-1 stage, the quality of TCR signaling driven by self-pMHC interactions governs both positive and negative selection, as well as the development of nonconventional T cell lineages. We hypothesize that in transgenic NOD8.3 mice, which express pre-rearranged Tcra and Tcrb transgenes derived from the islet-reactive CD8<sup>+</sup>T cell clone NY8.3, thymocytes undergo allelic exclusion and lack the clonal diversity seen in non-transgenic mice. As a result, NOD8.3 thymocytes may receive strong TCR signals from early developmental stages (DN3 and DP-1) even without undergoing normal selection checkpoints. While the elevated TCR signal observed in NOD8.3 is indeed artificial, this model provides a unique system to test our hypothesis—namely, whether a strongly self-reactive TCR can generate high basal signaling during thymic development that overrides the negative regulatory effects of phosphatases like Pep. This possibility has been acknowledged in the revised Discussion section, along with a plan to validate the hypothesis experimentally (line 455–471).

      (9) Figure 7, single-cell TCR-seq would be much more appropriate to tackle the question of self-reactivity of CD5hi vs. CD5low CD8 T cells.

      Thanks a lot for this useful comment. The limitations of bulk TCR-seq are acknowledged, and single-cell TCR-seq is proposed as a future direction (line 455–471).

      Note, for Reviewer #2 (Recommendations For The Authors) (7) (8) (9), the discussion paragraphs are included to address the reviewers’ questions (line 455–471).

      Reviewer #3 (Recommendations For The Authors):

      (1) Positive controls (activated T cells from PLN or spleen), gating controls (whole naïve T cells), and representative flow-cytometry plots are needed for T-bet, EOMES, GzmB, and cytokine staining in Figure 1.

      As Reviewer suggested, we added representative gating controls for T-bet, EOMES, GzmB and cytokine staining in Supplementary Figure 1 of revised manuscript.

      (2) For Figure 1F, MFI for activation markers for the CD44hiCD62Llo cells should be provided for the comparison of PLN data.

      As Reviewer suggested, MFI data for these markers have been included in Figure 1F of revised manuscript.

      (3) In many places and figure legends, it is not mentioned from which organ cells were collected, i.e., spleen or PLN.

      As Reviewer suggested, the origin of cells for each experiment has been explicitly indicated in the figure legends or figure content to ensure clarity.

      (4) In the pancreatic lymph node, autoreactive T cells might be upregulating CD5 because they are encountering antigens. This should be addressed in the discussion.

      As Reviewer suggested, this issue has been included in the discussion of revised manuscript (line 440-450).

      (5) It is not clear if T cells from the spleen and PLN were stimulated to detect the production of pro-inflammatory cytokines.

      Thanks for the critical comment. The stimulation protocol and cytokine staining method have been added to the Supplementary material’s Supplementary methods section Cytokine staining in revised manuscript.

      (6) Figure 4C-D: It is not clear if analysis was done on naïve T cells or if they were stimulated.

      Thanks for the comment. Additionally, the stimulation and cytokine staining methods used in Figure 4C-D have been described in detail in the Supplementary Materials section Cytokine staining of revised manuscript.

      (7) IGRP gating in Figure 4F should be revisited with negative controls.

      Thanks for the critical comment. Negative controls have been added and used to adjust IGRP gating, and this is now mentioned in the figure legend of revised manuscript.

      (8) Interpretation that only CD5hi cells form a central memory T cell population (Figure 4F) could be misleading.

      Thanks for this valuable comment. We agree with that in conventional CD8<sup>+</sup> T cell immune responses, both CD5<sup>hi</sup> and CD5<sup>lo</sup> subsets have the potential to differentiate into central memory T cells. In our experimental approach, we adoptively transferred sorted CD5<sup>hi</sup>CD8<sup>+</sup> or CD5<sup>lo</sup>CD8<sup>+</sup>cells into Rag1<sup>-/-</sup> recipients and specifically analyzed PLNs four weeks after transfer. Using CD44 and CD62L expression as conventional markers for central memory T cells, we barely observed a CD44<sup>hi</sup>CD62L<sup>hi</sup> population in CD5<sup>lo</sup>CD8<sup>+</sup>transferred group. Based on these results, we stated: “This analysis underscores that the central memory T cell population and the frequency of islet autoantigen-specific CD8<sup>+</sup>T cells are higher in the CD5<sup>hi</sup> transferred subset within the PLNs, implying more robust immune responses initiated by the CD5<sup>hi</sup>cells” (line 272–274). Importantly, we did not intend to imply that only CD5<sup>hi</sup> cells can form central memory T cells, but rather that they were more enriched for this phenotype under the specific conditions and time point analyzed. 

      (9) IL-2 gating representative plot should be provided for Figure 5A.

      As Reviewer suggested, a representative IL-2 gating plot has been included in the revised Supplementary Figure 3B.

    1. Author response:

      (1) General Statements

      The goal of our study was to mechanistically connect microbiota to host longevity. We have done so using a combination of genetic and physiological experiments, which outline a role for a neuroendocrine relay mediated by the intestinal neuropeptide Tachykinin, and its receptor TkR99D in neurons. We also show a requirement for these genes in metabolic and healthspan effects of microbiota.

      The referees' comments suggest they find the data novel and technically sound. We have added data in response to numerous points, which we feel enhance the manuscript further, and we have clarified text as requested. Reviewer #3 identified an error in Figure 4, which we have rectified. We felt that some specific experiments suggested in review would not add significant further depth, as we articulate below.

      Altogether our reviewers appear to agree that our manuscript makes a significant contribution to both the microbiome and ageing fields, using a large number of experiments to mechanistically outline the role(s) of various pathways and tissues. We thank the reviewers for their positive contributions to the publication process.

      (2) Description of the planned revisions

      Reviewer #2:

      Not…essential for publication…is it possible to look at Tk protein levels?

      We have acquired a small amount of anti-TK antibody and we will attempt to immunostain guts associated with A. pomorum and L. brevis. We are also attempting the equivalent experiment in mouse colon reared with/without a defined microbiota. These experiments are ongoing, but we note that the referee feels that the manuscript is a publishable unit whether these stainings succeed or not.

      (3) Description of the revisions that have already been incorporated in the transferred manuscript

      Reviewer #1:

      Can the authors state in the figure legends the numbers of flies used for each lifespan and whether replicates have been done?

      We have incorporated the requested information into legends for lifespan experiments.

      Do the interventions shorten lifespan relative to the axenic cohort? Or do they prevent lifespan extension by axenic conditions? Both statements are valid, and the authors need to be consistent in which one they use to avoid confusing the reader.

      We read these statements differently. The only experiment in which a genetic intervention prevented lifespan extension by axenic conditions is neuronal TkR86C knockdown (Figure 6B-C). Otherwise, microbiota shortened lifespan relative to axenic conditions, and genetic knockdowns extend blocked this effect (e.g. see lines 131-133). We have ensured that the framing is consistent throughout, with text edited at lines 198-199, 298-299, 311-312, 345-347, 407-408, 424-425, 450, 497-503.

      TkRNAi consistently reduces lipid levels in axenic flies (Figs 2E, 3D), essentially phenocopying the loss of lipid stores seen in control conventionally reared (CR) flies relative to control axenic. This suggests that the previously reported role of Tk in lipid storage - demonstrated through increased lipid levels in TkRNAi flies (Song et al (2014) Cell Rep 9(1): 40) - is dependent on the microbiota. In the absence of the microbiota TkRNAi reduces lipid levels. The lack of acknowledgement of this in the text is confusing

      We have added text at lines 219-222 to address this point. We agree that this effect is hard to interpret biologically, since expressing RNAi in axenics has no additional effect on Tk expression (Figure S7). Consequently we can only interpret this unexpected effect as a possible off-target effect of RU feeding on TAG, specific to axenic flies. However, this possibility does not void our conclusion, because an off-target dimunition of TAG cannot explain why CR flies accumulate TAG following Tk<sup>RNAi</sup> induction. We hope that our added text clarifies.

      I have struggled to follow the authors logic in ablating the IPCs and feel a clear statement on what they expected the outcome to be would help the reader.

      We have added the requested statement at lines 423-424, explaining that we expected the IPC ablation to render flies constitutively long-lived and non-responsive to A pomorum.

      Can the authors clarify their logic in concluding a role for insulin signalling, and qualify this conclusion with appropriate consideration of alternative hypotheses?

      We have added our logic at lines 449-454. In brief, we conclude involvement for insulin signalling because FoxO mutant lifespan does not respond to Tk<sup>RNAi</sup>, and diminishes the lifespan-shortening effect of A. pomorum. However, we cannot state that the effects are direct because we do not have data that mechanistically connects Tk/TkR99D signalling directly in insulin-producing cells. The current evidence is most consistent with insulin signalling priming responses to microbiota/Tk/TkR99D, as per the newly-added text.

      Typographical errors

      We have remedied the highlighted errors, at lines 128-140.

      Reviewer #2:

      it would be good to show that the bacterial levels are not impacted [by TkRNAi]

      We have quantified CFUs in CR flies upon ubiquitous TkRNAi (Figure S5), finding that the RNAi does not affect bacterial load. New text at lines 138-139 articulates this point.

      The effect of Tk RNAi on TAG is opposite in CR and Ax or CR and Ap flies, and the knockdown shows an effect in either case (Figure 2E, Figure 3D). Why is this?

      As per response to Reviewer #1, we have added text at lines 219-222 to address this point.

      Is it possible to perform at least one lifespan repeat with the other Tk RNAi line mentioned?

      We have added another experiment showing longevity upon knockdown in conventional flies, using an independent TkRNAi line (Figure S3).

      Reviewer #3:

      In Line243, the manuscript states that the reporter activity was not increased in the posterior midgut. However, based on the presented results in Fig4E, there is seemingly not apparent regional specificity. A more detailed explanation is necessary.

      We thank the reviewer sincerely for their keen eye, which has highlighted an error in the previous version of the figure. In revisiting this figure we have noticed, to our dismay, that the figures for GFP quantification were actually re-plots of the figures for (ac)K quantification. This error led to the discrepancy between statistics and graphics, which thankfully the reviewer noticed. We have revised the figure to remedy our error, and the statistics now match the boxplots and results text.

      Fig1C uses Adh for normalization. Given the high variability of the result, the authors should (1) check whether Adh expression levels changed via bacterial association

      We selected Adh on the basis of our RNAseq analysis, which showed it was not different between AX and CV guts, whereas many commonly-used “housekeeping” genes were. We have now added a plot to demonstrate (Figure S2).

      The statement in Line 82 that EEs express 14 peptide hormones should be supported with an appropriate reference

      We have added the requested reference (Hung et al, 2020) at line 86.

      (4) Description of analyses that authors prefer not to carry out

      Reviewer #1:

      I'd encourage the authors to provide lifespan plots that enable comparison between all conditions

      We have avoided this approach because the number of survival curves that would need to be presented on the same axis (e.g. 16 for Figure 5) is not legible. However we have ensured that axes on faceted plots are equivalent and with grid lines for comparison. Moreover, our approach using statistical coefficients (EMMs) enables direct quantitative comparison of the differences among conditions.

      Reviewer #2:

      Is it possible that this driver is simply not resulting in an efficient KD of the receptor? I would be inclined to check this

      This comment relates to Figure 7G. We do see an effect of the knockdown in this experiment, so we believe that the knockdown is effective. However the direction of response is not consistent with our hypothesis so the experiment is not informative about the role of these cells. We therefore feel there is little to be gained by testing efficacy of knockdown, which would also be technically challenging because the cells are a small population in a larger tissue which expresses the same transcripts elsewhere (i.e. necessitating FISH).

      Would it be possible to use antibodies for acetylated histones?

      The comment relates to Figure 4C-E. The proposed studies would be a significant amount of work because, to our knowledge, the specific histone marks which drive activation in TK+ cells remain unknown. On the other hand, we do not see how this information would enrich the present story, rather such experiments would appear to be the beginning of something new. We therefore agree with Reviewer #1 (in cross-commenting) that this additional work is not justified.

      Reviewer #3:

      Tk+ EEC activity should be assessed directly, rather than relying solely on transcript levels. Approaches such as CaLexA or GCaMP could be used.

      We agree with reviewers 1-2 (in cross-commenting) that this proposal is non-trivial and not justified by the additional insight that would be gained. As described above, we are attempting to immunostain Tk, which if successful will provide a third line of evidence for regulation of Tk+ cells. However we note that we already have the strongest possible evidence for a role of these cells via genetic analysis (Figure 5).

      While the difficulty of maintaining lifelong axenic conditions is understandable, it may still be feasible to assess the induction of Tk (ie. Tk transcription or EE activity upregulation) by the microbiome on males.

      As the reviewer recognises, maintaining axenic experiments for months on end is not trivial. Given the tendency for males either to simply mirror female responses to lifespan-extending interventions, or to not respond at all, we made the decision in our work to only study females. We have instead emphasised in the manuscript that results are from female flies.

      TkR86C, in addition to TkR99D, may be involved in the A. pomorum-lifespan interaction. Consider revising the title to refer more generally to the "tachykinin receptor" rather than only TkR99D.

      We disagree with this interpretation: the results do not show that TkR86C-RNAi recapitulates the effect of enteric Tk-RNAi. A potentially interesting interaction is apparent, but the data do not support a causal role for TkR86C. A causal role is supported only for TkR99D, knockdown of which recapitulates the longevity of axenic flies and Tk<sup>RNAi</sup> flies_._ Therefore we feel that our current title is therefore justified by the data, and a more generic version would misrepresent our findings.

      The difference between "aging" and "lifespan" should also be addressed.

      The smurf phenotype is a well-established metric of healthspan. Moreover, lifespan is the leading aggregate measure of ageing. We therefore feel that the use of “ageing” in the title is appropriate.

      If feasible, assessing foxo activation would add mechanistic depth. This could be done by monitoring foxo nuclear localization or measuring the expression levels of downstream target genes.

      Foxo nuclear localisation has already been shown in axenic flies (Shin et al, 2011). We have added text and citation at lines 401-402.

    1. Author response:

      We thank the reviewers for their thoughtful, constructive, and generous evaluations of our manuscript. We are encouraged by their overall assessment of the clarity, novelty, and significance of the work, and we appreciate the opportunity to further strengthen the manuscript.

      Both reviewers highlight the central contribution of this study: a developmental, circuitlevel dissection of how heart–brain signaling emerges in a vertebrate. We are pleased that the evidence supporting the staggered assembly of vagal motor, sympathetic, and sensory pathways was found to be compelling, and that the computational and experimental framework was viewed as appropriate and informative.

      Below, we briefly outline how we plan to address the main points raised in the reviews.

      Heart rate variability and temporal structure

      Both reviewers note that heart rate variability (HRV) changes across development and suggest that HRV may provide additional insight into the function of autonomic circuits. We agree that HRV is an important physiological readout and that its developmental changes are consistent with the progressive emergence of autonomic control.

      In the revised manuscript, we plan to (i) discuss heart rate variability more explicitly in the context of circuit maturation and (ii) clarify the temporal scales captured by our experiments and modeling framework. In particular, we will emphasize that our analyses focus on relationships between neural activity and heart-rate trajectories at timescales accessible given imaging rate and indicator kinetics, rather than beat-to-beat variability. We will also consider adding a supplementary analysis of the variability that can be reliably measured within these constraints, and, where appropriate, how neural activity predicts that measurable variation.

      Scope and interpretation of the computational models

      Reviewer #2 raises thoughtful points regarding what the generalized linear models can and cannot disambiguate, particularly when multiple efferent pathways may contribute to heart-rate dynamics. We will revise the text to more clearly distinguish between functional encoding relationships inferred from the models and anatomical connectivity that is directly demonstrated.

      Our intent is to frame the kernels identified in the motor and sympathetic pathways as computational motifs that capture distinct dynamical contributions, rather than as exclusive or complete explanations of heart-rate control. We will clarify these limitations explicitly in the Results and Discussion.

      Circuit diagram and anatomical interpretation

      We appreciate the reviewer’s careful reading of the proposed circuit schematic. In the revised manuscript, we will revise the figure and accompanying text to clearly annotate which connections are directly observed, which are functionally inferred, and which remain hypothetical. We will also expand the Discussion to explicitly address open questions, including unresolved feedback pathways and the potential for additional nodes in the circuit.

      We believe these revisions will improve clarity without altering the core conclusions of the study. We thank the reviewers again for their insightful feedback and look forward to submitting a revised version of the manuscript that addresses these points in detail.

    1. Author response:

      We thank the editors and reviewers for their generally positive and thoughtful feedback on this work. Below are provisional responses to some of the concerns raised:

      Reviewer 1:

      At a total scan duration of 2 minutes, the ASL sequence utilized in this cohort is much shorter than that of a typical ASL sequence (closer to 5 minutes as mentioned by the authors). However, this implementation also included multiple (n=5) PLDs. As currently described, it is unclear how any repetitions were acquired at each PLD and whether these were acquired efficiently (i.e., with a Look-Locker readout) or whether individual repetitions within this acquisition were dedicated to a single PLD. If the latter, the number of repetitions per PLD (and consequently signal-to-noise-ratio, SNR) is likely to be very low. Have the authors performed any analyses to determine whether the signal in individual subjects generally lies above the noise threshold? This is particularly relevant for white matter, which is the focus of several findings discussed in the study.

      We agree that this was a short acquisition compared to most ASL protocols, necessitated by the strict time-keeping requirements for running such a large study. We apologise if this was not clear in the original manuscript, but due to this time constraint and the use of a segmented readout (which was not Look-Locker) there was only time available for a single average at each PLD. This does mean that the perfusion weighted images at each PLD are relatively noisy, although the image quality with this sequence was still reasonable, as demonstrated in Figure 1, with perfusion weighted images visibly above the noise floor. In addition, as has been demonstrated theoretically and experimentally in recent work (Woods et al., 2023, 2020), even though the SNR of each individual PLD image might be low in multi-PLD acquisitions, this is effectively recovered during the model fitting process, giving it comparable or greater accuracy than a protocol which collects many averages at a single (long) PLD. As also noted by the reviewers, this approach has the further benefit of allowing ATT estimation, which has proven to provide useful and complementary information to CBF. Finally, the fact that many of the findings in this study pass strict statistical thresholds for significance, despite the many multiple comparisons performed, and that the spatial patterns of these relationships are consistent with expectations, even in the white matter (e.g. Figure 6B), give us confidence that the perfusion estimation is robust. However, we will consider adding some additional metrics around SNR or fitting uncertainty in a revised manuscript, as well as clarifying details of the acquisition.

      Hematocrit is one of the variables regressed out in order to reduce the effect of potential confounding factors on the image-derived phenotypes. The effect of this, however, may be more complex than accounting for other factors (such as age and sex). The authors acknowledge that hematocrit influences ASL signal through its effect on longitudinal blood relaxation rates. However, it is unclear how the authors handled the fact that the longitudinal relaxation of blood (T1Blood) is explicitly needed in the kinetic model for deriving CBF from the ASL data. In addition, while it may reduce false positives related to the relationships between dietary factors and hematocrit, it could also mask the effects of anemia present in the cohort. The concern, therefore, is two-fold: (1) Were individual hematocrit values used to compute T1Blood values? (2) What effect would the deconfounding process have on this?

      We agree this is an important point to clarify. In this work we decided not to use the haematocrit to directly estimate the T1 of blood for each participant a) because this would result in slight differences in the model fitting for each subject, which could introduce bias (e.g. the kinetic model used assumes instantaneous exchange between blood water and tissue, so changing the T1 of blood for each subject could make us more sensitive to inaccuracies in this assumption); and b) because typically the haematocrit measures were quite some time (often years) prior to the imaging session, leading to an imperfect correction. We therefore took the pragmatic approach to simply regress each subject’s average haematocrit reading out of the IDP and voxelwise data to prevent it contributing to apparent correlations caused by indirect effects on blood T1. However, we agree with the reviewer that this certainly would mask the effects of anaemia in this cohort, so for researchers interested in this condition a different approach should be taken. We will update the revised manuscript to try to clarify these points.

      The authors leverage an observed inverse association between white matter hyperintensity volume and CBF as evidence that white matter perfusion can be sensitively measured using the imaging protocol utilized in this cohort. The relationship between white matter hyperintensities and perfusion, however, is not yet fully understood, and there is disagreement regarding whether this structural imaging marker necessarily represents impaired perfusion. Therefore, it may not be appropriate to use this finding as support for validation of the methodology.

      We appreciate the reviewer’s point that there is still debate about the relationship between white matter hyperintensities and perfusion. We therefore agree that this observed relationship therefore does not validate the methodology in the sense that it is an expected finding, but it does demonstrate that the data quality is sufficient to show significant correlations between white matter hyperintensity volume and perfusion, even in white matter regions, which would not be the case if the signal there were dominated by noise. Similarly, the clear spatial pattern of perfusion changes in the white matter that correlate with DTI measures in the same regions also suggests there is sensitivity to white matter perfusion. However, we will update the wording in the revised manuscript to try to clarify this point.

      Reviewer 2:

      This study primarily serves to illustrate the efficacy and potential of ASL MRI as an imaging parameter in the UK Biobank study, but some of the preliminary observations will be hypothesis-generating for future analyses in larger sample sizes. However, a weakness of the manuscript is that some of the reported observations are difficult to follow. In particular, the associations between ASL and resting fMRI illustrated in Figure 7 and described in the accompanying Results text are difficult to understand. It could also be clearer whether the spatial maps showing ASL correlates of other image-derived phenotypes in Figure 6B are global correlations or confined to specific regions of interest. Finally, while addressing partial volume effects in gray matter regions by covarying for cortical thickness is a reasonable approach, the Methods section seems to imply that a global mean cortical thickness is used, which could be problematic given that cortical thickness changes may be localized.

      We apologise if any of the presented information was unclear and will try to improve this in our revised manuscript. To clarify, the spatial maps associated with other (non-ASL) IDPs were generated by calculating the correlation between the ASL CBF or ATT in every voxel in standard space with the non-ASL IDP of interest, not the values of the other imaging modality in the same voxel. No region-based masking was used for this comparison. This allowed us to examine whether the correlation with this non-ASL IDP was only within the same brain region or if the correlations extended to other regions too.

      We also agree that the associations between ASL and resting fMRI are not easy to interpret. We therefore tried to be clear in the manuscript that these were preliminary findings that may be of interest to others, but clearly further study is required to explore this complex relationship further. However, we will try to clarify how the results are presented in the revised manuscript.

      In relation to partial volume effects, we did indeed use only a global measure of cortical thickness in the deconfounding and we acknowledged that this could be improved in the discussion: [Partial volume effects were] “mitigated here by the inclusion of cortical thickness in the deconfounding process, although a region-specific correction approach that is aware of the through-slice blurring (Boscolo Galazzo et al., 2014) is desirable in future iterations of the ASL analysis pipeline.” As suggested here, although this is a coarse correction, we did not feel that a more comprehensive partial volume correction approach could be used without properly accounting for the through-slice blurring effects from the 3D-GRASE acquisition (that will vary across different brain regions), which is not currently available, although this is an area we are actively working on for future versions of the image analysis pipeline. We again will try to clarify this point further in the revised manuscript.

      References

      Woods JG, Achten E, Asllani I, Bolar DS, Dai W, Detre J, Fan AP, Fernández-Seara M, Golay X, Günther M, Guo J, Hernandez-Garcia L, Ho M-L, Juttukonda MR, Lu H, MacIntosh BJ, Madhuranthakam AJ, Mutsaerts HJ, Okell TW, Parkes LM, Pinter N, Pinto J, Qin Q, Smits M, Suzuki Y, Thomas DL, Van Osch MJP, Wang DJ, Warnert EAH, Zaharchuk G, Zelaya F, Zhao M, Chappell MA. 2023. Recommendations for Quantitative Cerebral Perfusion MRI using Multi-Timepoint Arterial Spin Labeling: Acquisition, Quantification, and Clinical Applications (preprint). Open Science Framework. doi:10.31219/osf.io/4tskr

      Woods JG, Chappell MA, Okell TW. 2020. Designing and comparing optimized pseudo-continuous Arterial Spin Labeling protocols for measurement of cerebral blood flow. NeuroImage 223:117246. doi:10.1016/j.neuroimage.2020.117246

    1. Author response:

      The following is the authors’ response to the current reviews.

      Public Reviews: 

      Reviewer #2 (Public review): 

      Summary: 

      This is an interesting study exploring methods for reconstructing visual stimuli from neural activity in the mouse visual cortex. Specifically, it uses a competition dataset (published in the Dynamic Sensorium benchmark study) and a recent winning model architecture (DNEM, dynamic neural encoding model) to recover visual information stored in ensembles of mouse visual cortex. 

      Strengths: 

      This is a great start for a project addressing visual reconstruction. It is based on physiological data obtained at a single-cell resolution, the stimulus movies were reasonably naturalistic and representative of the real world, the study did not ignore important correlates such as eye position and pupil diameter, and of course, the reconstruction quality exceeded anything achieved by previous studies. There appear to be no major technical flaws in the study, and some potential confounds were addressed upon revision. The study is an enjoyable read. 

      Weaknesses: 

      The study is technically competent and benchmark-focused, but without significant conceptual or theoretical advances. The inclusion of neuronal data broadens the study's appeal, but the work does not explore potential principles of neural coding, which limits its relevance for neuroscience and may create some disappointment to some neuroscientists. The authors are transparent that their goal was methodological rather than explanatory, but this raises the question of why neuronal data were necessary at all, as more significant reconstruction improvements might be achievable using noise-less artificial video encoders alone (network-to-network decoding approaches have been done well by teams such as Han, Poggio, and Cheung, 2023, ICML). Yet, even within the methodological domain, the study does not articulate clear principles or heuristics that could guide future progress. The finding that more neurons improve reconstruction aligns with well-established results in the literature that show that higher neuronal numbers improve decoding in general (for example, Hung, Kreiman, Poggio, and DiCarlo, 2005) and thus may not constitute a novel insight. 

      We thank the reviewer for this second round of comments and hope we were able to address the remaining points below. 

      Indeed, using surrogate noiseless data is interesting and useful when developing such methods, or to demonstrate that they work in principle. But in order to evaluate if they really work in practice, we need to use real neuronal data. While we did not try movie reconstruction from layers within artificial neural networks as surrogate data, in Supplementary Figure 3C we provide the performance of our method using simulated/predicted neuronal responses from the dynamic neural encoding model alongside real neuronal responses.

      Specific issues: 

      (1)The study showed that it could achieve high-quality video reconstructions from mouse visual cortex activity using a neural encoding model (DNEM), recovering 10-second video sequences and approaching a two-fold improvement in pixel-by-pixel correlation over attempts. As a reader, I was left with the question: okay, does this mean that we should all switch to DNEM for our investigations of mouse visual cortex? What makes this encoding model special? It is introduced as "a winning model of the Sensorium 2023 competition which achieved a score of 0.301...single trial correlation between predicted and ground truth neuronal activity," but as someone who does not follow this competition (most eLife readers are not likely to do so, either), I do not know how to gauge my response. Is this impressive? What is the best theoretical score, given noise and other limitations? Is the model inspired by the mouse brain in terms of mechanisms or architecture, or was it optimized to win the competition by overfitting it to the nuances of the data set? Of course, I know that as a reader, I am invited to read the references, but the study would stand better on its own, if it clarified how its findings depended on this model. 

      The revision helpfully added context to the Methods about the range of scores achieved by other models, but this information remains absent from the Abstract and other important sections. For instance, the Abstract states, "We achieve a pixel-level correlation of 0.57 between the ground truth movie and the reconstructions from single-trial neural responses," yet this point estimate (presented without confidence intervals or comparisons to controls) lacks meaning for readers who are not told how it compares to prior work or what level of performance would be considered strong. Without such context, the manuscript undercuts potentially meaningful achievements. 

      We appreciate that the additional information about the performance of the SOTA DNEM to predict neural responses could be made more visible in the paper and will therefore move it from the methods to the results section instead: 

      Line 348 “This model achieved an average single-trial correlation between predicted and ground truth neural activity of 0.291 during the competition, this was later improved to 0.301. The competition benchmark models achieved 0.106, 0.164 and 0.197 single-trial correlation, while the third and second place models achieved 0.243 and 0.265. Across the models, a variety of architectural components were used, including 2D and 3D convolutional layers, recurrent layers, and transformers, to name just a few.” will be moved to the results.

      With regard to the lack of context for the performance of our reconstruction in the abstract, we may have overcorrected in the previous revision round and have tried to find a compromise which gives more context to the pixel-level correlation value: 

      Abstract: “We achieve a pixel-level correlation of 0.57 (95% CI [0.54, 0.60]) between ground-truth movies and single-trial reconstructions. Previous reconstructions based on awake mouse V1 neuronal responses to static images achieved a pixel-level correlation of 0.238 over a similar retinotopic area.”

      (2) Along those lines, the authors conclude that "the number of neurons in the dataset and the use of model ensembling are critical for high-quality reconstructions." If true, these principles should generalize across network architectures. I wondered whether the same dependencies would hold for other network types, as this could reveal more general insights. The authors replied that such extensions are expected (since prior work has shown similar effects for static images) but argued that testing this explicitly would require "substantial additional work," be "impractical," and likely not produce "surprising results." While practical difficulty alone is not a sufficient reason to leave an idea untested, I agree that the idea that "more neurons would help" would be unsurprising. The question then becomes: given that this is a conclusion already in the field, what new principle or understanding has been gained in this study? 

      As mentioned in our previous round of revisions, we chose not to pursue the comparison of reconstructions using different model architectures in this manuscript because we did not think it would add significant insights to the paper given the amount of work it would require, and we are glad the reviewer agrees. 

      While the fact that more neurons result in better reconstructions is unsurprising, how quickly performance drops off will depend on the robustness of the method, and on the dimensionality of the decoding/reconstruction task (decoding grating orientation likely requires fewer neurons than gray scale image reconstruction, which in turn likely requires fewer neurons than full color movie reconstruction). How dependent input optimization based image/movie reconstruction is on population size has not been shown, so we felt it was useful for readers to know how well movie reconstruction works with our method when recording from smaller numbers of neurons. 

      (3) One major claim was that the quality of the reconstructions depended on the number of neurons in the dataset. There were approximately 8000 neurons recorded per mouse. The correlation difference between the reconstruction achieved by 1000 neurons and 8000 neurons was ~0.2. Is that a lot or a little? One might hypothesize that 7000 additional neurons could contribute more information, but perhaps, those neurons were redundant if their receptive fields are too close together or if they had the same orientation or spatiotemporal tuning. How correlated were these neurons in response to a given movie? Why did so many neurons offer such a limited increase in correlation? Originally, this question was meant to prompt deeper analysis of the neural data, but the authors did not engage with it, suggesting a limited understanding of the neuronal aspects of the dataset. 

      We apologize that we did not engage with this comment enough in the previous round. We assumed that the question arose because there was a misunderstanding about figure 5: 1000 not 1 neuron is sufficient to reconstruct the movies to a pixel-level correlation of 0.344. Of course, the fact that increasing the number of neurons from 1000 to 8000 only increased the reconstruction performance from 0.344 to 0.569 (65% increase in correlation) is still worth discussing. To illustrate this drop in performance qualitatively, we show 3 example frames from movie reconstructions using 1000-8000 neurons in Author response image 1.

      Author response image 1.

      3 example frames from reconstructions using different numbers of neurons. 

      As the reviewer points out, the diminishing returns of additional neurons to reconstruction performance is at least partly because there is redundancy in how a population of neurons represents visual stimuli. In supplementary figure S2, we inferred the on-off receptive fields of the neurons and show that visual space is oversampled in terms of the receptive field positions in panel C. However, the exact slope/shape of the performance vs population size curve we show in Figure 5 will also depend on the maximum performance of our reconstruction method, which is limited in spatial resolution (Figure 4 & Supplementary Figure S5). It is possible that future reconstruction approaches will require fewer neurons than ours, so we interpret this curve rather as a description of the reconstruction method itself than a feature of the underlying neuronal code. For that reason, we chose caution and refrained from making any claims about neuronal coding principles based on this plot. 

      (4) We appreciated the experiments testing the capacity of the reconstruction process, by using synthetic stimuli created under a Gaussian process in a noise-free way. But this originally further raised questions: what is the theoretical capability for reconstruction of this processing pipeline, as a whole? Is 0.563 the best that one could achieve given the noisiness and/or neuron count of the Sensorium project? What if the team applied the pipeline to reconstruct the activity of a given artificial neural network's layer (e.g., some ResNet convolutional layer), using hidden units as proxies for neuronal calcium activity? In the revision, this concern was addressed nicely in the review in Supplementary Figure 3C. Also, one appreciates that as a follow up, the team produced error maps (New Figure 6) that highlight where in the frames the reconstruction are likely to fail. But the maps went unanalyzed further, and I am not sure if there was a systematic trend in the errors. 

      We are happy to hear that we were able to answer the reviewers’ question of what the maximum theoretical performance of our reconstruction process is in figure 3C. Regarding systematic trends in the error maps, we also did not observe any clear systematic trends. If anything, we noticed that some moving edges were shifted, but we do not think we can quantify this effect with this particular dataset. 

      (5) I was encouraged by Figure 4, which shows how the reconstructions succeeded or failed across different spatial frequencies. The authors note that "the reconstruction process failed at high spatial frequencies," yet it also appears to struggle with low spatial frequencies, as the reconstructed images did not produce smooth surfaces (e.g., see the top rows of Figures 4A and 4B). In regions where one would expect a single continuous gradient, the reconstructions instead display specular, high-frequency noise. This issue is difficult to overlook and might deserve further discussion. 

      Thank you for pointing this out, this is indeed true. The reconstructions do have high frequency noise. We mention this briefly in line 102 “Finally, we applied a 3D Gaussian filter with sigma 0.5 pixels to remove the remaining static noise (Figure S3) and applied the evaluation mask.” In revisiting this sentence, we think it is more appropriate to replace “remove” with “reduce”. This noise is more visible in the Gaussian noise stimuli (Figure 4) because we did not apply the 3D Gaussian filter to these reconstructions, in case it interfered with the estimates of the reconstruction resolution limits. 

      Given that the Gaussian noise and drifting grating stimuli reconstructions were from predicted activity (“noise-free”), this high-frequency noise is not biological in origin and must therefore come from errors in our reconstruction process. This kind of high-frequency noise has previously been observed in feature visualization (optimizing input to maximize the activity of a specific node within a neural network to visualize what that node encodes; Olah, et al., "Feature Visualization", https://distill.pub/2017/feature-visualization/, 2017). It is caused by a kind of overfitting, whereby a solution to the optimization is found that is not “realistic”. Ways of combating this kind of noise include gradient smoothing, image smoothing, and image transformations during optimization, but these methods can restrict the resolution of the features that are recovered. Since we were more interested in determining the maximum resolution of stimuli that can be reconstructed in Figure 4 and Supplementary Figures 5-6, we chose not to apply these methods.

      Reviewer #3 (Public review): 

      Summary: 

      This paper presents a method for reconstructing input videos shown to a mouse from the simultaneously recorded visual cortex activity (two-photon calcium imaging data). The publicly available experimental dataset is taken from a recent brain-encoding challenge, and the (publicly available) neural network model that serves to reconstruct the videos is the winning model from that challenge (by distinct authors). The present study applies gradient-based input optimization by backpropagating the brain-encoding error through this selected model (a method that has been proposed in the past, with other datasets). The main contribution of the paper is, therefore, the choice of applying this existing method to this specific dataset with this specific neural network model. The quantitative results appear to go beyond previous attempts at video input reconstruction (although measured with distinct datasets). The conclusions have potential practical interest for the field of brain decoding, and theoretical interest for possible future uses in functional brain exploration. 

      Strengths: 

      The authors use a validated optimization method on a recent large-scale dataset, with a state-of-the-art brain encoding model. The use of an ensemble of 7 distinct model instances (trained on distinct subsets of the dataset, with distinct random initializations) significantly improves the reconstructions. The exploration of the relation between reconstruction quality and number of recorded neurons will be useful to those planning future experiments. 

      Weaknesses: 

      The main contribution is methodological, and the methodology combines pre-existing components without any new original component. 

      We thank the reviewer for their balanced assessment of our manuscript.


      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review): 

      Summary: 

      This paper presents a method for reconstructing videos from mouse visual cortex neuronal activity using a state-of-the-art dynamic neural encoding model. The authors achieve high-quality reconstructions of 10-second movies at 30 Hz from two-photon calcium imaging data, reporting a 2-fold increase in pixel-by-pixel correlation compared to previous methods. They identify key factors for successful reconstruction including the number of recorded neurons and model ensembling techniques. 

      Strengths: 

      (1) A comprehensive technical approach combining state-of-the-art neural encoding models with gradient-based optimization for video reconstruction. 

      (2) Thorough evaluation of reconstruction quality across different spatial and temporal frequencies using both natural videos and synthetic stimuli. 

      (3) Detailed analysis of factors affecting reconstruction quality, including population size and model ensembling effects. 

      (4) Clear methodology presentation with well-documented algorithms and reproducible code. 

      (5) Potential applications for investigating visual processing phenomena like predictive coding and perceptual learning. 

      We thank the reviewer for taking the time to provide this valuable feedback. We would like to add that in our eyes one additional main contribution is the step of going from reconstruction of static images to dynamic videos. We trust that in the revised manuscript, we have now made the point more explicit that static image reconstruction relies on temporally averaged responses, which negates the necessity of having to account for temporal dynamics altogether. 

      Weaknesses: 

      The main metric of success (pixel correlation) may not be the most meaningful measure of reconstruction quality: 

      High correlation may not capture perceptually relevant features.

      Different stimuli producing similar neural responses could have low pixel correlations The paper doesn't fully justify why high pixel correlation is a valuable goal 

      This is a very relevant point. In retrospect, perhaps we did not justify this enough. Sensory reconstruction typically aims to reconstruct sensory input based on brain activity as faithfully as possible. A brain-to-image decoder might therefore be trained to produce images as close to the original input as possible. The loss function to train the decoder would therefore be image similarity on the pixel level. In that case, evaluating reconstruction performance based on pixel correlation is somewhat circular. 

      However, when reconstructing videos, we optimize the input video in terms of its perceptual similarity to the original video and only then evaluate pixel-level similarity. The perceptual similarity metric we optimize for is the estimate of how the neurons in mouse V1 respond to that video. We then evaluate the similarity of this perceptually optimized video to the original input video with pixel-level correlation. In other words, we optimize for perceptual similarity and then evaluate pixel similarity. If our method optimized pixel-level similarity, then we would agree that perceptual similarity is a more relevant evaluation metric. We do not think it was clear in our original submission that our optimization loss function is a perceptual loss function, and have now made this clearer in Figure 1C-D and have clarified this in the results section, line 70:

      “In effect, we optimized the input video to be perceptually similar with respect to the recorded neurons.”

      And in line 110: 

      “Because our optimization of the movies was based on a perceptual loss function, we were interested in how closely these movies matched the originals on the pixel level.”

      We chose to use pixel correlation to measure pixel-level similarity for several reasons. 1) It has been used in the past to evaluate reconstruction performance (Yoshida et al., 2020), 2) It is contrast and luminance insensitive, 3) correlation is a common metric so most readers will have an intuitive understanding of how it relates to the data. 

      To further highlight why pixel similarity might be interesting to visualize, we have included additional analysis in Figure 6 illustrating pixel-level differences between reconstructions from experimentally recorded activity and predicted activity. 

      We expect that the type of perceptual similarity the reviewer is alluding to is pretrained neural network image embedding similarity (Zhang et al., 2018: https://doi.org/10.48550/arXiv.1801.03924). While these metrics seem to match human perceptual similarity, it is unclear if they reflect mouse vision. We did try to compare the embedding similarity from pretrained networks such as VGG16, but got results suggesting the reconstructed frames were no more similar to the ground truth than random frames, which is obviously not true. This might be because the ground truth videos were too different in resolution from the training data of these networks and because these metrics are typically very sensitive to decreases in resolution. 

      The best alternative approach to evaluate mouse perceptual similarity would be to show the reconstructed videos to the same animals while recording the same neurons and to compare these neural activation patterns to those evoked by the original ground truth videos. This has been done for static images in the past: Cobos et al., bioRxiv 2022, found that static image reconstructions generated using gradient descent evoked more similar trial-averaged (40 trials) responses to those evoked by ground truth images compared to other reconstruction methods. Unfortunately, we are currently not able to perform these in vivo experiments, which is why we used publicly available data for the current paper. We plan to use this method in the future. But this method is also not flawless as it assumes that the average response to an image is the best reflection of how that image is represented, which may not be the case for an individual trial.

      As far as we are aware, there is currently no method that, given a particular activity pattern in response to an image/video, can produce an image/video that induces a neural activity pattern that is closer to the original neural response than simply showing the same image/video again. Hypothetically, such a stimulus exists because of various visual processing phenomena we mention in our discussion (e.g., predictive coding and selective attention), which suggest that the image that is represented by a population of neurons likely differs from the original sensory input. In other words, what the brain represents is an interpretation of reality not a pure reflection. Experimentally verifying this is difficult, as these variations might be present on a single trial level. The first step towards establishing a method that captures the visual representation of a population of neurons is sensory reconstruction, where the aim is to get as close as possible to the original sensory input. We think pixel-level correlation is a stringent and interpretable metric for this purpose, particularly when optimizing for perceptual similarity rather than image similarity directly.

      Comparison to previous work (Yoshida et al.) has methodological concerns: Direct comparison of correlation values across different datasets may be misleading; Large differences in the number of recorded neurons (10x more in the current study); Different stimulus types (dynamic vs static) make comparison difficult; No implementation of previous methods on the current dataset or vice versa. 

      Yes, we absolutely agree that direct comparison to previous static image reconstruction methods is problematic. We primarily do so because we think it is standard practice to give related baselines. We agree that direct comparison of the performance of video reconstruction methods to image reconstruction methods is not really possible. It does not make sense to train and apply a dynamic model on a static image data set where neural activity is time-averaged, as the temporal kernels could not be learned. Conversely, for a static model, which expects a single image as input and predicts time averaged responses, it does not make sense to feed it a series of temporally correlated movie frames and to simply concatenate the resulting activity perdition. The static model would need to be substantially augmented to incorporate temporal dynamics, which in turn would make it a new method. This puts us in the awkward position of being expected to compare our video reconstruction performance to previous image reconstruction methods without a fair way of doing so. We have now added these caveats in line 119:

      “However, we would like to stress that directly comparing static image reconstruction methods with movie reconstruction approaches is fundamentally problematic, as they rely on different data types both during training and evaluation (temporally averaged vs continuous neural activity, images flashed at fixed intervals vs continuous movies).”

      We have also toned down the language, emphasising the comparison to previous image reconstruction performance in the abstract, results, and conclusion. 

      Abstract: We removed “We achieve a ~2-fold increase in pixel-by-pixel correlation compared to previous state-of-the-art reconstructions of static images from mouse V1, while also capturing temporal dynamics.” and replaced with “We achieve a pixel-level correction of 0.57 between the ground truth movie and the reconstructions from single-trial neural responses.”

      Discussion: we removed “In conclusion, we reconstruct videos presented to mice based on the activity of neurons in the mouse visual cortex, with a ~2-fold improvement in pixel-by-pixel correlation compared to previous static image reconstruction methods.” and replaced with “In conclusion, we reconstruct videos presented to mice based on single-trial activity of neurons in the mouse visual cortex.”

      We have also removed the performance table and have instead added supplementary figure 3 with in-depth comparison across different versions of our reconstruction method (variations of masking, ensembling, contrast & luminance matching, and Gaussian blurring). 

      Limited exploration of how the reconstruction method could provide insights into neural coding principles beyond demonstrating technical capability. 

      The aim of this paper was not to reveal principles of neural coding. Instead, we aimed to achieve the best possible performance of video reconstructions and to quantify the limitations. But to highlight its potential we have added two examples of how sensory reconstruction has been applied in human vision research in line 321: 

      “Although fMRI-based reconstruction techniques are starting to be used to investigate visual phenomena in humans (such as illusions [Cheng et al., 2023] and mental imagery [Shen et al., 2019; Koide-Majima et al., 2024; Kalantari et al., 2025]), visual processing phenomena are likely difficult to investigate using existing fMRI-based reconstruction approaches, due to the low spatial and temporal resolution of the data.”

      We have also added a demonstration of how this method could be used to investigate which parts of a reconstruction from a single trial response differs from the model's prediction (Figure  6). We do this by calculating pixel-level differences between reconstructions from the recorded neural activity and reconstructions from the expected neural activity (predicted activity by the neural encoding model). Although difficult to interpret, this pixel-by-pixel error map could represent trial-by-trial deviations of the neural code from pure sensory representation. But at this point we cannot know whether these errors are nothing more than errors in the reconstruction process. To derive meaningful interpretations of these maps would require a substantial amount of additional work and in vivo experiments and so is outside the scope of this paper, but we include this additional analysis now to highlight a) why pixel-level similarity might be interesting to quantify and visualize and b) to demonstrate how video reconstruction could be used to provide insights into neural coding, namely as a tool to identify how sensory representations differ from a pure reflection of the visual input.  

      The claim that "stimulus reconstruction promises a more generalizable approach" (line 180) is not well supported with concrete examples or evidence. 

      What we mean by generalizable is the ability to apply reconstruction to novel stimuli, which is not possible for stimulus classification. We now explain this better in the paragraph in line 211: 

      “Stimulus identification, i.e. identifying the most likely stimulus from a constrained set, has been a popular approach for quantifying whether a population of neurons encodes the identity of a particular stimulus [Földiák, 1993, Kay et al., 2008]. This approach has, for instance, been used to decode frame identity within a movie [Deitch et al., 2021, Xia et al., 2021, Schneider et al., 2023, Chen et al.,2024]. Some of these approaches have also been used to reorder the frames of the ground truth movie [Schneider et al., 2023] based on the decoded frame identity. Importantly, stimulus identification methods are distinct from stimulus reconstruction where the aim is to recreate what the sensory content of a neuronal code is in a way that generalizes to new sensory stimuli [Rakhimberdina et al., 2021]. This is inherently a more demanding task because the range of possible solutions is much larger. Although stimulus identification is a valuable tool for understanding the information content of a population code, stimulus reconstruction could provide a more generalizable approach, because it can be applied to novel stimuli.”

      All the stimuli we reconstructed were not in the training set of the model, i.e., novel. We have also downed down the claim: we have replaced “promises” with “could provide”. 

      The paper would benefit from addressing how the method handles cases where different stimuli produce similar neural responses, particularly for high-speed moving stimuli where phase differences might be lost in calcium imaging temporal resolution. 

      Thank you for this suggestion, we think this is a great question. Calcium dynamics are slow and some of the high temporal frequency information could indeed be lost, particularly phase information. In other words, when the stimulus has high temporal frequency information, it is harder to decode spatial information because of the slow calcium dynamics. Ideally, we would look at this effect using the drifting grating stimuli; however, this is problematic because we rely on predicted activity from the SOTA DNEM, and due to the dilation of the first convolution, the periodic grating stimulus causes aliasing. At 15Hz, when the temporal frequency of the stimulus is half the movie frame rate, the model is actually being given two static images, and so the predicted activity is the interleaved activity evoked by two static images. We therefore do not think using the grating stimuli is a good idea. But we have used the Gaussian stimuli as it is not periodic, and is therefore less of a problem. 

      We have now also reconstructed phase-inverted Gaussian noise stimuli and plotted the video correlation between the reconstructions from activity evoked by phase-inverted stimuli. On the one hand, we find that even for the fastest changing stimuli, the correlation between the reconstructions from phase inverted stimuli are negative, meaning phase information is not lost at high temporal frequencies. On the other hand, for the highest spatial frequency stimuli, the correlation is negative. So, the predicted neural activity (and therefore the reconstructions) are phase-insensitive when the spatial frequency is higher than the reconstruction resolution limit we identified (spatial length constant of 1 pixel, or 3.38 degrees). Beyond this limit, the DNEM predicts activity in response to phase-inverted stimuli, which, when used for reconstruction, results in movies which are more similar to each other than the stimulus that actually evokes them. 

      However, not all information is lost at these high spatial frequencies. If we plot the Shannon entropy in the spatial domain or the motion energy in the temporal domain, we find that even when the reconstructions fail to capture the stimulus at a pixel-specific level (spatial length constant of 1 pixel, or 3.38 degrees), they do capture the general spatial and temporal qualities of the videos. 

      We have added these additional analyses to Figure 4 and Supplementary Figure 5.

      Reviewer #2 (Public review): 

      This is an interesting study exploring methods for reconstructing visual stimuli from neural activity in the mouse visual cortex. Specifically, it uses a competition dataset (published in the Dynamic Sensorium benchmark study) and a recent winning model architecture (DNEM, dynamic neural encoding model) to recover visual information stored in ensembles of the mouse visual cortex. 

      This is a great project - the physiological data were measured at a single-cell resolution, the movies were reasonably naturalistic and representative of the real world, the study did not ignore important correlates such as eye position and pupil diameter, and of course, the reconstruction quality exceeded anything achieved by previous studies. Overall, it is great that teams are working towards exploring image reconstruction. Arguably, reconstruction may serve as an endgame method for examining the information content within neuronal ensembles - an alternative to training interminable numbers of supervised classifiers, as has been done in other studies. Put differently, if a reconstruction recovers a lot of visual features (maybe most of them), then it tells us a lot about what the visual brain is trying to do: to keep as much information as possible about the natural world in which its internal motor circuits may act consequently. 

      While we enjoyed reading the manuscript, we admit that the overall advance was in the range of those that one finds in a great machine learning conference proceedings paper. More specifically, we found no major technical flaws in the study, only a few potential major confounds (which should be addressable with new analyses), and the manuscript did not make claims that were not supported by its findings, yet the specific conceptual advance and significance seemed modest. Below, we will go through some of the claims, and ask about their potential significance. 

      We thank the reviewer for the positive feedback on our paper.

      (1) The study showed that it could achieve high-quality video reconstructions from mouse visual cortex activity using a neural encoding model (DNEM), recovering 10-second video sequences and approaching a two-fold improvement in pixel-by-pixel correlation over attempts. As a reader, I am left with the question: okay, does this mean that we should all switch to DNEM for our investigations of the mouse visual cortex? What makes this encoding model special? It is introduced as "a winning model of the Sensorium 2023 competition which achieved a score of 0.301... single-trial correlation between predicted and ground truth neuronal activity," but as someone who does not follow this competition (most eLife readers are not likely to do so, either), I do not know how to gauge my response. Is this impressive? What is the best achievable score, in theory, given data noise? Is the model inspired by the mouse brain in terms of mechanisms or architecture, or was it optimized to win the competition by overfitting it to the nuances of the data set? Of course, I know that as a reader, I am invited to read the references, but the study would stand better on its own if clarified how its findings depended on this model. 

      This is a very good point. We do not think that everyone should switch to using this particular DNEM to investigate the mouse visual cortex, but we think DNEMs and stimulus reconstruction in general has a lot of potential. We think static neural encoding models have already been demonstrated to be an extremely valuable tool to investigate visual coding (Walker et al., 2019; Yoshida et al., 2021; Willeke et al., bioRxiv 2023). DNEMs are less common, largely because they are very large and are technically more demanding to train and use. That makes static encoding models more practical for some applications, but they do not have temporal kernels and are therefore only used for static stimuli. They cannot, for instance, encode direction tuning, only orientation tuning. But both static and dynamic encoding models have advantages over stimulus classification methods which we outline in our discussion. Here we provide the first demonstration that previous achievements in static image reconstruction are transferable to movies.

      It has been shown in the past for static neural encoding models that choosing a better-performing model produces reconstructed static images that are closer to the original image (Pierzchlewicz et al., 2023). The factors in choosing this particular DNEM were its capacity to predict neural activity (benchmarked against other models), it was open source, and the data it was designed for was also available. 

      To give more context to the model used in the paper, we have included the following, line 348:

      “This model achieved an average single-trial correlation between predicted and ground truth neural activity of 0.291 during the competition, this was later improved to 0.301. The competition benchmark models achieved 0.106, 0.164 and 0.197 single-trial correlation, while the third and second place models achieved 0.243 and 0.265. Across the models, a variety of architectural components were used, including 2D and 3D convolutional layers, recurrent layers, and transformers, to name just a few.” 

      Concerning biologically inspired model design. The winning model contained 3 fully connected layers comprising the “Cortex” just before the final readout of neural activity, but we would consider this level of biological inspiration as minor. We do not think that the exact architecture of the model is particularly important, as the crucial aspect of such neural encoders is their ability to predict neural activity irrespective of how they achieve it. There has been a move towards creating foundation models of the brain (Wang et al., 2025) and the priority so far has been on predictive performance over mechanistic interpretability or similarity to biological structures and processes. 

      Finally, we would like to note that we do not know what the maximum theoretical score for single-trial responses might be, and don't think there is a good way of estimating it in this context. 

      (2) Along those lines, two major conclusions were that "critical for high-quality reconstructions are the number of neurons in the dataset and the use of model ensembling." If true, then these principles should be applicable to networks with different architectures. How well can they do with other network types? 

      This is a good question. Our method critically relies on the accurate prediction of neural activity in response to new videos. It is therefore expected that a model that better predicts neural responses to stimuli will also be better at reconstructing those stimuli given population activity. This was previously shown for static images (Pierzchlewicz et al., 2023). It is also expected that whenever the neural activity is accurately predicted, the corresponding reconstructed frames will also be more similar to the ground truth frames. We have now demonstrated this relationship between prediction accuracy and reconstruction accuracy in supplementary figure 4.

      Although it would be interesting to compare the movie reconstruction performance of many different models with different architectures and activity prediction performances, this would involve quite substantial additional work because movie reconstruction is very resource- and time-intensive. Finding optimal hyperparameters to make such a comparison fair and informative would therefore be impractical and likely not yield surprising results. 

      We also think it is unlikely that ensembling would not improve reconstruction performance in other models because ensembling across model predictions is a common way of improving single-model performance in machine learning. Likewise, we think it is unlikely that the relationship between neural population size and reconstruction performance would differ substantially when using different models, because using more neurons means that a larger population of noisy neurons is “voting” on what the stimulus is. However, we would expect that if the model were worse at predicting neural activity, then more neurons are needed for an equivalent reconstruction performance. In general, we would recommend choosing the best possible DNEM available, in terms of neural activity prediction performance, when reconstructing movies using input optimization through gradient descent. 

      (3) One major claim was that the quality of the reconstructions depended on the number of neurons in the dataset. There were approximately 8000 neurons recorded per mouse. The correlation difference between the reconstruction achieved by 1 neuron and 8000 neurons was ~0.2. Is that a lot or a little? One might hypothesize that ~7,999 additional neurons could contribute more information, but perhaps, those neurons were redundant if their receptive fields were too close together or if they had the same orientation or spatiotemporal tuning. How correlated were these neurons in response to a given movie? Why did so many neurons offer such a limited increase in correlation? 

      In the population ablation experiments, we compared the performance using ~1000, ~2000, ~4000, ~8000 neurons, and found an attenuation of 39.5% in video correlation when dropping 87.5% of the neurons (~1000 neurons remaining), we did not try reconstruction using just 1 neuron. 

      (4) On a related note, the authors address the confound of RF location and extent. The study resorted to the use of a mask on the image during reconstruction, applied during training and evaluation (Line 87). The mask depends on pixels that contribute to the accurate prediction of neuronal activity. The problem for me is that it reads as if the RF/mask estimate was obtained during the very same process of reconstruction optimization, which could be considered a form of double-dipping (see the "Dead salmon" article, https://doi.org/10.1016/S1053-8119(09)71202-9). This could inflate the reconstruction estimate. My concern would be ameliorated if the mask was obtained using a held-out set of movies or image presentations; further, the mask should shift with eye position, if it indeed corresponded to the "collective receptive field of the neural population." Ideally, the team would also provide the characteristics of these putative RFs, such as their weight and spatial distribution, and whether they matched the biological receptive fields of the neurons (if measured independently). 

      We can reassure the reviewer that there is no double-dipping. We would like to clarify that the mask was trained only on videos from the training set of the DNEM and not the videos which were reconstructed. We have added the sentence, line 91: 

      “None of the reconstructed movies were used in the optimization of this transparency mask.”

      Making the mask dependent on eye position would be difficult to implement with the current DNEM, where eye position is fed to the model as an additional channel. When using a model where the image is first transformed into retinotopic coordinates in an eye position-dependent manner (such as in Wang et al., 2025) the mask could be applied in retinotopic coordinates and therefore be dependent on eye position. 

      Effectively, the alpha mask defines the relative level of influence each pixel contributes to neural activity prediction. We agree it is useful to compare the shape of the alpha mask with the location of traditional on-off receptive fields (RFs) to clarify what the alpha mask represents and characterise the neural population available for our reconstructions. We therefore presented the DNEM with on-off patches to map the receptive fields of single neurons in an in silico experiment (the experimentally derived RF are not available). As expected, there is a rough overlap between the alpha mask (Supplementary Figure 2D), the average population receptive field (Supplementary Figure 2B), and the location of receptive field peaks (Supplementary Figure 2C). In principle, all three could be used during training or evaluation for masking, but we think that defining a mask based on the general influence of images on neural activity, rather than just on off patch responses, is a more elegant solution.

      One idea of how to go a step further would be to first set the alpha mask threshold during training based on the % loss of neural activity prediction performance that threshold induces (in our case alpha=0.5 corresponds to ~3% loss in correlation between predicted vs recorded neural responses, see Supplementary Figure 3D), and second base the evaluation mask on a pixel correlation threshold (see example pixel correlation map in Supplementary Figure 2E) instead to avoid evaluating areas of the image with low image reconstruction confidence. 

      We referred to this figure in the result section, line 83:

      “The transparency masks are aligned with but not identical to the On-Off receptive field distribution maps using sparse-noise (Figure S2).” 

      We have also done additional analysis on the effect of masking during training and evaluation with different thresholds in Supplementary Figure 3.

      (5) We appreciated the experiments testing the capacity of the reconstruction process, by using synthetic stimuli created under a Gaussian process in a noise-free way. But this further raised questions: what is the theoretical capability for the reconstruction of this processing pipeline, as a whole? Is 0.563 the best that one could achieve given the noisiness and/or neuron count of the Sensorium project? What if the team applied the pipeline to reconstruct the activity of a given artificial neural network's layer (e.g., some ResNet convolutional layer), using hidden units as proxies for neuronal calcium activity? 

      That’s a very interesting point. It is very hard to know what the theoretical best reconstruction performance of the model would be. Reconstruction performance could be decreased due to neural variability, experimental noise, the temporal kernel of the calcium indicator and the imaging frame rate, information compression along the visual hierarchy, visual processing phenomena (such as predictive coding and selective attention), failure of the model to predict neural activity correctly, or failure of the reconstruction process to find the best possible image which explains the neural activity. We don't think we can disentangle the contribution of all these sources, but we can provide a theoretical maximum assuming that the model and the reconstruction process are optimal. To that end, we performed additional simulations and reconstructed the natural videos using the predicted activity of the neurons in response to the natural videos as the target (similar to the synthetic stimuli) and got a correlation of 0.766. So, the single trial performance of 0.569 is ~75% of this theoretical maximum. This difference can be interpreted as a combination of the losses due to neuronal variability, measurement noise, and actual deviations in the images represented by the brain compared to reality. 

      We thank the reviewer for this suggestion, as it gave us the idea of looking at error maps (Figure 6), where the pixel-level deviation of the reconstructions from recorded vs predicted activity is overlaid on the ground truth movie.

      (6) As the authors mentioned, this reconstruction method provided a more accurate way to investigate how neurons process visual information. However, this method consisted of two parts: one was the state-of-the-art (SOTA) dynamic neural encoding model (DNEM), which predicts neuronal activity from the input video, and the other part reconstructed the video to produce a response similar to the predicted neuronal activity. Therefore, the reconstructed video was related to neuronal activity through an intermediate model (i.e., SOTA DNEM). If one observes a failure in reconstructing certain visual features of the video (for example, high-spatial frequency details), the reader does not know whether this failure was due to a lack of information in the neural code itself or a failure of the neuronal model to capture this information from the neural code (assuming a perfect reconstruction process). Could the authors address this by outlining the limitations of the SOTA DNEM encoding model and disentangling failures in the reconstruction from failures in the encoding model? 

      To test if a better neural prediction by the DNEM would result in better reconstructions, we ran additional simulations and now show that neural activity prediction performance correlates with reconstruction performance (Supplementary Figure 4B). This is consistent with Pierzchlewicz et al., (2023) who showed that static image reconstructions using better encoding models leads to better reconstruction performance. As also mentioned in the answer to the previous comment, untangling the relative contributions of reconstruction losses is hard, but we think that improvements to the DNEM performance are key. Two suggestions to improving the DNEM we used would be to translate the input image into retinotopic coordinates and shift this image relative to eye position before passing it to the first convolutional layer (as is done in Wang et al. 2025), to use movies which are not spatially down sampled as heavily, to not use a dilation of 2 in the temporal convolution of the first layer and to train on a larger dataset. 

      (7) The authors mentioned that a key factor in achieving high-quality reconstructions was model assembling. However, this averaging acts as a form of smoothing, which reduces the reconstruction's acuity and may limit the high-frequency content of the videos (as mentioned in the manuscript). This averaging constrains the tool's capacity to assess how visual neurons process the low-frequency content of visual input. Perhaps the authors could elaborate on potential approaches to address this limitation, given the critical importance of high-frequency visual features for our visual perception. 

      This is exactly what we also thought. To answer this point more specifically, we ran additional simulations where we also reconstruct the movies using gradient ensembling instead of reconstruction ensembling. Here, the gradients of the loss with respect to each pixel of the movie is calculated for each of the model instances and are averaged at every iteration of the reconstruction optimization. In essence, this means that one reconstruction solution is found, and the averaging across reconstructions, which could degrade high-frequency content, is skipped. The reconstructions from both methods look very similar, and the video correlation is, if anything, slightly worse (Supplemental Figure 3A&C). This indicates that our original ensembling approach did not limit reconstruction performance, but that both approaches can be used, depending on what is more convenient given hardware restrictions. 

      Reviewer #3 (Public review): 

      Summary: 

      This paper presents a method for reconstructing input videos shown to a mouse from the simultaneously recorded visual cortex activity (two-photon calcium imaging data). The publicly available experimental dataset is taken from a recent brain-encoding challenge, and the (publicly available) neural network model that serves to reconstruct the videos is the winning model from that challenge (by distinct authors). The present study applies gradient-based input optimization by backpropagating the brain-encoding error through this selected model (a method that has been proposed in the past, with other datasets). The main contribution of the paper is, therefore, the choice of applying this existing method to this specific dataset with this specific neural network model. The quantitative results appear to go beyond previous attempts at video input reconstruction (although measured with distinct datasets). The conclusions have potential practical interest for the field of brain decoding, and theoretical interest for possible future uses in functional brain exploration. 

      Strengths: 

      The authors use a validated optimization method on a recent large-scale dataset, with a state-of-the-art brain encoding model. The use of an ensemble of 7 distinct model instances (trained on distinct subsets of the dataset, with distinct random initializations) significantly improves the reconstructions. The exploration of the relation between reconstruction quality and the number of recorded neurons will be useful to those planning future experiments. 

      Weaknesses: 

      The main contribution is methodological, and the methodology combines pre-existing components without any new original components. 

      We thank the reviewer for taking the time to review our paper and for their overall positive assessment. We would like to emphasise that combining pre-existing machine learning techniques to achieve top results in a new modality does require iteration and innovation. While gradient-based input optimization by backpropagating the brain-encoding error through a neural encoding model has been used in 2D static image optimization to generate maximally exciting images and reconstruct static images, we are the first to have applied it to movies which required accounting for the time domain. Previous methods used time averaged responses and were limited to the reconstruction of static images presented with fixed image intervals.

      The movie reconstructions include a learned "transparency mask" to concentrate on the most informative area of the frame; it is not clear how this choice impacts the comparison with prior experiments. Did they all employ this same strategy? If not, shouldn't the quantitative results also be reported without masking, for a fair comparison? 

      Yes, absolutely. All reconstruction approaches limit the field of view in some way, whether this is due to the size of the screen, the size of the image on the screen, or cropping of the presented/reconstructed images during analysis due to the retinotopic coverage of the recorded neurons. Note that we reconstruct a larger field of view than Yoshida et al. In Yoshida et al., the reconstructed field of view was 43 by 43 retinal degrees. we show the size of an example evaluation mask in comparison. 

      To address the reviewer’s concern more specifically, we performed additional simulations and now also show the performance using a variety of different training and evaluation masks, including different alpha thresholds for training and evaluation masks as well as the effective retinotopic coverage at different alpha thresholds. Despite these comparisons, we would also like to highlight that the comparison to the benchmark is problematic itself. This is because image and movie reconstruction are not directly comparable. It does not make sense to train and apply a dynamic model on a static image dataset where neural activity is time averaged. Conversely, it does not make sense to train or apply a static model that expects time-averaged neural responses on continuous neural activity unless it is substantially augmented to incorporate temporal dynamics, which in turn would make it a new method. This puts us in the awkward position of being expected to compare our video reconstruction performance to previous image reconstruction methods without a fair way of doing so. We have therefore de-emphasised the phrasing comparing our method to previous publications in the abstract, results, and discussion. 

      Abstract: “We achieve a ~2-fold increase in pixel-by-pixel correlation compared to previous state-of-the-art reconstructions of static images from mouse V1, while also capturing temporal dynamics.” with “We achieve a pixel-level correction of 0.57 between the ground truth movie and the reconstructions from single-trial neural responses.”

      Results: “This represents a ~2x higher pixel-level correlation over previous single-trial static image reconstructions from V1 in awake mice (image correlation 0.238 +/- 0.054 s.e.m for awake mice) [Yoshida et al., 2020] over a similar retinotopic area (~43° x 43°) while also capturing temporal dynamics. However, we would like to stress that directly comparing static image reconstruction methods with movie reconstruction approaches is fundamentally problematic, as they rely on different data types both during training and evaluation (temporally averaged vs continuous neural activity, images flashed at fixed intervals vs continuous movies).”

      Discussion: “In conclusion, we reconstruct videos presented to mice based on the activity of neurons in the mouse visual cortex, with a ~2-fold improvement in pixel-by-pixel correlation compared to previous static image reconstruction methods.” with “In conclusion, we reconstruct videos presented to mice based on single-trial activity of neurons in the mouse visual cortex.”

      We have also removed the performance table and have instead added supplementary figure 3 with in-depth comparison across different versions of our reconstruction method (variations of masking, ensembling, contrast & luminance matching, and Gaussian blurring). 

      We believe that we have given enough information in our paper now so that readers can make an informed decision whether our movie reconstruction method is appropriate for the questions they are interested in.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors): 

      (1) "Reconstructions have been luminance (mean pixel value across video) and contrast (standard deviation of pixel values across video) matched to ground truth." This was not clear: was it done by the investigating team? I imagine that one of the most easily captured visual features is luminance and contrast, why wouldn't the optimization titrate these well? 

      The contrast and luminance matching of the reconstructions to the ground truth videos was done by us, but this was only done to help readers assess the quality of the reconstructions by eye. Our performance metrics (frame and video correlation) are contrast and luminance insensitive. To clarify this, we have also added examples of non-adjusted frames in Supplementary Figure 3A, and added a sentence in the results, line 103: 

      “When presenting videos in this paper we normalize the mean and standard deviation of the reconstructions to the average and standard deviation of the corresponding ground truth movie before applying the evaluation masks, but this is not done for quantification except in Supplementary Figure 3D.”

      We were also initially surprised that contrast and luminance are not captured well by our reconstruction method, but this makes sense as V1 is largely luminance invariant (O’Shea et al., 2025 https://doi.org/10.1016/j.celrep.2024.115217 ) and contrast only has a gain effect on V1 activity (Tring et al., 2024 https://journals.physiology.org/doi/full/10.1152/jn.00336.2024). Decoding absolute contrast is likely unreliable because it is probably not the only factor modulating the overall gain of the neural population.

      To address the reviewer’s comment more fully, we ran additional experiments. More specifically, to test why contrast and luminance are not recovered in the reconstructions, we checked how the predicted activity between the reconstruction and the contrast/luminance corrected reconstructions differs. Contrast and luminance adjustment had little impact on predicted response similarity on average. This makes the reconstruction optimization loss function insensitive to overall contrast and luminance so it cannot be decoded. There is a small effect on activity correlation, however, so we cannot completely rule out that contrast and luminance could be reconstructed with a different loss function. 

      (2) The authors attempted to investigate the variability in reconstruction quality across different movies and 10-second snippets of a movie by correlating various visual features, such as video motion energy, contrast, luminance, and behavioral factors like running speed, pupil diameter, and eye movement, with reconstruction success. However, it would also be beneficial if the authors correlated the response loss (Poisson loss between neural responses) with reconstruction quality (video correlation) for individual videos, as these metrics are expected to be correlated if the reconstruction captures neural variance. 

      We thank the reviewer for this suggestion. We have now included this analysis and find that if the neural activity was better predicted by the DNEM then the reconstruction of the video was also more similar to the ground truth video. We further found that this effect is shift-dependent (in time), meaning the prediction of activity based on proximal video frames is more influential on reconstruction performance. 

      Reviewer #3 (Recommendations for the authors): 

      (1) I was confused about the choice of applying a transparency mask thresholded with alpha>0.5 during training and alpha>1 during evaluation. Why treat the two situations differently? Also, shouldn't we expect alpha to be in the [0,1] range, in which case, what is the meaning of alpha>1? (And finally, as already described in "Weaknesses", how does this choice impact the comparison with prior experiments? Did they also employ a similar masking strategy?) 

      We found that applying a mask during training increased performance regardless of the size of the evaluation mask. Using a less stringent mask during training than during evaluation increases performance slightly, but also allows inspection of the reconstruction in areas where the model will be less confident without sacrificing performance, if this is desired. The thresholds of 0.5 and 1 were chosen through trial and error, but the exact values do not hold intrinsic meaning. The alpha mask values can go above 1 during their optimization. We could have clipped alpha during the training procedure (algorithm 1), but we decided this was not worth redoing at this stage, as the alphas used for testing were not above 1. All reconstruction approaches in previous publications limit the field of view in some form, whether this is due to the size of the screen, the size of the image on the screen, or the cropping of the presented/reconstructed images during analysis. 

      To address the reviewer’s comment in detail, we have added extensive additional analysis to evaluate the coverage of the reconstruction achieved in this paper and how different masking strategies affect performance, as well as how the mask relates to more traditional receptive field mapping.  

      (2) I would not use the word "imagery" in the first sentence of the abstract, because this might be interpreted by some readers as reconstruction of mental imagery, a very distinct question. 

      We changed imagery to images in the abstract.

      (3) Line 145-146: "<1 frame, or <30Hz" should be "<1 frame, or >30Hz". 

      We have corrected the error.

      (4) Algorithm 1, Line 5, a subscript variable 'g' should be changed to 'h'

      We have corrected the error.

      Additional Changes

      (1) Minor grammatical errors

      (2) Addition of citations: We were previously not aware of a bioRxiv preprint from 2022 (Cobos et al., 2022), which used gradient descent-based input optimization to reconstruct static images but without the addition of a diffusion model. Instead, we had cited for this method Pierzchlewicz et al., 2023 bioRxiv/NeurIPS. In Cobos et al., 2022, they compare static image reconstruction similarity to ground truth images and the similarity of the in vivo evoked activity across multiple reconstruction methods. Performance values are only given for reconstructions from trial-averaged responses across ~40 trials (in the absence of original data or code we are also not able to retrospectively calculate single-trial performance). The authors find that optimizing for evoked activity rather than image similarity produces image reconstructions that evoke more similar in vivo responses compared to reconstructions optimized for image similarity itself. We have now added and discussed the citation in the main text. 

      (3) Workaround for error in the open-source code from https://github.com/lRomul/sensorium for video hashing function in the SOTA DNEM: By checking the most correlated first frame for each reconstructed movie, we discovered there was a bug in the open-source code and 9/50 movies we originally used for reconstruction were not properly excluded from the training data between DNEM instances. The reason for this error was that some of the movies are different by only a few pixels, and the video hashing function used to split training and test set folds in the original DNEM code classified these movies as different and split them across folds. We have replaced these 9 movies and provide a figure below showing the next closest first frame for every movie clip we reconstruct. This does not affect our claims. Excluding these 9 movie clips, did not affect the reconstruction performance (video correlation went from 0.563 to 0.568), so there was no overestimation of performance due to test set contamination. However, they should still be removed so some of the values in the paper have changed slightly. The only statistical test that was affected was the correlation between video correlation and mean motion energy (Supplementary Figure 4A), which went from p = 0.043 to 0.071. 

      Author response image 2.

      exclusion of movie clips with duplicates in the DNEM training data. A) example frame of a reconstructed movie (ground truth) and the most correlated first frame from the training data. b) all movie clips and their corresponding most correlated clip from the training data. Red boxes indicate excluded duplicates. 

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review)

      Major:

      (1) In line 76, the authors make a very powerful statement: 'σRNN simulation achieves higher similarity with unseen recorded trials before perturbation, but lower than the bioRNN on perturbed trials.' I couldn't find a figure showing this. This might be buried somewhere and, in my opinion, deserves some spotlight - maybe a figure or even inclusion in the abstract.

      We agree with the reviewer that these results are important. The failure of σRNN on perturbed data could be inferred from the former Figures 1E, 2C-E, and 3D. Following the reviewers' comments, we have tried to make this the most prominent message of Figure 1, in particular with the addition of the new panel E. We also moved Table 1 from the  Supplementary to the main text to highlight this quantitatively. 

      (2) It's mentioned in the introduction (line 84) and elsewhere (e.g., line 259) that spiking has some advantage, but I don't see any figure supporting this claim. In fact, spiking seems not to matter (Figure 2C, E). Please clarify how spiking improves performance, and if it does not, acknowledge that. Relatedly, in line 246, the authors state that 'spiking is a better metric but not significant' when discussing simulations. Either remove this statement and assume spiking is not relevant, or increase the number of simulations.

      We could not find the exact quote from the reviewer, and we believe that he intended to quote “spiking is better on all metrics, but without significant margins”. Indeed, spiking did not improve the fit significantly on perturbed trials, this is particularly true in comparison with the benefits of Dale’s law and local inhibition. As suggested by the reviewer, we rephrased the sentence from this quote and more generally the corresponding paragraphs in the intro (lines 83-87) and in the results (lines 245-271). Our corrections in the results sections are also intended to address the minor point (4) raised by the same reviewer.

      (3) The authors prefer the metric of predicting hits over MSE, especially when looking at real data (Figure 3). I would bring the supplementary results into the main figures, as both metrics are very nicely complementary. Relatedly, why not add Pearson correlation or R2, and not just focus on MSE Loss?

      In Figure 3 for the in-vivo data, we do not have simultaneous electrophysiological recordings and optogenetic stimulation in this dataset.  The two are performed on different recording sessions. Therefore, we can only compare the effect of optogenetics on the behavior, and we cannot compute Pearson correlation or R2 of the perturbed network activity. To avoid ambiguity, we wrote “For the sessions of the in vivo dataset with optogenetic perturbation that we considered, only the behavior of an animal is recorded” on line 294. 

      (4) I really like the 'forward-looking' experiment in closed loop! But I felt that the relevance of micro perturbations is very unclear in the intro and results. This could be better motivated: why should an experimentalist care about this forward-looking experiment? Why exactly do we care about micro perturbation (e.g., in contrast to non-micro perturbation)? Relatedly, I would try to explain this in the intro without resorting to technical jargon like 'gradients'.

      As suggested, we updated the last paragraph of the introduction (lines 88 - 95) to give better motivation for why algorithmically targeted acute spatio-temporal perturbations can be important to dissect the function of neural circuits. We also added citations to recent studies with targeted in vivo optogenetic stimulation. As far as we know the existing previous work targeted network stimulation mostly using linear models, while we used non-linear RNNs and their gradients.

      Minor:

      (1) In the intro, the authors refer to 'the field' twice. Personally, I find this term odd. I would opt for something like 'in neuroscience'.

      We implemented the suggested change: l.27 and l.30

      (2) Line 45: When referring to previous work using data-constrained RNN models, Valente et al. is missing (though it is well cited later when discussing regularization through low-rank constraints)

      We added the citation: l.45

      (3) Line 11: Method should be methods (missing an 's').

      We fixed the typo.

      (4) In line 250, starting with 'So far', is a strange choice of presentation order. After interpreting the results for other biological ingredients, the authors introduce a new one. I would first introduce all ingredients and then interpret. It's telling that the authors jump back to 2B after discussing 2C.

      We restructured the last two paragraphs of section 2.1, and we hope that the presentation order is now more logical.

      (5) The black dots in Figure 3E are not explained, or at least I couldn't find an explanation.

      We added an explanation in the caption of Figure 3E.

      Reviewer #2 (Public review):

      (1) Some aspects of the methods are unclear. For comparisons between recurrent networks trained from randomly initialized weights, I would expect that many initializations were made for each model variant to be compared, and that the performance characteristics are constructed by aggregating over networks trained from multiple random initializations. I could not tell from the methods whether this was done or how many models were aggregated.

      The expectation of the reviewer is correct, we trained multiple models with different random seeds (affecting both the weight initialization and the noise of our model) for each variant and aggregated the results. We have now clarified this in Methods 4.6. lines 658-662.

      (2) It is possible that including perturbation trials in the training sets would improve model performance across conditions, including held-out (untrained) perturbations (for instance, to units that had not been perturbed during training). It could be noted that if perturbations are available, their use may alleviate some of the design decisions that are evaluated here.

      In general, we agree with the reviewer that including perturbation trials in the training set would likely improve model performance across conditions. One practical limitation explaining partially why we did not do it with our dataset is the small quantity of perturbed trials for each targeted cortical area: the number of trials with light perturbations is too scarce to robustly train and test our models.

      More profoundly, to test hard generalizations to perturbations (aka perturbation testing), it will always be necessary that the perturbations are not trivially represented in the training data. Including perturbation trials during training would compromise our main finding: some biological model constraints improve the generalization to perturbation. To test this claim, it was necessary to keep the perturbations out of the training data.

      We agree that including all available data of perturbed and non-perturbed recordings would be useful to build the best generalist predictive system. It could help, for instance, for closed-loop circuit control as we studied in Figure 5. Yet, there too, it will be important for the scientific validation process to always keep some causal perturbations of interest out of the training set. This is necessary to fairly measure the real generalization capability of any model. Importantly, this is why we think out-of-distribution “perturbation testing” is likely to have a recurring impact in the years to come, even beyond the case of optogenetic inactivation studied in detail in our paper.

      Recommendation for the authors:

      Reviewer #1 (Recommendation for the authors):

      The code is not very easy to follow. I know this is a lot to ask, but maybe make clear where the code is to train the different models, which I think is a great contribution of this work? I predict that many readers will want to use the code and so this will improve the impact of this work.

      We updated the code to make it easier to train a model from scratch.

      Reviewer #2 (Recommendation for the authors):

      The figures are really tough to read. Some of that small font should be sized up, and it's tough to tell in the posted paper what's happening in Figure 2B.

      We updated Figures 1 and 2 significantly, in part to increase their readability. We also implemented the "Superficialities" suggestions.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review): 

      Summary: 

      The authors analyzed the expression of ATAD2 protein in post-meiotic stages and characterized the localization of various testis-specific proteins in the testis of the Atad2 knockout (KO). By cytological analysis as well as the ATAC sequencing, the study showed that increased levels of HIRA histone chaperone, accumulation of histone H3.3 on post-meiotic nuclei, defective chromatin accessibility and also delayed deposition of protamines. Sperm from the Atad2 KO mice reduces the success of in vitro fertilization. The work was performed well, and most of the results are convincing. However, this manuscript does not suggest a molecular mechanism for how ATAD2 promotes the formation of testis-specific chromatin. 

      We would like to take this opportunity to highlight that the present study builds on our previously published work, which examined the function of ATAD2 in both yeast S. pombe and mouse embryonic stem (ES) cells (Wang et al., 2021). In yeast, using genetic analysis we showed that inactivation of HIRA rescues defective cell growth caused by the absence of ATAD2. This rescue could also be achieved by reducing histone dosage, indicating that the toxicity depends on histone over-dosage, and that HIRA toxicity, in the absence of ATAD2, is linked to this imbalance.

      Furthermore, HIRA ChIP-seq performed in mouse ES cells revealed increased nucleosome-bound HIRA, particularly around transcription start sites (TSS) of active genes, along with the appearance of HIRA-bound nucleosomes within normally nucleosome-free regions (NFRs). These findings pointed to ATAD2 as a major factor responsible for unloading HIRA from nucleosomes. This unloading function may also apply to other histone chaperones, such as FACT (see Wang et al., 2021, Fig. 4C).

      In the present study, our investigations converge on the same ATAD2 function in the context of a physiologically integrated mammalian system—spermatogenesis. Indeed, in the absence of ATAD2, we observed H3.3 accumulation and enhanced H3.3-mediated gene expression. Consistent with this functional model of ATAD2— unloading chaperones from histone- and non-histone-bound chromatin—we also observed defects in histone-toprotamine replacement.

      Together, the results presented here and in Wang et al. (2021) reveal an underappreciated regulatory layer of histone chaperone activity. Previously, histone chaperones were primarily understood as factors that load histones. Our findings demonstrate that we must also consider a previously unrecognized regulatory mechanism that controls assembled histone-bound chaperones. This key point was clearly captured and emphasized by Reviewer #2 (see below).

      Strengths:

      The paper describes the role of ATAD2 AAA+ ATPase in the proper localization of sperm-specific chromatin proteins such as protamine, suggesting the importance of the DNA replication-independent histone exchanges with the HIRA-histone H3.3 axis. 

      Weaknesses: 

      (1) Some results lack quantification. 

      We will consider all the data and add appropriate quantifications where necessary.

      (2) The work was performed well, and most of the results are convincing. However, this manuscript does not suggest a molecular mechanism for how ATAD2 promotes the formation of testis-specific chromatin. 

      Please see our comments above.

      Reviewer #2 (Public review): 

      Summary:

      This manuscript by Liakopoulou et al. presents a comprehensive investigation into the role of ATAD2 in regulating chromatin dynamics during spermatogenesis. The authors elegantly demonstrate that ATAD2, via its control of histone chaperone HIRA turnover, ensures proper H3.3 localization, chromatin accessibility, and histone-toprotamine transition in post-meiotic male germ cells. Using a new well-characterized Atad2 KO mouse model, they show that ATAD2 deficiency disrupts HIRA dynamics, leading to aberrant H3.3 deposition, impaired transcriptional regulation, delayed protamine assembly, and defective sperm genome compaction. The study bridges ATAD2's conserved functions in embryonic stem cells and cancer to spermatogenesis, revealing a novel layer of epigenetic regulation critical for male fertility. 

      Strengths:

      The MS first demonstration of ATAD2's essential role in spermatogenesis, linking its expression in haploid spermatids to histone chaperone regulation by connecting ATAD2-dependent chromatin dynamics to gene accessibility (ATAC-seq), H3.3-mediated transcription, and histone eviction. Interestingly and surprisingly, sperm chromatin defects in Atad2 KO mice impair only in vitro fertilization but not natural fertility, suggesting unknown compensatory mechanisms in vivo. 

      Weaknesses:

      The MS is robust and there are not big weaknesses 

      Reviewer #3 (Public review): 

      Summary: 

      The authors generated knockout mice for Atad2, a conserved bromodomain-containing factor expressed during spermatogenesis. In Atad2 KO mice, HIRA, a chaperone for histone variant H3.3, was upregulated in round spermatids, accompanied by an apparent increase in H3.3 levels. Furthermore, the sequential incorporation and removal of TH2B and PRM1 during spermiogenesis were partially disrupted in the absence of ATAD2, possibly due to delayed histone removal. Despite these abnormalities, Atad2 KO male mice were able to produce offspring normally. 

      Strengths:

      The manuscript addresses the biological role of ATAD2 in spermatogenesis using a knockout mouse model, providing a valuable in vivo framework to study chromatin regulation during male germ cell development. The observed redistribution of H3.3 in round spermatids is clearly presented and suggests a previously unappreciated role of ATAD2 in histone variant dynamics. The authors also document defects in the sequential incorporation and removal of TH2B and PRM1 during spermiogenesis, providing phenotypic insight into chromatin transitions in late spermatogenic stages. Overall, the study presents a solid foundation for further mechanistic investigation into ATAD2 function. 

      Weaknesses:

      While the manuscript reports the gross phenotype of Atad2 KO mice, the findings remain largely superficial and do not convincingly demonstrate how ATAD2 deficiency affects chromatin dynamics. Moreover, the phenotype appears too mild to elucidate the functional significance of ATAD2 during spermatogenesis. 

      We respectfully disagree with the statement that our findings are largely superficial. Based on our investigations of this factor over the years, it has become evident that ATAD2 functions as an auxiliary factor that facilitates mechanisms controlling chromatin dynamics (see, for example, Morozumi et al., 2015). These mechanisms can still occur in the absence of ATAD2, but with reduced efficiency, which explains the mild phenotype we observed.

      This function, while not essential, is nonetheless an integral part of the cell’s molecular biology and should be studied and brought to the attention of the broader biological community, just as we study essential factors. Unfortunately, the field has tended to focus primarily on core functional actors, often overlooking auxiliary factors. As a result, our decade-long investigations into the subtle yet important roles of ATAD2 have repeatedly been met with skepticism regarding its functional significance, which has in turn influenced editorial decisions.

      We chose eLife as the venue for this work specifically to avoid such editorial barriers and to emphasize that facilitators of essential functions do exist. They deserve to be investigated, and the underlying molecular regulatory mechanisms must be understood.

      (1) Figures 4-5: The analyses of differential gene expression and chromatin organization should be more comprehensive. First, Venn diagrams comparing the sets of significantly differentially expressed genes between this study and previous work should be shown for each developmental stage. Second, given the established role of H3.3 in MSCI, the effect of Atad2 knockout on sex chromosome gene expression should be analyzed. Third, integrated analysis of RNA-seq and ATAC-seq data is needed to evaluate how ATAD2 loss affects gene expression. Finally, H3.3 ChIP-seq should be performed to directly assess changes in H3.3 distribution following Atad2 knockout.  

      (1) In the revised version, we will include Venn diagrams to illustrate the overlap in significantly differentially expressed genes between this study and previous work. However, we believe that the GSEAs presented here provide stronger evidence, as they indicate the statistical significance of this overlap (p-values). In our case, we observed p-value < 0.01 (**) and p < 0.001 (***).

      (2) Sex chromosome gene expression was analyzed and is presented in Fig. 5C.

      (3) The effect of ATAD2 loss on gene expression is shown in Fig. 4A, B, and C as histograms, with statistical significance indicated in the middle panels.

      (4) Although mapping H3.3 incorporation across the genome in wild-type and Atad2 KO cells would have been informative, the available anti-H3.3 antibody did not work for ChIP-seq, at least in our hands. The authors of Fontaine et al., 2022, who studied H3.3 during spermatogenesis in mice, must have encountered the same problem, since they tagged the endogenous H3.3 gene to perform their ChIP experiments.

      (2) Figure 3: The altered distribution of H3.3 is compelling. This raises the possibility that histone marks associated with H3.3 may also be affected, although this has not been investigated. It would therefore be important to examine the distribution of histone modifications typically associated with H3.3. If any alterations are observed, ChIP-seq analyses should be performed to explore them further.

      Based on our understanding of ATAD2’s function—specifically its role in releasing chromatin-bound HIRA—in the absence of ATAD2 the residence time of both HIRA and H3.3 on chromatin increases. This results in the detection of H3.3 not only on sex chromosomes but across the genome. Our data provide clear evidence of this phenomenon. The reviewer is correct in suggesting that the accumulated H3.3 would carry H3.3-associated histone PTMs; however, we are unsure what additional insights could be gained by further demonstrating this point.

      (3) Figure 7: While the authors suggest that pre-PRM2 processing is impaired in Atad2 KO, no direct evidence is provided. It is essential to conduct acid-urea polyacrylamide gel electrophoresis (AU-PAGE) followed by western blotting, or a comparable experiment, to substantiate this claim. 

      Figure 7 does not suggest that pre-PRM2 processing is affected in Atad2 KO; rather, this figure—particularly Fig. 7B—specifically demonstrates that pre-PRM2 processing is impaired, as shown using an antibody that recognizes the processed portion of pre-PRM2. ELISA was used to provide a more quantitative assessment; however, in the revised manuscript we will also include a western blot image.

      (4) HIRA and ATAD2: Does the upregulation of HIRA fully account for the phenotypes observed in Atad2 KO? If so, would overexpression of HIRA alone be sufficient to phenocopy the Atad2 KO phenotype? Alternatively, would partial reduction of HIRA (e.g., through heterozygous deletion) in the Atad2 KO background be sufficient to rescue the phenotype? 

      These are interesting experiments that require the creation of appropriate mouse models, which are not currently available.

      (5) The mechanism by which ATAD2 regulates HIRA turnover on chromatin and the deposition of H3.3 remains unclear from the manuscript and warrants further investigation. 

      The Reviewer is absolutely correct. In addition to the points addressed in response to Reviewer #1’s general comments (see above), it would indeed have been very interesting to test the segregase activity of ATAD2 (likely driven by its AAA ATPase activity) through in vitro experiments using the Xenopus egg extract system described by Tagami et al., 2004. This system can be applied both in the presence and absence (via immunodepletion) of ATAD2 and would also allow the use of ATAD2 mutants, particularly those with inactive AAA ATPase or bromodomains. However, such experiments go well beyond the scope of this study, which focuses on the role of ATAD2 in chromatin dynamics during spermatogenesis.

      References:

      (1) Wang T, Perazza D, Boussouar F, Cattaneo M, Bougdour A, Chuffart F, Barral S, Vargas A, Liakopoulou A, Puthier D, Bargier L, Morozumi Y, Jamshidikia M, Garcia-Saez I, Petosa C, Rousseaux S, Verdel A, Khochbin S. ATAD2 controls chromatin-bound HIRA turnover. Life Sci Alliance. 2021 Sep 27;4(12):e202101151. doi: 10.26508/lsa.202101151. PMID: 34580178; PMCID: PMC8500222.

      (2) Morozumi Y, Boussouar F, Tan M, Chaikuad A, Jamshidikia M, Colak G, He H, Nie L, Petosa C, de Dieuleveult M, Curtet S, Vitte AL, Rabatel C, Debernardi A, Cosset FL, Verhoeyen E, Emadali A, Schweifer N, Gianni D, Gut M, Guardiola P, Rousseaux S, Gérard M, Knapp S, Zhao Y, Khochbin S. Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells. J Mol Cell Biol. 2016 Aug;8(4):349-62. doi: 10.1093/jmcb/mjv060. Epub 2015 Oct 12. PMID: 26459632; PMCID: PMC4991664.

      (3) Fontaine E, Papin C, Martinez G, Le Gras S, Nahed RA, Héry P, Buchou T, Ouararhni K, Favier B, Gautier T, Sabir JSM, Gerard M, Bednar J, Arnoult C, Dimitrov S, Hamiche A. Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation. Nucleic Acids Res. 2022 Jul 22;50(13):7350-7366. doi: 10.1093/nar/gkac541. PMID: 35766398; PMCID: PMC9303386.

      (4) Tagami H, Ray-Gallet D, Almouzni G, Nakatani Y. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell. 2004 Jan 9;116(1):51-61. doi: 10.1016/s0092-8674(03)01064-x. PMID: 14718166.

      Recommendations for the authors:

      Reviewing Editor Comments:

      I note that the reviewers had mixed opinions about the strength of the evidence in the manuscript. A revision that addresses these points would be welcome.

      Reviewer #1 (Recommendations for the authors):  

      Major points: 

      (1) No line numbers: It is hard to point out the issues.

      The revised version harbors line numbers.

      (2) Given the results shown in Figure 3 and Figure 4, it is nice to show the chromosomal localization of histone H3.3 in spermatocytes or post-meiotic cells by Chromatin-immunoprecipitation sequencing (ChIP-seq).

      Although mapping H3.3 incorporation across the genome in wild-type and Atad2 KO cells would have been informative, the available anti-H3.3 antibody did not work for ChIP-seq in our hands. In fact, this antibody is not well regarded for ChIP-seq. For example, Fontaine et al. (2022), who investigated H3.3 during spermatogenesis in mice, circumvented this issue by tagging the endogenous H3.3 genes for their ChIP experiments.

      (3) Figure 7B and 8: Why the authors used ELISA for the protein quantification. At least, western blotting should be shown.

      ELISA is a more quantitative method than traditional immunoblotting. Nevertheless, as requested by the reviewer, we have now included a corresponding western blot in Fig. S3.

      (4) For readers, please add a schematic pathway of histone-protamine replacement in sperm formation in Fig.1 and it would be nice to have a model figure, which contains the authors' idea in the last figure.

      As requested by this reviewer, we have now included a schematic model in Figure 9 to summarize the main conclusions of our work.

      Minor points: 

      (1) Page 2, the second paragraph, "pre-PRM2: Please explain more about pre-PRM2 and/or PRM2 as well as PRM1 (Figure 6).

      More detailed descriptions of PRM2 processing are now given in this paragraph. 

      (2) Page 3, bottom paragraph, line 1: "KO" should be "knockout (KO)".

      Done.

      (3) Page 4, second paragraph bottom: Please explain more about the protein structure of germ-line-specific ATAD2S: how it is different from ATAD2L. Germ-line specific means it is also expressed in ovary?

      As Atad2 is predominantly expressed in embryonic stem cells and in spermatogenic cells, we replaced all through the text germ-line specific by more appropriate terms.

      (4) Figure 1C, western blotting: Wild-type testis extracts, both ATAD2L and -S are present. Does this mean that ATADS2L is expressed in both germ line as well as supporting cells. Please clarify this and, if possible, show the western blotting of spermatids well as spermatocytes.

      Figure 1D shows sections of seminiferous tubules from Atad2 KO mice, in which lacZ expression is driven by the endogenous Atad2 promoter. The results indicate that Atad2 is expressed mainly in post-meiotic cells. Most labeled cells are located near the lumen, whereas the supporting Sertoli cells remain unlabeled. Sertoli cells, which are anchored to the basal lamina, span the entire thickness of the germinal epithelium from the basal lamina to the lumen. Their nuclei, however, are usually positioned closer to the basal membrane. Thus, the observed lacZ expression pattern argues against substantial Atad2 expression in Sertoli cells. 

      (5) Figure 1C: Please explain a bit more about the reduction of ATAD2 proteins in heterozygous mice.

      Done

      (6) Figure 1C: Genotypes of the mice should be shown in the legend.

      Done 

      (7) Figure 1D: Please add a more magnified image of the sections to see the staining pattern in the seminiferous tubules.

      The magnification does not bring more information since we lose the structure of cells within tubules due the nature of treatment of the sections for X-gal staining. Please see comments to question 1C to reviewer 2

      (8) Page 5, first paragraph, line 2, histone dosage: What do the authors meant by the histone dosage? Please explain more or use more appropriate word.

      "Histone dosage" refers to the amount or relative abundance of histone proteins in a cell.

      (9) Figure 2A: Figure 2A: Given the result in Figure 1C, it is interesting to check the amount of HIRA in Atad2 heterozygous mice.

      In Atad2 heterozygous mice, we would expect an increase in HIRA, but only to about half the level seen in the Atad2 homozygous knockout shown in Figure 2A, which is relatively modest. Therefore, we doubt that detecting such a small change—approximately half of that in Figure 2A—would yield clear or definitive results. 

      (10) Figure 2A, legend (n=5): What does this "n" mean? The extract of testes from "5" male mice like Figure 2B. Or 5 independent experiments. If the latter is true, it is important to share the other results in the Supplements.

      “n” refers to five WT and five Atad2 KO males. The legend has been clarified as suggested by the reviewer.

      (11) Figure 2A, legend, line 2, Atad2: This should be italicized.

      Done

      (12) Figure 2B: Please show the quantification of amounts of HIRA protein like Fig. 2A.

      As indicated in the legend, what is shown is a pool of testes from 3 individuals per genotype.

      (13) Figure 2B shows an increased level of HIRA in Atad2 KO testis. This suggests the role of ATAD2 in the protein degradation of HIRA. This possibility should be mentioned or tested since ATAD2 is an AAA+ ATPase. 

      The extensive literature on ATAD2 provides no indication that it is involved in protein degradation. In our early work on ATAD2 in the 2000s, we hypothesized that, as a member of the AAA ATPase family, ATAD2 might associate with the 19S proteasome subunit (through multimerization with the other AAA ATPase member of this regulatory subunit). However, both our published pilot studies (Caron et al., PMID: 20581866) and subsequent unpublished work ruled out this possibility. Instead, since the amount of nucleosome-bound HIRA increases in the absence of ATAD2, we propose that chromatin-bound HIRA is more stable than soluble HIRA once it has been released from chromatin by ATAD2.

      (14) Page 6, second paragraph, line 5, ko: KO should be capitalized.

      Done

      (15) Page 6, second paragraph, line 2 from the bottom, chromatin dynamics: Throughout the text, the authors used "chromatin dynamics". However, all the authors analyzed in the current study is the localization of chromatin protein.  So, it is much easier to explain the results by using "chromatin status," etc. In this context, "accessibility" is better. 

      We changed the term “chromatin dynamics” into a more precise term according to the context used all through the text.

      (16) Figure 3: Please provide the quantification of signals of histone H3.3 in a nucleus or nuclear cytoplasm.

      This request is not clear to us since we do not observe any H3.3 signal in the cytoplasm.

      (17) Figure 3: As the control of specificity in post-meiotic cells, please show the image and quantification of the H3.3 signals in spermatocyte, for example.

      This request is not clear to us. What specificity is meant? 

      (18) Figure 3, bottom panels: Please show what the white lines indicate? 

      The white lines indicate the limit of cell nucleus and estimated by Hoechst staining. This is now indicated in the legend of the figure. 

      (19) Figure 4A: Please explain more about what kind of data is here. Is this wild-type and/or Atad2 KO? The label of the Y-axis should be "mean expression level". What is the standard deviation (SD) here on the X-axis. Moreover, there is only one red open circle, but the number of this class is 5611. All 5611 genes in this group show NO expression. Please explain more.

      The plot displays the mean expression levels (y-axis, labeled as "mean expression level") versus the corresponding standard deviations (x-axis), both calculated from three independent biological replicates of isolated round spermatids (Atad2 wild-type and Atad2 KO). The standard deviation reflects the variability of gene expression across biological replicates. Genes were grouped into four categories (grp1: blue, grp2: cyan, grp3: green, grp4: orange) according to the quartile of their mean expression. For grp4, all genes have no detectable expression, resulting in a mean expression of zero and a standard deviation of zero; consequently, the 5611 genes in this group are represented by a single overlapping point (red open circle) at the origin. 

      (20) Figure 4C: If possible, it would be better to have a statistical comparison between wild-type and the KO.  

      The mean profiles are displayed together with their variability (± 2 s.e.m.) across the four replicates for both ATAD2 WT (blue) and ATAD2 KO (red). For groups 1, 2, and 3, the envelopes of the curves remain clearly separated around the peak, indicating a consistent difference in signal between the two conditions. In contrast, group 4 does not present a strong signal and, accordingly, no marked difference is observed between WT and KO in this group.

      (21) Figure 5, GSEA panels: Please explain more about what the GSEA is in the legend.  The legend has been updated as follows:

      (A) Expression profiles of post-meiotic H3.3-activated genes. The heatmap (left panel) displays the normalized expression levels of genes identified by Fontaine and colleagues as upregulated in the absence of histone H3.3 (Fontaine et al. 2022) for Atad2 WT (WT) and Atad2 KO (KO) samples at days 20, 22, 24, and 26 PP (D20 to D26). The colour scale represents the z-score of log-transformed DESeq2-normalized counts. The middle panel box plots display, pooled, normalized expression levels, aggregated across replicates and genes, for each condition (WT and KO) and each time point (D20 to D26). Statistical significance between WT and KO conditions was determined using a two-sided t-test, with p-values indicated as follows: * for p-value<0.05, ** for p-value<0.01 and *** for p-value<0.001. The right panel shows the results of gene set enrichment analysis (GSEA), which assesses whether predefined groups of genes show statistically significant differences between conditions. Here, the post-meiotic H3.3-activated genes set, identified by Fontaine et al. (2022), is significantly enriched in Atad2 KO compared with WT samples at day 26 (p < 0.05, FDR < 0.25). Coloured vertical bars indicate the “leading edge” genes (i.e., those contributing most to the enrichment signal), located before the point of maximum enrichment score.  (B) As shown in (A) but for the "post-meiotic H3.3-repressed genes" gene set. (C) As shown in (A) but for the " sex chromosome-linked genes " gene set.

      (22) Figure 6. In the KO, the number of green cells is more than red and yellow cells, suggesting the delayed maturation of green (TH2B-positive) cells. It is essential to count the number of each cell and show the quantification.

      The green cells correspond to those expressing TH2B but lacking transition proteins (TP) and protamine 1 (Prm1), indicating that they are at earlier stages than elongating–condensing spermatids. Counting these green cells simply reflects the ratio of elongating/condensing spermatids to earlier-stage cells, which varies depending on the field examined. The key point in this experiment is that in wild-type mice, only red cells (elongating/condensing spermatids) and green cells (earlier stages) are observed. By contrast, in Atad2 KO testes, a significant proportion of yellow cells appears, which are never seen in wild-type tissue. The crucial metric here is the percentage of yellow cells relative to the total number of elongating/condensing spermatids (red cells). In wild-type testes, this value is consistently 0%, whereas in Atad2 KO testes it always ranges between 50% and 100% across all fields containing substantial numbers of elongating/condensing spermatids.

      (23) Figure 8A: Please show the images of sperm (heads) in the KO mice with or without decompaction.

      The requested image is now displayed in Figure S5.

      (24) Figure 8C: In the legend, it says n=5. However, there are more than 5 plots on the graph. Please explain the experiment more in detail.

      The experiment is now better explained in the legend of this Figure.

      Reviewer #2 (Recommendations for the authors): 

      While the study is rigorous and well performed, the following minor points could be addressed to strengthen the manuscript: 

      Figure 1C should indicate each of the different types of cells present in the sections. It would be of interest to show specifically the different post-meiotic germ cells.

      With this type of sample preparation, it is difficult to precisely distinguish the different cell types within the sections. Nevertheless, the staining pattern strongly indicates that most of the intensely stained cells are post-meiotic, situated near the tubule lumens and extending roughly halfway toward the basal membrane.

      In the absence of functional ATAD2, the accumulation of HIRA primarily occurs in round spermatids (Fig. 2B). If technically possible, it would be of great interest to show this by IHC of testis section. 

      Unfortunately, our antibody did not satisfactorily work in IHC.

      The increased of H3.3 signal in Atad2 KO spermatids (Fig. 3) is interpreted because of a reduced turnover. However, alternative explanations (e.g., H3.3 misincorporation or altered chaperone affinity) should not be ruled out. 

      The referee is correct that alternative explanations are possible. However, based on our previous work (Wang et al., 2021; PMID: 34580178), we demonstrated that in the absence of ATAD2, there is reduced turnover of HIRAbound nucleosomes, as well as reduced nucleosome turnover, evidenced by the appearance of nucleosomes in regions that are normally nucleosome-free at active gene TSSs. We have no evidence supporting any other alternative hypothesis.

      In the MS the reduced accessibility at active genes (Fig. 4) is attributed to H3.3 overloading. However, global changes in histone acetylation (e.g., H4K5ac) or other remodelers in KO cells could be also consider.

      In fact, we meant that histone overloading could be responsible for the altered accessibility. This has been clearly demonstrated in case of S. cerevisiae in the absence of Yta7 (S.  cerevisiae’ ATAD2) (PMID: 25406467).

      In relation with the sperm compaction assay (Fig. 8A), the DTT/heparin/Triton protocol may not fully reflect physiological decompaction. This could be validated with alternative methods (e.g., MNase sensitivity). 

      The referee is right, but since this is a subtle effect as it can be judged by normal fertility, we doubt that milder approaches could reveal significant differences between wildtype and Atad2 KO sperms.

      It is surprising that despite the observed alterations in the genome organization of the sperm, the natural fertility of the KO mice is not affected (Fig. 8C). This warrants deeper discussion: Is functional compensation occurring (e.g., by p97/VCP)? Analysis of epididymal sperm maturation or uterine environment could provide insights.

      As detailed in the Discussion section, this work, together with our previous study (Wang et al., 2021; PMID: 34580178), highlights an overlooked level of regulation in histone chaperone activity: the release of chromatinbound factors following their interaction with chromatin. This is an energy-dependent process, driven by ATP and the associated ATPase activity of these factors. Such activity could be mediated by various proteins, such as p97/VCP or DNAJC9–HSP70, as discussed in the manuscript, or by yet unidentified factors. However, most of these mechanisms are likely to occur during the extensive histone-to-histone variant exchanges of meiosis and post-meiotic stages. To the best of our knowledge, epididymal sperm maturation and the uterine environment do not involve substantial histone-to-histone or histone-to-protamine exchanges.

      The authors showed that MSCI genes present an enhancement of repression in the absence of ATAD2 by enhancing H3.3 function. It would be also of interest to analyze the behavior of the Sex body during its silencing (zygotene to pachytene) by looking at different markers (i.e., gamma-H2AX phosphorylation, Ubiquitylation etc). 

      The referee is correct that this is an interesting question. Accordingly, in our future work, we plan to examine the sex body in more detail during its silencing, using a variety of relevant markers, including those suggested by the reviewer. However, we believe that such investigations fall outside the scope of the present study, which focuses on the molecular relationship between ATAD2 and H3.3, rather than on the role of H3.3 in regulating sex body transcription. For a comprehensive analysis of this aspect, studies should primarily focus on the H3.3 mouse models reported by Fontaine and colleagues (PMID: 35766398).

      Fig. 6: Co-staining of TH2B/TP1/PRM1 is convincing but would benefit from quantification (% cells with overlapping signals).

      The green cells correspond to those expressing TH2B but lacking transition proteins (TP) and protamine 1 (Prm1), indicating that they are at earlier stages than elongating–condensing spermatids. Counting these green cells simply reflects the ratio of elongating/condensing spermatids to earlier-stage cells, which varies depending on the field examined. The key point is that in wild-type mice, only red cells (elongating/condensing spermatids) and green cells (earlier stages) are observed. By contrast, in Atad2 KO testes, a significant proportion of yellow cells appears, which are never seen in wild-type tissue. The crucial metric is the percentage of yellow cells relative to the total number of elongating/condensing spermatids (red cells). In wild-type testes, this value is consistently 0%, whereas in Atad2 KO testes it always ranges between 50% and 100% across all fields containing substantial numbers of elongating/condensing spermatids.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      In the manuscript by Fu et al., the authors developed a chemo-immunological method for the reliable detection of Kacac, a novel post-translational modification, and demonstrated that acetoacetate and AACS serve as key regulators of cellular Kacac levels. Furthermore, the authors identified the enzymatic addition of the Kacac mark by acyltransferases GCN5, p300, and PCAF, as well as its removal by deacetylase HDAC3. These findings indicate that AACS utilizes acetoacetate to generate acetoacetyl-CoA in the cytosol, which is subsequently transferred into the nucleus for histone Kacac modification. A comprehensive proteomic analysis has identified 139 Kacac sites on 85 human proteins. Bioinformatics analysis of Kacac substrates and RNA-seq data reveal the broad impacts of Kacac on diverse cellular processes and various pathophysiological conditions. This study provides valuable additional insights into the investigation of Kacac and would serve as a helpful resource for future physiological or pathological research.

      The authors have made efforts to revise this manuscript and address my concerns. The revisions are appropriate and have improved the quality of the manuscript.

      We appreciate the constructive and thoughtful feedbacks, which have been invaluable in enhancing the quality of our manuscript.

      Reviewer #3 (Public review):

      Summary:

      This paper presents a timely and significant contribution to the study of lysine acetoacetylation (Kacac). The authors successfully demonstrate a novel and practical chemoimmunological method using the reducing reagent NaBH4 to transform Kacac into lysine βhydroxybutyrylation (Kbhb).

      Thank you for the positive and insightful comments.

      Strengths:

      This innovative approach enables simultaneous investigation of Kacac and Kbhb, showcasing its potential in advancing our understanding of post-translational modifications and their roles in cellular metabolism and disease.

      We are grateful for the reviewer’s comments, which has contributed to enhancing the quality of our study.

      Weaknesses:

      The experimental evidence presented in the article is insufficient to fully support the authors' conclusions. In the in vitro assays, the proteins used appear to be highly inconsistent with their expected molecular weights, as shown by Coomassie Brilliant Blue staining (Figure S3A). For example, p300, which has a theoretical molecular weight of approximately 270 kDa, appeared at around 37 kDa; GCN5/PCAF, expected to be ~70 kDa, appeared below 20 kDa. Other proteins used in the in vitro experiments also exhibited similarly large discrepancies from their predicted sizes. These inconsistencies severely compromise the reliability of the in vitro findings. Furthermore, the study lacks supporting in vivo data, such as gene knockdown experiments, to validate the proposed conclusions at the cellular level.

      We appreciate the reviewer’s comments. In the biochemical assays, we used the expressed catalytic domains of HATs—rather than the full-length proteins for activity testing. Specifically, the following constructs were expressed and purified: p300 (1287– 1666), GCN5 (499-663), PCAF (493-658), MOF (125-458), MOZ (497-780), MBP-MORF (361-716), Tip60 (221-512), HAT1 (20-341), and HBO1 (full length). This resulted in the observed discrepancies in molecular weight in Figure S3A compared to the expected fulllength weights. 

      Although a recent study (PMID: 37382194) reported the acetoacetyltransferase activities of p300 and GCN5 in cells, we recognize that additional knockdown experiments would be necessary to substantiate their contributions to in vivo Kacac generation and to explore the functional roles of Kacac in an enzyme-specific context. We plan to address these kinds of research issues in our future work.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review)

      The Cx3cr1/EGFP line labels all myeloid cells, which makes it difficult to conclude that all observed behaviors are attributable to microglia rather than infiltrating macrophages. The authors refer to this and include it as a limitation. Nonetheless, complementary confirmation by additional microglia markers would strengthen their claims. 

      We appreciate the reviewer’s insightful comment regarding the cellular identity of the enveloping myeloid cells. As suggested, we performed triple co-immunostaining of SSLOW-infected Cx3cr1/EGFP mice using markers for neurons (NeuN), myeloid cells (IBA1), and resident microglia (TMEM119 or P2Y12). Because formic acid treatment used to deactivate prions abolishes the EGFP signal, we relied on IBA1 staining to identify the myeloid population. Our results confirmed that IBA1⁺ cells exhibiting the envelopment behavior are also TMEM119⁺ and P2Y12⁺, consistent with a resident microglial phenotype. These new data are presented in Figures S3 and S4 and described in the final section of the Results.

      Although the authors elegantly describe dynamic surveillance and envelopment hypothesis, it is unclear what the role of this phenotype is for disease progression, i.e., functional consequences. For example, are the neurons that undergo sustained envelopment more likely to degenerate? 

      We appreciate this important question regarding the functional implications of neuronal envelopment. At present, technical limitations prevent us from continuously tracking the fate of individual enveloped neurons in prion-infected mice. Nevertheless, our recent study demonstrated that P2Y12 knockout increases the prevalence of neuronal envelopment and accelerates disease progression (Makarava et al., 2025, J. Neuroinflammation). These findings suggest that while microglial envelopment may represent an adaptive response to increased neuronal surveillance demands, excessive envelopment, as observed in the absence of P2Y12, appears to be maladaptive. A new paragraph has been added to the Discussion to address this point.

      Moreover, although the increase in mobility is a relevant finding, it would be interesting for the authors to further comment on what the molecular trigger(s) is/are that might promote this increase. These adaptations, which are at least long-lasting, confer apparent mobility in the absence of external stimuli. 

      We thank the reviewer for this thoughtful suggestion. The molecular mechanisms underlying the increased mobility of microglia in prion-infected brains remain to be identified, and we plan to pursue this question in future studies. One possibility we briefly discuss in the revised manuscript is that proinflammatory signaling, mediated by secreted cytokines or interleukins, may drive this phenotype. Supporting this hypothesis, recent work has shown that IFNγ enhances microglial migration in the adult mouse cortex (doi:10.1073/pnas.2302892120). This work has been cited in the revised manuscript.

      The authors performed, as far as I could understand, the experiments in cortical brain regions. There is no clear rationale for this in the manuscript, nor is it clear whether the mobility is specific to a particular brain region. This is particularly important, as microglia reactivity varies greatly depending on the brain region. 

      We appreciate this insightful comment highlighting the importance of regional determinants of microglial reactivity, which indeed aligns with our ongoing research interests. In our previous studies, neuronal envelopment by microglia was observed consistently across all prion-affected brain regions exhibiting neuroinflammation. Assuming that envelopment requires microglial mobility, it is reasonable to speculate that microglia are mobile in all brain regions affected by prions and displaying neuroinflammatory responses. In the current study, we focused exclusively on the cortex because this region was used for quantifying the prevalence of neuronal envelopment as a function of disease progression in our prior work (DOI: 10.1172/JCI181169), which guided the present study design. Our ongoing investigations indicate that the prevalence of envelopment is region-dependent and correlates with microglial reactivity/the degree of neuroinflammation. In prion diseases, the degree of microglial reactivity is dictated by the tropism of specific prion strains to distinct brain regions. Notably, our prior studies have shown that strain-specific sialylation patterns of PrP<sup>Sc</sup> glycans play a key role in determining both regional strain tropism and the extent of neuroinflammatory activation (DOI: 10.3390/ijms21030828, DOI: 10.1172/JCI138677). In response to this comment, we have added a brief rationale for using the cortex in the Results section.

      It would be relevant information to have an analysis of the percentage of cells in normal, sub-clinical, early clinical, and advanced stages that became mobile. Without this information, the speed/distance alone can have different interpretations.

      We thank the reviewer for this valuable suggestion. The percentage of mobile cells across normal, sub-clinical, early clinical, and advanced disease stages is presented in Figure 3b and described in the final paragraph of the section “Enveloping behavior of reactive myeloid cells.”

      Reviewer #2 (Public review)

      The number of individual cells tracked has been provided, but not the number of individual mice. The sex of the mice is not provided. 

      We used N = 3 animals per group throughout the study; this information has now been added to the figure legends. Animals of both sexes were included in random proportions. The sex information is now listed for each experiment in the Animals subsection of the Methods.

      The statistical approach is not clear; was each cell treated as a single observation? 

      Yes, with the exception of the heat map in Figure 2d, all mobility parameters are analyzed and presented at the level of individual cells, with each cell treated as an independent observation. The primary aim of this study is to characterize behavioral patterns of single reactive myeloid cells. Analyzing data at the cell level allows us to capture the full distribution of cell behaviors and to preserve biologically meaningful heterogeneity within and across animals. By contrast, averaging values per animal would largely mask this variability. In the heat map in Figure 2d, data are averaged per animal, specifically to illustrate inter-animal variability within each group and to visualize changes across disease progression.

      The potential for heterogeneity among animals has not been addressed. 

      To address this concern, we now include a new Supplemental Figure (Figure S4)  presenting the data using Superplots, in which individual cells are shown as dots, animal-level average as circles, and group means calculated based on animals as black horizontal lines. These plots demonstrate that cell mobility measures are highly consistent across animals within each group, indicating limited inter-animal heterogeneity.

      Validation of prion accumulation at each clinical stage of the disease is not provided. 

      We now provide validation of PrP<sup>Sc</sup> accumulation across disease stages by Western blot, along with quantitative analysis, in a new Supplemental Figure (Figure S2). This confirms progressive PrP<sup>Sc</sup> accumulation with advancing disease.

      How were the numerous captures of cells handled to derive morphological quantitative values? Based on the videos, there is a lot of movement and shape-shifting.

      The following description has been added to Methods to clarify morphology analysis: For microglial morphology analysis, we quantified morphological parameters (radius, area, perimeter, and shape index) for individual EGFP⁺ cells in each time frame of the time-lapse recordings using the TrackMate 7.13.2 plugin in FIJI. Parameter values for each cell were then averaged across the entire three-hour imaging period to obtain a single mean value per cell.

      While it is recognized that there are limits to what can be measured simultaneously with live imaging, the authors appear to have fixed tissues from each time point too - it would be very interesting to know if the extent or prion accumulation influences the microglial surveillance - i.e., do the enveloped ones have greater pathology. 

      This is very interesting question which is difficult to answer due to technical challenges in monitoring the pathology or faith of individual neuronal cells as a function of their envelopment in live prion-infected animals. Our previous work revealed that both accumulation of total PrP<sup>Sc</sup> in a brain and  accumulation of PrP<sup>Sc</sup> specifically in lysosomal compartments of microglia due to phagocytosis precedes the onset of neuronal envelopment (DOI: 10.1172/JCI181169).  Moreover, the onset of neuronal envelopment occurred after a noticeable decline in neuronal levels of Grin1, a subunit of the NMDA receptor essential for synaptic plasticity. Reactive microglia were observed to envelop Grin1-deficient neurons, suggesting that microglia respond to neuronal dysfunction. However, considering that envelopment is very dynamic and - in most cases - reversible, correlating the degree of envelopment with dysfunction of individual neurons is technically challenging.

      Recommendations for the authors

      Reviewer #1 (Recommendations for the authors): 

      (1) I recommend performing additional immunostaining using microglial markers to address specificity. 

      These new data showing immunostaining for markers of resident microglia TMEM119 and P2Y12 are presented in Figures S6 and S7 and described in the final section of the Results.

      (2) The authors can at least further discuss the functional consequences of their findings in further detail. 

      A new paragraph has been added to the Discussion to address this point.

      (3) Quantify the % of cells that become mobile in the different conditions. 

      The percentage of mobile cells across normal, sub-clinical, early clinical, and advanced disease stages is presented in Figure 3b and described in the final paragraph of the section “Enveloping behavior of reactive myeloid cells.”

      (4) Improve method details on the brain regions used and further expand the statistical section. 

      We have expanded the Statistical Analysis section to indicate whether statistical comparisons and mean values were calculated at the single-cell level or the animal level for each analysis. The specific statistical tests used and the number of animals (N) are now reported in the corresponding figure legends. The sex of animals is provided in Table 1 (Methods). Only the cortical region was examined in this study; this information is stated in the Methods and is now also noted in the figure legends for clarity.

      Reviewer #2 (Recommendations for the authors): 

      (1) More details on members of the PY2 receptor family expressed in microglia would be helpful. The study highlights a previously published prion-induced decline in the expression of P2Y12, a microglial marker that is required for intracellular neuron-microglial contacts, and P2Y6, involved in calcium transients, which is required for hypermotility. How are members of this family of receptors regulated at the gene and/or protein level in microglial and given their responsiveness to nucleotide ligands, are other members implicated in the properties being quantified here? 

      We appreciate the reviewer’s insightful comment. To address this point, we examined the expression of multiple P2Y receptors and ATP-gated P2X channels known to contribute to microglial surveillance, activation, motility, and phagocytosis, alongside the activation markers Tlr2, Cd68, and Trem2. Bulk brain transcript analyses indicated that all examined genes were upregulated in SSLOW-infected mice relative to controls (new Figure S5a). However, because microglial proliferation substantially increases microglial numbers during prion disease progression, bulk tissue measurements do not necessarily reflect per-cell expression levels. Therefore, we normalized gene expression values to the microglia-specific marker Tmem119, whose per-cell expression remains stable across disease stages (Makarava et al., 2025, J. Neuroinflammation). After normalization, Tlr2, Cd68, and Trem2 were increased approximately 10-, 6-, and 4-fold, respectively. In contrast, P2 receptor genes showed more modest changes: P2ry6 increased ~3-fold, P2ry13 ~2-fold, and P2rx7 ~1.3-fold, while P2rx4 remained unchanged (Figure S5a). Within the scope of the present study, we focused on P2Y6 due to (i) its role in regulating calcium transients, (ii) the magnitude of its upregulation relative to other P2 receptors, and (iii) its highly microglia-specific expression in the CNS. We note that currently available commercial P2Y6 antibodies lack sufficient specificity, making reliable assessment of protein-level expression challenging.

      (2) Is P2Y6 expressed in any other cell type that might account for the blunted mobility of the microglia? The authors mention P2Y12 also identifies the GFP cells; however, it would be beneficial to highlight the specificity of the target in the ex vivo treatment of the infected slices.

      In the brain, both P2Y12 and P2Y6 are considered highly specific to resident microglia under physiological and neuroinflammatory conditions. P2Y12 is, in fact, widely used as a canonical marker of homeostatic and resident microglia. While P2Y6 is also expressed in peripheral myeloid cells such as macrophages, our phenotypic characterization indicates that the cells exhibiting neuronal envelopment are TMEM119⁺ and P2Y12⁺, consistent with a resident microglial identity. These data, including new analyses added to the revised manuscript, support that the cells responding to P2Y6 signaling in our ex vivo slice experiments are resident microglia.

      (3) The fluorescent mouse lacks Cx3cr1 - have the authors investigated why there were no apparent consequences, at least in the context of prion infection? Are there functional redundancies that might be harnessed? Does this impact the generalizability of the findings here?

      The role of Cx3cr1 in prion disease has been directly examined in two independent studies (doi: 10.1099/jgv.0.000442; doi: 10.1186/1471-2202-15-44). One study reported no effect of Cx3cr1 deficiency on disease incubation time, whereas the other observed only a minor difference. Importantly, both studies found no detectable alterations in microglial activation patterns, cytokine expression, or PrP<sup>Sc</sup> deposition in Cx3cr1-deficient mice compared to wild-type controls. Our own data (Figure S1) are consistent with these findings: disease course and PrP<sup>Sc</sup> deposition were comparable between Cx3cr1/EGFP and wild-type mice. Moreover, we observed reactive microglial envelopment of neurons in both genotypes. Microglia isolated from SSLOW-infected Cx3cr1/EGFP mice also displayed similarly elevated mobility in vitro, in agreement with our previous observations of high mobility of microglia isolated from SSLOW-infected wild-type mice (Makarava et al., 2025, J. Neuroinflammation). Taken together, these results indicate that Cx3cr1 is not a key determinant of reactive microglial mobility or envelopment behavior in prion disease. Thus, the use of the Cx3cr1/EGFP reporter line does not compromise the generalizability of our conclusions.

      (4) The distinction between high mobility and low mobility microglia is interesting - is there any evidence to suggest that the slow-moving microglia are actually a separate class - do enveloping microglia exhibit both mobility states - can the authors comment on plasticity here? 

      We appreciate this insightful comment, which closely aligns with our ongoing interests. At present, we do not have evidence to support that high- versus low-mobility microglia represent distinct molecular phenotypes. Given that our time-lapse imaging spans only a three-hour window, it remains unclear whether these mobility states reflect stable cell-intrinsic properties or transient phases within a dynamic surveillance process. Notably, we observed that individual cells can transition between more stationary, neuron-associated states and highly mobile states within the same imaging session. In future work, we intend to investigate whether prolonged interactions with neuronal somas or other microenvironmental cues may drive diversification of reactive myeloid cell phenotypes.

      (5) In the discussion, the authors speculate about "collective coordinated decision making" - that seems a stretch unless greater context is provided. The fact that several microglia can be found in contact with an individual neuron and that each microglia can connect with multiple neurons simultaneously is certainly interesting; however, evidence for hive behavior is entirely lacking.

      We agree with the reviewer that our previous wording overstated the interpretation. The statement regarding collective decision-making has been removed.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment:

      This is an important study, supported by solid to convincing data, that suggests a model for diet selection in C. elegans. The significance is that while C. elegans has long been known to be attracted to bacterial volatiles, what specific bacterial volatiles may signify to C. elegans is largely unknown. This study also provides evidence for a possible odorant/GPCR pairing.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Siddiqui et al., investigate the question of how bacterial metabolism contributes to the attraction of C. elegans to specific bacteria. They show that C. elegans prefers three bacterial species when cultured in a leucine-enriched environment. These bacterial species release more isoamyl alcohol, a known C. elegans attractant, when cultured with leucine supplement than without leucine supplement. The study shows correlative evidence that isoamyl alcohol is produced from leucine by the Ehrlich pathway. In addition, they show that SRD-12 (SNIF-1) is likely a receptor for isoamyl alcohol because a null mutant of this receptor exhibits lower chemotaxis to isoamyl alcohol and lower preference for leucine-enriched bacteria.

      Strengths:

      (1) This study takes a creative approach to examine the question of what specific volatile chemicals released by bacteria may signify to C. elegans by examining both bacterial metabolism and C. elegans preference behavior. Although C. elegans has long been known to be attracted to bacterial metabolites, this study may be one of the first to examine the role of a specific bacterial metabolic pathway in mediating attraction.

      (2)  A strength of the paper is the identification of SRD-12 (SNIF-1) as a likely receptor for isoamyl alcohol. The ligands for very few olfactory receptors have been identified in C. elegans and so this is a significant addition to the field. The srd-12 (snif-1) null mutant strain will likely be a useful reagent for many labs examining olfactory and foraging behaviors.

      Weaknesses:

      (1) The authors write that the leucine metabolism via the Ehrlich pathway is required for the production of isoamyl alcohol by three bacteria (CEent1, JUb66, BIGb0170), but their evidence for this is correlation and not causation. They write that the gene ilvE is a bacterial homolog of the first gene in the yeast Ehrlich pathway (it would be good to include a citation for this) and that the gene is present in these three bacterial strains. In addition, they show that this gene, ilvE, is upregulated in CEent1 bacteria upon exposure to leucine. To show causation, they need to knockout ilvE from one of these strains, show that the bacteria does not have increased isoamyl alcohol production when cultured on leucine, and that the bacteria is no longer attractive to C. elegans.

      Thank you for the comment. We have added the appropriate citation [1,2]. We agree that worms’ diet preference for the preferred strains upon ilvE knockout will further strengthen the claim for IAA being used as a proxy for leucine-enriched diet. Currently, protocols and tools for genetic manipulations for CeMbio strains are not available, making this experiment not feasible at this time.  

      (2) The authors examine three bacterial strains that C. elegans showed increased preference when grown with leucine supplementation vs. without leucine supplementation. However, there also appears to be a strong preference for another strain, JUb0393, when grown on plus leucine (Figure 1B). It would be good to include statistics and criteria for selecting the three strains.

      Thanks for your comment. We agree that for Pantoea nemavictus, JUb393, worms seem to prefer the leucine supplemented (+ LEU) bacteria over unsupplemented (-LEU). However, when given a choice between the individual CeMbio bacteria and E. coli OP50, worms showed preference for only CEent1, JUb66, and BIGb0170 (Figure 1F). Consequently, CEent1, JUb66, and BIGb0170 were selected for further analyses. We have included statistics for Figure 1B-C and Figure S1A-G with details mentioned in the figure legend. 

      (3) Although the behavioral evidence that srd-12 (snif-1) gene encodes a receptor for isoamyl alcohol is compelling, it does not meet the standard for showing that it is an olfactory receptor in C. elegans. To show it is indeed a likely receptor one or more of the following should be done:

      (a) Calcium imaging of AWC neurons in response to isoamyl alcohol in the receptor mutant with the expectation that the response would be reduced or abolished in the mutant compared to wildtype.

      (b)"A receptor swap" experiment where the SRD-12 (SNIF-1) receptor is expressed in AWB repulsive neuron in SRD-12 (SNIF-1) receptor mutant background with the expectation that with receptor swap C. elegans will now be repulsed from isoamyl alcohol in chemotaxis assays (experiment from Sengupta et al., 1996 odr-10 paper).

      Thanks for all your comments and suggestions. While the lab currently does not have the necessary expertise to conduct calcium imaging of neurons, we have performed additional experiments to confirm the requirements of AWC neurons for SNIF-1 function. We generated transgenic worms with extrachromosomal array expressing snif-1 under (a) AWC-specific promoter, odr-1, and (b) AWB-specific promoter, str-1. As shown in new panel 6H in the revised manuscript and Author response image 1, we found that overexpression of snif-1 in AWC neurons completely rescues the chemotaxis defect of snif-1 mutant (referred at VSL2401), whereas upon the “receptor swap" in AWB neurons IAA is sensed as a repellent.  

      Author response image 1.

      (A) Chemotaxis index (CI) of WT, VSL2401, VSL2401 [AWCp::snif-1] and VSL2401 [AWBp::snif-1] worms to IAA at 1:1000 dilution. Significant differences are indicated as **** P ≤ 0.0001 determined by one-way ANOVA followed by post hoc Dunnett’s multiple comparison test. Error bars indicate SEM (n≥15).

      (4) The authors conclude that C. elegans cannot detect leucine in chemotaxis assays. It is important to add the method for how leucine chemotaxis assay was done in order to interpret these results. Because leucine is not volatile if leucine is put on the plates immediately before the worms are added (as in a traditional odor chemotaxis assay), there is no leucine gradient for the worm to detect. It would be good to put leucine on the plate several hours before worms are introduced so worms have the possibility to be able to detect the gradient of leucine (for example, see Wakabayashi et al., 2009).

      Previously, the chemotaxis assays with leucine were performed like traditional odor chemotaxis assays. We also performed chemotaxis assay as detailed in Shingai et al 2005[3]. Leucine was spotted on the assay plates 5 hours prior to the introduction of worms on the plates. As shown in new panel S1H in the revised manuscript, wild-type worms do not show response to leucine in the modified chemotaxis assay.

      We have included the experimental details for leucine chemotaxis assays in the revised manuscript.  

      (5) The bacterial preference assay entitled "odor-only assay" is a misleading name. In the assay, C. elegans is exposed to both volatile chemicals (odors) and non-volatile chemicals because the bacteria are grown on the assay plate for 12 hours before the worms are introduced to the assay plate. In that time, the bacteria is likely releasing non-volatile metabolites into the plate which may affect the worm's preference. A true odor-only assay would have the bacteria on the lid and the worms on the plate.

      The ‘odor-only’ diet preference assay does not allow for non-volatile chemicals to reach worms. We achieved this by using tripartite dishes where the compartments containing worms and bacterial odors are separated by polystyrene barriers. At the time of the assay, worms were spotted in a separate compartment from that of bacteria (as shown in schematic 1A). The soluble metabolites released by the bacteria during their growth will accumulate in the agar within the bacterial compartment alone such that worms only encounter the volatile metabolites produced by bacteria wafting past the polystyrene barrier.

      (6) The findings of the study should be discussed more in the context of prior literature. For example, AWC neurons have been previously shown to be involved in bacterial preference (Harris et al., 2014; Worthy et al., 2018). In addition, CeMbio bacterial strains (the strains examined in this study) have been previously shown to release isoamyl alcohol (Chai et al. 2024).

      Thanks for the suggestion. We have modified the Discussion section to discuss the study in the light of relevant prior literature.  

      Reviewer #2 (Public review):

      Summary:

      Siddiqui et al. show that C. elegans prefers certain bacterial strains that have been supplemented with the essential amino acid (EEA) leucine. They convincingly show that some leucine enriched bacteria stimulate the production of isoamyl alcohol (IAA). IAA is an attractive odorant that is sensed by the AWC. The authors an identify a receptor, SRD-12 (SNIF-1), that is expressed in the AWC chemosensory neurons and is required for chemotaxis to IAA. The authors propose that IAA is a predominant olfactory cue that determines diet preference in C. elegans. Since leucine is an EAA, the authors propose that worm IAA sensing allows the animal provides a proxy mechanism to identify EAA rich diets.

      Strengths:

      The authors propose IAA as a predominant olfactory cue that determines diet preference in C. elegans providing molecular mechanism underlying diet selection. They show that wild isolates of C. elegans have a strong chemotactic response to IAA indicating that IAA is an ecologically relevant odor for the worm. The paper is well written, and the presented data are convincing and well organized. This is an interesting paper that connects chemotactic response with bacterially produced odors and thus provides an understanding of how animals adapt their foraging behavior through the perception of molecules that may indicate the nutritional value.

      Weaknesses:

      Major:

      While I do like the way the authors frame C. elegans IAA sensing as mechanisms to identify leucine (EAA) rich diets it is not fully clear whether bacterial IAA production is a proxy for bacterial leucine levels.

      (1) Can the authors measure leucine (or other EAA) content of the different CeMbio strains? This would substantiate the premise in the way they frame this in the introduction. While the authors convincingly show that leucine supplementation induces IAA production in some strains, it is not clear if there are lower leucine levels in the different in non-preferred strains.

      Thanks for your suggestion. Estimating leucine levels in various bacteria will provide useful information, and we hope to do so in future studies.

      (2) It is not clear whether the non-preferred bacteria in Figure 1A and 1B have the ability to produce IAA. To substantiate the claim that C. elegans prefers CEent1, JUb66, and BIGb0170 due to their ability to generate IAA from leucine, it would measure IAA levels in non-preferred bacteria (+ and - leucine supplementation). If the authors have these data it would be good to include this.

      Thanks for the suggestion. We have included the table indicating the presence or absence of IAA production by all the bacteria under + LEU and – LEU conditions (Table S2). Some of the nonpreferred bacteria indeed produce isoamyl alcohol. However, the abundance of IAA in these strains is significantly less than in the preferred bacteria.  

      Using the available genomic sequence data, we found that all CeMbio strains encode IlvE-like transaminase enzymes[4]. This suggests that presumably all the bacteria have the metabolic capacity to make alpha-ketoisocaproate (an intermediate in IAA biosynthetic pathway) from leucine. However, the regulation of metabolic flux is likely to be quite complex in various bacteria.  

      (3) The authors would strengthen their claim if they could show that deletion or silencing ilvE enzyme reduces IAA levels and eliminates the increased preference upon leucine supplementation.

      We agree that testing worms’ diet preference for the preferred strains upon ilvE knockout will further strengthen the claim for IAA being crucial for finding leucine-enriched diet. Currently the lab does not have the necessary expertise and standardize protocols to do genetic manipulations for the CeMbio strains.

      (4) While the three preferred bacteria possess the ilvE gene, it is not clear whether this enzyme is present in the other non-preferred bacterial strains. As far as I know, the CeMbio strains have been sequenced so it should be easy to determine if the non-preferred bacteria possess the capacity to make IAA. Does the expression of ilvE in e.g. E. coli increase its preference index or are the other genes in the biosynthesis pathway missing?

      Thanks for the suggestion. Using the available genomic sequence data, we find that all the bacteria in the CeMbio collection possess IlvE-like transaminase necessary for synthesis of alphaketoisocaproate, key metabolite in leucine turn over as well as precursor for IAA [4]. E. coli has an IlvE encoding gene in its genome [2]. However, we do not find IAA in the headspace of E. coli either with or without leucine supplementation. This indicates either (i) E. coli lacks enzymes for subsequent steps in IAA biosynthesis or (ii) leucine provided under the experimental regime is not sufficient to shift the metabolic flux to IAA production.  

      Previous studies have suggested that in yeast, the final two steps leading to IAA production are catalyzed by decarboxylase and dehydrogenase enzymes1. The genomic and metabolic flux data available for CeMbio do not describe specific enzymes leading up to IAA synthesis [4].  

      (5) It is strongly implied that leucine-rich diets are beneficial to the worm. Do the authors have data to show the effect on leucine supplementation on C. elegans healthspan, life-span or broodsize?

      Edwards et al. 2015 reported a 15% increase in the lifespan of worms upon 1 mM leucine supplementation [5]. Wang et al 2018 also showed lifespan extension upon 1 mM and 10 mM leucine supplementation. They also reported that while leucine supplementation did not have any effect on brood size, it did make worms more resistant to heat, paraquat, and UV-stress [6]. These studies have been included in the discussion section.

      Other comments:

      Page 6. Figure 2c. While the authors' conclusions are correct based on AWC expts. it would be good at this stage to include the possibility that odors that enriched in the absence of leucine may be aversive.

      Thanks for the comment. We have tested the chemotaxis response of the worms for most of the odors produced by CeMbio strains without leucine supplementation. We did not find any odor that is aversive to worms. However, we cannot completely rule out the possibility that a low abundance of aversive odor in the headspace of the bacteria was missed.

      Interestingly, we did identify 2-nonanone, a known repellent, in the headspace of the preferred bacteria upon leucine supplementation. However, the abundance of 2-nonanone in headspace of bacteria is relatively low (less than 1% for CEent1, and JUb66, and ~10% for BIGb0170). This suggests that the relative abundance of odors in an odor bouquet may be a relevant factor in determining worms’ reference.  

      Page 6. IAA increases 1.2-4 folds upon leucine supplementation. If the authors perform a chemotaxis assay with just IAA with 1-2-4 fold differences do you get the shift in preference index as seen with the bacteria? i.e. is the difference in IAA concentration sufficient to explain the shift in bacterial PI upon leucine supplementation? Other attractants such as Acetoin and isobutanol go up in -Leu conditions.

      Thanks for the suggestion. As shown in Figure S2H and S2I, when given a choice between a concentration of IAA (1:1000 dilution) attractive to worms and a 4-fold higher amount of IAA, worms chose the latter. This result suggests that worms can distinguish between relatively small difference in concentrations of IAA.

      We agree that the relative abundance of Acetoin and Isobutanol is high in -LEU conditions. The presence of other attractants in - LEU conditions should skew the preference of worms for – LEU bacteria. However, we found that worms prefer + LEU bacteria (Figure 1B), suggesting that the abundance of IAA mainly influences the diet preference of the worms.  

      Page 14-15. The authors identify a putative IAA receptor based on expression studies. I compliment the authors for isolating two CRISPR deletion alleles. They show that the srd-12 (snif-1) mutants have obvious defects in IAA chemotaxis. Very few ligand-odorant receptors combinations have been identified so this is an important discovery. CenGen data indicate that srd-12 (snif-1) is expressed in a limited set of neurons. Did the authors generate a reporter to show the expression of srd-12 (snif-1)? This is a simple experiment that would add to the characterization of the SRD-12 (SNIF-1) receptor. Rescue experiments would be nice even though the authors have independent alleles. To truly claim that SRD-12 (SNIF-1) is the ligand for IAA and activates the AWC neurons would require GCamp experiments in the AWC neuron or heterologous expression system. I understand that GCamp imaging might not be part of the regular arsenal of the lab but it would be a great addition (even in collaboration with one of the many labs that do this regularly). Comparing AWC activity using GCaMP in response IAA-producing bacteria with high leucine levels in both wild-type and SRD-12 (SNIF-1) deficient backgrounds, would further support their narrative. I leave that to the authors.

      Thanks for your comments and suggestions. To address this comment, we rescued snif-1 mutant (referred as VSL2401) with extrachromosomal array expressing snif-1 under AWC-specific promoter as well as its native promoter. As shown in Figure 6H and Author response image 2, we find that both transgenic lines show a complete rescue of chemotaxis response to isoamyl alcohol. To find where snif-1 is expressed, we generated a transgenic line of worms expressing GFP under snif-1 promoter, and mCherry under odr-1 promoter (to mark AWC neurons). As shown in Figure 6I, we found that snif-1 is expressed faintly in many neurons, with strong expression in one of the two AWC neurons marked by odr-1::mCherry. This result suggests that SNIF-1 is expressed in AWC neuron.

      We hope to perform GCaMP assay and further characterization of SNIF-1 in the future.

      Author response image 2.

      Chemotaxis index (CI) of WT, VSL2401, VSL2401 [AWCp:: snif-1] and VSL2401 [snif-1p::snif-1] worms to IAA at 1:1000 dilution. Significant differences are indicated as **** P ≤ 0.0001 determined by one-way ANOVA followed by post hoc Dunnett’s multiple comparison test. Error bars indicate SEM (n≥15).

      Minor:

      Page 4 "These results suggested that worms can forage for diets enriched in specific EAA, leucine...." More precise at this stage would be to state " These results indicated that worms can forage for diets supplemented with specific EAA...".

      We have changed the statement in the revised manuscript.

      Page 5."these findings suggested that worms not only rely on odors to choose between two bacteria but also to find leucine enriched bacteria" This statement is not clear to me and doesn't follow the data in Fig. S2. Preferred diets in odorant assays are the IAA producing strains.

      Thanks for your comment. We have revised the manuscript to make it clear. “Altogether, these findings suggested that worms rely on odors to distinguish different bacteria and find leucineenriched bacteria”. This statement concludes all the data shown in Figure 1 and Figure S1.  

      Page 5. Figure S2A provides nice and useful data that can be part of the main Figure 1.

      Thanks for the comment. We have incorporated the data from Figure S2A to main Figure 1.

      Reviewer #3 (Public review):

      Summary:

      The authors first tested whether EAA supplementation increases olfactory preference for bacterial food for a variety of bacterial strains. Of the EAAs, they found only leucine supplementation increased olfactory preference (within a bacterial strain), and only for 3 of the bacterial strains tested. Leucine itself was not found to be intrinsically attractive.

      They determined that leucine supplementation increases isoamyl alcohol (IAA) production in the 3 preferred bacterial strains. They identify the biochemical pathway that catabolizes leucine to IAA, showing that a required enzyme for this pathway is upregulated upon supplementation.

      Consistent with earlier studies, they find that AWC olfactory neuron is primarily responsible for increased preference for IAA-producing bacteria.

      Testing volatile compounds produced by bacteria and identified by GC/MS, and identified several as attractive, most of them require AWC for the full effect. Adaptation assays were used to show that odorant levels produced by bacterial lawns were sufficient to induce olfactory adaptation, and adaptation to IAA reduced chemotaxis to leucine-supplemented lawns. They then showed that IAA attractiveness is conserved across wild strains, while other compounds are more variable, suggesting IAA is a principal foraging cue.

      Finally, using the CeNGEN database, they developed a list of candidate IAA receptors. Using behavioral tests, they show that mutation of srd-12 (snif-1) greatly impairs IAA chemotaxis without affecting locomotion or attraction to another AWC-sensed odor, PEA.

      Comments

      This study will be of great interest in the field of C. elegans behavior, chemical senses and chemical ecology, and understanding of the sensory biology of foraging.

      Strengths:

      The identification of a receptor for IAA is an excellent finding. The combination of microbial metabolic chemistry and the use of natural bacteria and nematode strains makes an extremely compelling case for the ecological and adaptive relevance of the findings.

      Weaknesses:

      AWC receives synaptic input from other chemosensory neurons, and thus could potentially mediate navigation behaviors to compounds detected in whole or in part by those neurons. Language concluding detection by AWC should be moderated (e.g. p9 "worms sense an extensive repertoire...predominantly using AWC") unless it has been demonstrated.

      Thanks for your comment. We have modified the manuscript to incorporate the suggestion.

      srd-12 (snif-1) is not exclusively expressed in AWC. Normally, cell-specific rescue or knockdown would be used to demonstrate function in a specific cell. The authors should provide such a demonstration or explain why they are confident srd-12 (snif-1) acts in AWC.

      Thanks for the comment. We have performed AWC-specific rescue of snif-1 in mutant worms. As shown in Figure 6H, we found that AWC neurons specific rescue completely recovered the chemotaxis defect of the snif-1 mutant (referred as VSL2401) for IAA. In addition, snif-1 is expressed in one of the AWC neurons.

      A comparison of AWC's physiological responses between WT and srd-12 (snif-1), preferably in an unc13 background, would be nice. Even further, the expression of srd-12 (snif-1) in a different neuron type and showing that it confers responsiveness to IAA (in this case, inhibition) would be very convincing.

      Thanks for the suggestion. We have performed a receptor swap experiment, where snif-1 is misexpressed in AWB neurons. We find that these worms show slight but significant repulsion to IAA compared to WT and snif-1 mutant worms (Author response image 1).

      Recommendations for the authors:

      Reviewing Editor:

      Please consider all of the reviewer comments. In particular, as noted in the individual reviews, the strength of the evidence would be bolstered by additional experiments to demonstrate that the iLvE enzyme affects IAA levels in the preferred bacteria. The reviewers note that the authors haven't shown that IAA production is a reflection of leucine content. Are the non-preferred bacteria low on leucine or lack iLvE or IAA synthesis pathways? Further, more direct evidence that SRD-12 (SNIF-1) is in fact the primary IAA receptor would further strengthen the study. The authors should also be aware that geographic distance for wild isolate C. elegans may not directly correlate with phylogenetic distance. This should be assessed/discussed for the strains used.

      Thanks for the suggestions. Some of these have been addressed in response to reviewers. Thanks for your comments about possible disconnect between geographical and phylogenetic distances amongst natural isolates used here.

      By analyzing the phylogenetic tree generated using neighbor-joining algorithm available at CaeNDR database, we found that QX1211 and JU3226 are phylogenetically close, but the remaining isolates fall under different clades separated by long phylogenetic distances [7,8].  

      Reviewer #1 (Recommendations for the authors):

      (1) In the first sentence of the third paragraph of the introduction, C. elegans are described as "soildwelling." Although C. elegans has been described as soil-dwelling in the past, current research indicates they are most often found on rotten fruit, compost heaps and other bacterial-rich environments, not soil. "All Caenorhabditis species are colonizers of nutrient- and bacteria-rich substrates and none of them is a true soil nematode." from Kiontke, K. and Sudhaus, W. Ecology of Caenorhabditis species (WormBook).

      Your specific comment about C. elegans’ habitat is well received. However, in that sentence we are referring to the chemosensory system of soil-dwelling animals in general, and not particularly C. elegans.

      (2) Figure 3K, the model would be clearer if leucine-rich diet -> volatile chemicals ->AWC (instead of leucine-rich diet -> AWC <- volatile chemicals). The leucine-rich diet results in the production of volatile chemicals which are detected by AWC.

      We have modified the figure to make it clearer.

      (3) Figure 4 - it would help to include a table summarizing the volatile chemicals that each bacteria releases. Then the reader could more easily evaluate whether the adaptation to each specific odor is consistent with the change in preference for the specific bacteria based on what it releases in its headspace. In addition, Figure 4 would help to clarify whether bacteria in these experiments were cultured with or without leucine supplementation.

      Table S2 summarizes the odors released by all the bacteria under + LEU and – LEU conditions.

      In Figure 4, adaptation was performed by odors of bacteria when cultured under leucineunsupplemented conditions.

      Reviewer #2 (Recommendations for the authors):

      Page 9. Previous studies e.g. Bargmann Hartwieg and Horvitz have shown IAA is sensed by the AWC. Would be good to cite appropriately.

      Thanks for the comment. The reference has been cited at p9 and p16.

      References:

      (1) Yuan, J., Mishra, P., and Ching, C.B. (2017). Engineering the leucine biosynthetic pathway for isoamyl alcohol overproduction in Saccharomyces cerevisiae. Journal of Industrial Microbiology and Biotechnology 44, 107-117. 10.1007/s10295-016-1855-2 %J Journal of Industrial Microbiology and Biotechnology.

      (2) Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y., and Ishiguro-Watanabe, M. (2025). KEGG: biological systems database as a model of the real world. Nucleic Acids Res 53, D672-d677. 10.1093/nar/gkae909.

      (3) Shingai, R., Wakabayashi, T., Sakata, K., and Matsuura, T. (2005). Chemotaxis of Caenorhabditis elegans during simultaneous presentation of two water-soluble attractants, llysine and chloride ions. Comparative biochemistry and physiology. Part A, Molecular & integrative physiology 142, 308-317. 10.1016/j.cbpa.2005.07.010.

      (4) Dirksen, P., Assié, A., Zimmermann, J., Zhang, F., Tietje, A.M., Marsh, S.A., Félix, M.A., Shapira, M., Kaleta, C., Schulenburg, H., and Samuel, B.S. (2020). CeMbio - The Caenorhabditis elegans Microbiome Resource. G3 (Bethesda, Md.) 10, 3025-3039. 10.1534/g3.120.401309.

      (5) Edwards, C., Canfield, J., Copes, N., Brito, A., Rehan, M., Lipps, D., Brunquell, J., Westerheide, S.D., and Bradshaw, P.C. (2015). Mechanisms of amino acid-mediated lifespan extension in Caenorhabditis elegans. BMC genetics 16, 8. 10.1186/s12863-015-0167-2.

      (6) Wang, H., Wang, J., Zhang, Z.J.J.o.F., and Research, N. (2018). Leucine Exerts Lifespan Extension and Improvement in Three Types of Stress Resistance (Thermotolerance, AntiOxidation and Anti-UV Irradiation) in C. elegans. 6, 665-673.

      (7) Crombie, T.A., McKeown, R., Moya, N.D., Evans, Kathryn S., Widmayer, Samuel J., LaGrassa, V., Roman, N., Tursunova, O., Zhang, G., Gibson, Sophia B., et al. (2023). CaeNDR, the Caenorhabditis Natural Diversity Resource. Nucleic Acids Research 52, D850-D858. 10.1093/nar/gkad887 %J Nucleic Acids Research.

      (8) Cook, D.E., Zdraljevic, S., Roberts, J.P., and Andersen, E.C. (2017). CeNDR, the Caenorhabditis elegans natural diversity resource. Nucleic Acids Res 45, D650-d657. 10.1093/nar/gkw893.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews: 

      Reviewer #1 (Public review): 

      Summary: 

      This work by Al-Jezani et al. focused on characterizing clonally derived MSC populations from the synovium of normal and osteoarthritis (OA) patients. This included characterizing the cell surface marker expression in situ (at time of isolation), as well as after in vitro expansion. The group also tried to correlate marker expression with trilineage differential potential. They also tested the ability of the different subpopulations for their efficacy in repairing cartilage in a rat model of OA. The main finding of the study is that CD47hi MSCs may have a greater capacity to repair cartilage than CD47lo MSCs, suggesting that CD47 may be a novel marker of human MSCs that have enhanced chondrogenic potential. 

      Strengths: 

      Studies on cell characterization of the different clonal populations isolated indicate that the MSC are heterogenous and traditional cell surface markers for MSCs do not accurately predict the differentiation potential of MSCs. While this has been previously established in the field of MSC therapy, the authors did attempt to characterize clones derived from single cells, as well as evaluate the marker profile at the time of isolation. While the outcome of heterogeneity is not surprising, the methods used to isolate and characterize the cells were well developed. The interesting finding of the study is the identification of CD47 as a potential MSC marker that could be related to chondrogenic potential. The authors suggest that MSCs with high CD47 repaired cartilage more effectively than MSC with low CD47 in a rat OA model. 

      Weaknesses: 

      While the identification of CD47 as a novel MSC marker could be important to the field of cell therapy and cartilage regeneration, there was a lack of robust data to support the correlation of CD47 expression to chondrogenesis. The authors indicated that the proteomics suggested that the MSC subtype expressed significantly more CD47 than the non-MSC subtype. However, it was difficult to appreciate where this was shown. It would be helpful to clearly identify where in the figure this is shown, especially since it is the key result of the study. The authors were able to isolate CD47hi and CD47 low cells. While this is exciting, it was unclear how many cells could be isolated and whether they needed to be expanded before being used in vivo. Additional details for the CD47 studies would have strengthened the paper. Furthermore, the CD47hi cells were not thoroughly characterized in vitro, particularly for in vitro chondrogenesis. More importantly, the in vivo study where the CD47hi and CD47lo MSCs were injected into a rat model of OA lacked experimental details regarding how many cells were injected and how they were labeled. No representative histology was presented and there did not seem to be a statistically significant difference between the OARSI score of the saline injected and MSC injected groups. The repair tissue was stained for Sox9 expression, which is an important marker of chondrogenesis but does not show production of cartilage. Expression of Collagen Type II would be needed to more robustly claim that CD47 is a marker of MSCs with enhanced repair potential. 

      Reviewer #2 (Public review): 

      Summary: 

      This is a compelling study that systematically characterized and identified clonal MSC populations derived from normal and osteoarthritis human synovium. There is immense growth in the focus on synovial-derived progenitors in the context of both disease mechanisms and potential treatment approaches, and the authors sought to understand the regenerative potential of synovial-derived MSCs. 

      Strengths: 

      This study has multiple strengths. MSC cultures were established from an impressive number of human subjects, and rigorous cell surface protein analyses were conducted, at both pre-culture and post-culture timepoints. In vivo experiments using a rat DMM model showed beneficial therapeutic effects of MSCs vs non-MSCs, with compelling data demonstrating that only "real" MSC clones incorporate into cartilage repair tissue and express Prg4. Proteomics analysis was performed to characterize non-MSC vs MSC cultures, and high CD47 expression was identified as a marker for MSC. Injection of CD47-Hi vs CD47-Low cells in the same rat DMM model also demonstrated beneficial effects, albeit only based on histology. A major strength of these studies is the direct translational opportunity for novel MSC-based therapeutic interventions, with high potential for a "personalized medicine" approach. 

      Weaknesses: 

      Weaknesses of this study include the rather cursory assessment of the OA phenotype in the rat model, confined entirely to histology (i.e. no microCT, no pain/behavioral assessments, no molecular readouts). It is somewhat unclear how the authors converged on CD47 vs the other factors identified in the proteomics screen, and additional information is needed to understand whether true MSCs only engraft in articular cartilage or also in ectopic cartilage (in the context of osteophyte/chondrophyte formation). Some additional discussion and potential follow-up analyses focused on other cell surface markers recently described to identify synovial progenitors is also warranted. A conceptual weakness is the lack of discussion or consideration of the multiple recent studies demonstrating that DPP4+ PI16+ CD34+ stromal cells (i.e. the "universal fibroblasts") act as progenitors in all mesenchymal tissues, and their involvement in the joint is actively being investigated. Thus, it seems important to understand how the MSCs of the present study are related to these DPP4+ progenitors. Despite these areas for improvement, this is a strong paper with a high degree of rigor, and the results are compelling, timely, and important. 

      Overall, the authors achieved their aims, and the results support not just the therapeutic value of clonally-isolated synovial MSCs but also the immense heterogeneity in stromal cell populations (containing true MSCs and non-MSCs) that must be investigated further. Of note, the authors employed the ISCT criteria to characterize MSCs, with mixed results in pre-culture and post-culture assessments. This work is likely to have a longterm impact on methodologies used to culture and study MSCs, in addition to advancing the field's knowledge about how synovial-derived progenitors contribute to cartilage repair in vivo.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors): 

      In all figures, it would be beneficial to report the sample number used for the data reported. It is difficult to appreciate the statistical analysis without that information.

      Understood, the sample number and replicates have been added to each figure legend.

      Please check that Table S7 is part of the manuscript. It could not be found.

      It was added as an additional excel file since it was too large to fit in the word document.

      Lines 377-379 (Figure 2E): the authors write that rats receiving MSCs had a significantly lower OARSI and Krenn score vs. rats injected with non-MSCs. However, none of the bars indicating statistical significance run between these two groups. Please verify the text and figure.

      This has been corrected

      The details surrounding the labeling of the cells with tdTomato were not presented in the methods. 

      This has been added to the methods

      The fluorescent antibodies used should be listed and more details provided in the methods rather than a general statement that fluorescent antibodies were used.

      Our apologies, the clones and companies have been added.

      Additional information on the CD47 experiments (# cells, # animals) would have strengthened the study.

      This has been added to the methods and figure legend.

      Reviewer #2 (Recommendations for the authors): 

      My comments span minor corrections, requests for additional analyses, some suggestions for additional experiments, and requests for additional discussion of recent important studies. 

      Introduction: 

      The introduction is thorough and well-written. I recommend a brief discussion about the emerging evidence demonstrating that DPP4+ PI16+ CD34+ synovial cells, i.e. the "universal fibroblasts", act as stromal progenitors in development, homeostasis, and disease. Relevant osteoarthritis-related papers encompass human and mouse studies (PMIDs: 39375009, 38266107, 38477740, 36175067, 36414376).

      This has been added.

      Relatedly, as DPP4 is CD26 and therefore useful as a cell-surface antigen for flow cytometry, sorting, etc, it would be interesting to understand the relationship and similarities between the CD47-High cells identified in this study and the DPP4/PI16+ cells previously described. Do they overlap in phenotype/identity?

      We have added a new flow cytometry figure for address this question. 

      Results: 

      Note type-o on Line 311: "preformed" instead of "performed". Line 313 "prolife" instead of "profile"

      Thank you for catching these.

      The identified convergence of the cell surface marker profile of all normal and OA clones in culture is a highly intriguing result. Do the authors have stored aliquots of these cells to demonstrate whether this would also occur in soft substrate, i.e. low stiffness culture conditions? This could be done with standard dishes coated with bulk collagen or with commercially available low-stiffness dishes (1 kPa). This is relevant to multiple studies demonstrating the induction of a myofibroblast-like phenotype by stromal cells cultured on high-stiffness plastic or glass. This is also the experiment where assessment of DPP4/CD26 could be added, if possible.

      While we agree it would be interesting to determine the mechanism by which the cells phenotypes converge, we would argue that it is outside of the scope of the current manuscript. We have instead added a sentence to the discussion. 

      Line 353 regarding the use of CD68 as a negative gate: can the authors pleasecomment on why they employed CD68 here and not CD45? While monocytes/macs/myeloid cells are the most abundant immune cells in synovium, CD45 would more comprehensively exclude all immune cells. 

      That is a fair point, and we really don’t have any reason to have picked CD68 over CD45. In our opinion either would be a fair negative marker to use based on the literature. 

      Fig 2, minor suggestion: consider adding "MSC vs non-MSC" on the experimental schematic to more comprehensively summarize the experiment. 

      This has been modified 

      Fig 2E should show all individual datapoints, not just bar graphs. 

      This has been modified

      Fig 2: Given the significant reduction in Krenn score in DMM-MSC injected knees compared to DMM-saline knees, Fig 2 should also show representative images of the synovial phenotype to demonstrate which aspects of synovial pathology were mitigated. Was the effect related to lining hyperplasia, subsynovial infiltrate, fibrosis, etc? Similarly, can the authors narrate which aspects of the OARSI score drove the treatment effect (proteoglycans vs structure vs osteophytes, etc). 

      We have added a new sup figure breaking down the Krenn score as well as higher magnification images of representative synovium.

      Fig 2: In the absence of microCT imaging, can the authors quantify subchondral bone morphometrics using multiple histological sections? The tibial subchondral bone in Fig 2D appears protected from sclerosis/thickening.

      Unfortunately, this is beyond what are able to add to the manuscript. 

      The Fig 3 results are highly compelling and interesting. Congratulations.

      Thank you very much.

      Fig 4A: the cell highlighted in the high-mag zoom box in Fig 4A appears to be localized within the joint capsule or patellar tendon (it is unclear which anatomic region this image represents). The highly aligned nature of the tissue and cells along a fibrillar geometry indicates that this is not synovium. The interface between synovium and the tissue in question can be clearly observed in this image. Please choose an image more representative of synovium.

      We completely agree with the reviewers assessment. However, it is the synovium that overlays this tissue (Fig 4A arrow). We are simply showing that there were very few MSCs that took up residence in the synovium or the adjacent tissues. 

      Fig 4C and F: please show individual data points.

      This has been added

      Fig 5D: I see DPP4 and ITGA5 were also hits in the proteomics analysis, which is intriguing. Besides my comments/suggestions regarding DPP4 above, please note this recent paper identifying a ITGA5+ synovial fibroblast subset that orchestrates pathological crosstalk with lymphocytes in RA, PMID: 39486872

      Thank you for the information. We have added the reference in the results section. 

      Fig 5B-D: How did the authors converge on CD47 as the target for follow-up study? It does not appear to be a differentially-expressed protein based on the Volcano plot in Fig 5B, and it's unclear why it is a more important factor than any of the other proteins shown in the network diagram in Fig 5D, e.g. CTSL, ITGA5, DPP4. Can the authors add a quantitative plot supporting their statement "the MSC sub-type expressed significantly more CD47 than the non-MSCs" on Line 458? 

      We have re-written this line. It was incorrect to discuss amount of CD47. That was shown later with the flow analysis.  

      Fig 6D: Please show individual data points and also representative histology images to demonstrate the nature of the phenotypic effect.

      This has been added. 

      Fig 6E-F: In what anatomic region are these images? Please add anatomic markers to clarify the location and allow the reader to interpret whether this is articular cartilage or ectopic cartilage

      We have redone the figure to show the area as requested.

      Relevant to this, do the authors observe this type of cellular engraftment in ectopic cartilage/osteophytes or only in articular cartilage? Understanding the contribution of these cells to the formation/remodeling of various cartilage types in the context of OA is a critical aspect of this line of investigation.

      We didn’t see any contribution of these cells to ectopic cartilage formation and are actively working on a follow up study discussing this point specifically. 

      Discussion: 

      Besides my comments regarding DPP4 and ITGA5 above, the authors may also consider discussing PMID: 37681409 (JCI Insight 2023), which demonstrates that adult Prg4+ progenitors derived from synovium contribute to articular cartilage repair in vivo. 

      We agree that there are numerous markers we could look at in future studies and that other people in the field are actively studying.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Review:

      Reviewer #1 (Public review):

      The authors used fluorescence microscopy, image analysis, and mathematical modeling to study the effects of membrane affinity and diffusion rates of MinD monomer and dimer states on MinD gradient formation in B. subtilis. To test these effects, the authors experimentally examined MinD mutants that lock the protein in specific states, including Apo monomer (K16A), ATP-bound monomer (G12V) and ATP-bound dimer (D40A, hydrolysis defective), and compared to wild-type MinD. Overall, the experimental results support the conclusions that reversible membrane binding of MinD is critical for the formation of the MinD gradient, but the binding affinities between monomers and dimers are similar.

      The modeling part is a new attempt to use the Monte Carlo method to test the conditions for the formation of the MinD gradient in B. subtilis. The modeling results provide good support for the observations and find that the MinD gradient is sensitive to different diffusion rates between monomers and dimers. This simulation is based on several assumptions and predictions, which raises new questions that need to be addressed experimentally in the future.  

      Reviewer #3 (Public review):

      This important study by Bohorquez et al examines the determinants necessary for concentrating the spatial modulator of cell division, MinD, at the future site of division and the cell poles. Proper localization of MinD is necessary to bring the division inhibitor, MinC, in proximity to the cell membrane and cell poles

      where it prevents aberrant assembly of the division machinery. In contrast to E. coli, in which MinD 50 oscillates from pole-to-pole courtesy of a third protein MinE, how MinD localization is achieved in B. 51 subtilis-which does not encode a MinE analog-has remained largely a mystery. The authors present 52 compelling data indicating that MinD dimerization is dispensable for membrane localization but required 53 for concentration at the cell poles. Dimerization is also important for interactions between MinD and MinC, 54 leading to the formation of large protein complexes. Computational modeling, specifically a Monte Carlo 55 simulation, supports a model in which differences in diffusion rates between MinD monomers and dimers 56 lead to concentration of MinD at cell poles. Once there, interaction with MinC increases the size of the 57 complex, further reinforcing diffusion differences. Notably, interactions with MinJ-which has previously 58 been implicated in MinCD localization, are dispensable for concentrating MinD at cell poles although MinJ may help stabilize the MinCD complex at those locations.

      Comments on revisions:  

      I believe the authors put respectable effort into revisions and addressing reviewer comments, particularly 64      those that focused on the strengths of the original conclusions. The language in the current version of the manuscript is more precise and the overall product is stronger.  

      We are happy to learn that the reviewer considers our manuscript ready for publication.  

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):  

      The author has adequately answered the questions that were raised in my previous comments. There are only few minor revisions needed for improvement.  

      Line 48−49: 'These proteins ensure that cell division occurs at midcell and not close to nascent division sites or cell poles'  

      delete 'nascent division site'  

      This has now been corrected as suggested.

      Line 64−65: 'MinC inhibits polymerization of FtsZ by direct protein-protein interactions and needs to bind to the Walker A-type ATPase MinD for its recruitment to septa or the polar regions of the cell'

      delete 'septa or', because MinD recruits MinC to the cell poles to block polar division, not septal formation.  

      This has now been corrected as suggested.

      Supplemental information:

      Some parameters in Table S1 are missing definitions. If these parameters relate to terms described in the "Methods" section, please add the corresponding parameter symbols after the terms.  

      We would like to thank the reviewer for pointing this out. We have improved Table S1 and corrected the related parameters in the Methods section (lines 605-619).

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review): 

      Summary: 

      This manuscript investigates the biological mechanism underlying the assembly and transport of the AcrAB-TolC efflux pump complex. By combining endogenous protein purification with cryo-EM analysis, the authors show that the AcrB trimer adopts three distinct conformations simultaneously and identify a previously uncharacterized lipoprotein, YbjP, as a potential additional component of the complex. The work aims to advance our understanding of the AcrAB-TolC efflux system in near-native conditions and may have broader implications for elucidating its physiological mechanism. 

      Strengths: 

      Overall, the manuscript is clearly presented, and several of the datasets are of high quality. The use of natively isolated complexes is a major strength, as it minimizes artifacts associated with reconstituted systems and enables the discovery of a novel subunit. The authors also distinguish two major assemblies-the TolC-YbjP sub-complex and the complete pump-which appear to correspond to the closed and open channel states, respectively. The conceptual advance is potentially meaningful, and the findings could be of broad interest to the field. 

      Weaknesses: 

      (1) As the identification of YbjP is a key contribution of this work, a deeper comparison with functional "anchor" proteins in other efflux pumps is needed. Including an additional supplementary figure illustrating these structural comparisons would be valuable. 

      We appreciate this helpful suggestion. We will expand the comparative analysis between YbjP and established anchoring or accessory components in other efflux pumps, and we will add a new supplementary figure illustrating these structural relationships.

      (2) The observation of the LTO states in the presence of TolC represents an important extension of previous findings. A more detailed discussion comparing these LTO states to those reported in earlier structural and biochemical studies would improve the clarity and significance of this point. 

      We agree. In the revised manuscript we will expand our discussion of the LTO conformations, including a direct comparison with previously reported structural and biochemical observations, to better contextualize the significance of our findings.

      Reviewer #2 (Public review): 

      Summary: 

      This manuscript reports the high-resolution cryo-EM structures of the endogenous TolC-YbjP-AcrABZ complex and a TolC-YbjP subcomplex from E. coli, identifying a novel accessory subunit. This work is an impressive effort that provides valuable structural insights into this native complex. 

      Strengths: 

      (1) The study successfully determines the structure of the complete, endogenously purified complex, marking a significant achievement. 

      (2) The identification of a previously unknown accessory subunit is an important finding. 

      (3) The use of cryo-EM to resolve the complex, including potential post-translational modifications such as N-palmitoyl and S-diacylglycerol, is a notable highlight. 

      Weaknesses: 

      (1) Clarity and Interpretation: Several points need clarification. Additionally, the description of the sample preparation method, which is a key strength, is currently misplaced and should be introduced earlier. 

      Thank you for pointing this out. We will reorganize the text to introduce the sample preparation strategy earlier and clarify the points that may cause ambiguity.

      (2) Data Presentation: The manuscript would benefit significantly from improved figures. 

      We agree and will revise the figures to improve clarity, consistency, and readability. Additional schematic illustrations will also be included where appropriate.

      (3) Supporting Evidence: The inclusion of the protein purification profile as a supplementary figure is essential. Furthermore, a discussion comparing the endogenous AcrB structure to those obtained in other systems (e.g., liposomes) and commenting on observed lipid densities would strengthen the overall analysis. 

      We appreciate these suggestions. We will add the purification profile and expand the comparison between our endogenous AcrB structure and previously reported structures from reconstituted systems, including a more detailed discussion of lipid densities.

      Reviewer #3 (Public review): 

      Summary: 

      The manuscript "Structural mechanisms of pump assembly and drug transport in the AcrAB-TolC efflux system" by Ge et al. describes the identification of a previously uncharacterized lipoprotein, YbjP, as a novel partner of the well-studied Enterobacterial tripartite efflux pump AcrAB-TolC. The authors present cryo-electron microscopy structures of the TolC-YbjP subcomplex and the complete AcrABZ-TolC-YbjP assembly. While the identification and structural characterization of YbjP are potentially novel, the stated focus of the manuscript-mechanisms of pump assembly and drug transport - is not sufficiently addressed. The manuscript requires reframing to emphasize the principal novelty associated with YbjP and significant development of the other aspects, especially the claimed novelty of the AcrB drug-efflux cycle. 

      Strengths: 

      The reported association of YbjP with AcrAB-TolC is novel; however, a recent deposition of a preceding and much more detailed manuscript to the BioRxiv server (Horne et al., https://doi.org/10.1101/2025.03.19.644130) removes much of the immediate novelty. 

      Weaknesses: 

      While the identification of YbjP is novel, the authors do not appear to acknowledge the precedence of another work (Horne et al., 2025), and it is not cited within the correct context in the manuscript. 

      We thank the reviewer for rasising this important point regarding the independent nature of our work.

      Our study indeed progressed independently. The process began with our purification of an endogenous protein sample containing the AcrAB-TolC efflux pump. During our cryo-EM analysis, we observed an unassigned density in the map, for which we built a preliminary main-chain model. A subsequent search of structural databases, including AlphaFold predictions, allowed us to identify this density as the protein YbjP. It was only after this identification that we became aware of the related preprint by Horne et al. on BioRxvi (Posted March 19, 2025).

      Therefore, our structural determination of YbjP was conducted entirely independently. We fully acknowledge and respect the work by Horne et al. and have already cited their reprint in our manuscript. While their detailed structural data, maps, and coordinates are not yet publicly available, we have described their findings appropriately. We agree that our manuscript can better reflect this context and will carefully check for any missing citations to ensure that their contribution is properly and clearly acknowledged.

      We also believe that the two studies are mutually complementary and collectively reinforce the emerging understanding of YbjP.

      Several results presented in the TolC-YbjP section do not represent new findings regarding TolC structure itself.

      We agree that the TolC features we describe are consistent with previously reported structural characteristics. However, these observations could only be confirmed in the context of the newly determined TolC–YbjP subcomplex, which was not available prior to this study. We will clarify this point in the revision to avoid overstating novelty.

      The structure and gating behaviour of TolC should be more thoroughly introduced in the Introduction, including prior work describing channel opening and conformational transitions.

      We appreciate this suggestion and agree that a more comprehensive overview of TolC gating and conformational transitions will strengthen the Introduction. We will revise the text to incorporate relevant prior structural and functional studies.

      The current manuscript does not discuss the mechanistic role of helices H3/H4 and H7/H8 in channel dilation, despite implying that YbjP binding may influence these features.

      Thank you for this comment. The primary novel contributions of this manuscript are the identification of YbjP and the structural characterization of AcrB in three distinct states. The discussion of the dilation mechanism, while included because we observed the closed TolC-YbjP state, is a secondary point. In the revised manuscript, we will expand this discussion as suggested.

      Only the original closed TolC structure is cited, and the manuscript does not address prior mutational studies involving the D396 region, though this residue is specifically highlighted in the presented structures. 

      We appreciate the reviewer drawing attention to this oversight. We will add citations to the relevant mutational and mechanistic studies, including those involving the D396 region, and more clearly discuss these findings in relation to our structural observations.

      The manuscript provides only a general structural alignment between the closed TolC-YbjP subcomplex and the open TolC observed in the full pump assembly. However, multiple open, closed, and intermediate conformations of AcrAB-TolC have already been reported. Thus, YbjP alone cannot be assumed to account for TolC channel gating. A systematic comparison with existing structures is necessary to determine whether YbjP contributes any distinct allosteric modulation. 

      We agree with the reviewer’s assessment and appreciate the constructive suggestion. In our revised manuscript, we will expand the structural comparison to include previously reported open, closed, and intermediate AcrAB–TolC conformations. This expanded analysis will more clearly position our findings within the existing structural framework.

      The analysis of AcrB peristaltic action is superficial, poorly substantiated and importantly, not novel. Several references to the ATP-synthase cycle have been provided, but this has been widely established already some 20 years ago - e.g. https://www.science.org/doi/10.1126/science.1131542

      We thank the reviewer for this comment. We fully acknowledge the foundational studies that established the AcrB functional cycle and its analogy to the ATP-synthase mechanism. While previous work indeed defined the LTO (Loose, Tight, Open) cycle of AcrB, those structures were obtained using AcrB in isolation. In contrast, our endogenous sample, which includes the native constraints of AcrA from above and the presence of AcrZ, reveals conformational changes in the transmembrane and porter domains that differ from those previously reported. We interpret these differences as reflecting a more physiologically relevant mechanism. In our revision, we will provide a detailed discussion to contextualize these distinctions within the existing literature.

      The most significant limitation of the study is the absence of functional characterization of YbjP in vivo or in vitro. While the structural association between YbjP and TolC is interesting, the biological role of YbjP remains unclear.

      We agree that the lack of functional characterization is a limitation of the present work. Our study focuses on structural elucidation and structural analysis. Although the recent preprint you mentioned suggests that YbjP deletion may not produce a strong phenotype, we are still interested in conducting additional experiments to explore its potential roles in future work. We will revise the text to clearly acknowledge this limitation.

      Moreover, the manuscript does not examine structural differences between the presented complex and previously solved AcrAB-TolC or MexAB-OprM assemblies that might support a mechanistic model.

      We thank the reviewer for this suggestion. We will incorporate a more detailed comparative analysis with existing AcrAB–TolC and MexAB–OprM structures and highlight similarities and differences that may inform mechanistic interpretation.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript by Lu and colleagues demonstrates convincingly that PRRT2 interacts with brain voltage-gated sodium channels to enhance slow inactivation in vitro and in vivo. The work is interesting and rigorously conducted. The relevance to normal physiology and disease pathophysiology (e.g., PRRT2-related genetic neurodevelopmental disorders) seems high. Some simple additional experiments could elevate the impact and make the study more complete.

      Strengths:

      Experiments are conducted rigorously, including experimenter blinding and appropriate controls. Data presentation is excellent and logical. The paper is well written for a general scientific audience.

      Weaknesses:

      There are a few missing experiments and one place where data are over-interpreted.

      (1) An in vitro study of Nav1.6 is conspicuously absent. In addition to being a major brain Na channel, Nav1.6 is predominant in cerebellar Purkinje neurons, which the authors note lack PRRT2 expression. They speculate that the absence of PRRT2 in these neurons facilitates the high firing rate. This hypothesis would be strengthened if PRRT2 also enhanced slow inactivation of Nav1.6. If a stable Nav1.6 cell were not available, then simple transient co-transfection experiments would suffice.

      We thank the reviewer for this suggestion. In the revised manuscript, we will examine whether PRRT2 modulates slow inactivation of Nav1.6 channels using heterologous co-expression experiments.

      (2) To further demonstrate the physiological impact of enhanced slow inactivation, the authors should consider a simple experiment in the stable cell line experiments (Figure 1) to test pulse frequency dependence of peak Na current. One would predict that PRRT2 expression will potentiate 'run down' of the channels, and this finding would be complementary to the biophysical data.

      We agree that examining pulse frequency-dependent changes in peak sodium current would provide a functional readout linking PRRT2-mediated enhancement of slow inactivation to use-dependent channel availability. In the revision, we will include a pulse-train protocol to quantify use-dependent attenuation (“run-down”) of peak sodium current across stimulation trains and will compare this adaptation between control and PRRT2-expressing conditions.

      (3) The study of one K channel is limited, and the conclusion from these experiments represents an over-interpretation. I suggest removing these data unless many more K channels (ideally with measurable proxies for slow inactivation) were tested. These data do not contribute much to the story.

      We agree with the reviewer’s assessment. To avoid over-interpretation and to maintain focus on PRRT2-dependent regulation of Nav channel slow inactivation, we will remove potassium channel dataset and the associated conclusions from the revised manuscript.

      (4) In Figure 2, the authors should confirm that protein is indeed expressed in cells expressing each truncated PRRT2 construct. Absent expression should be ruled out as an explanation for the enhancement of slow inactivation.

      We appreciate the reviewer’s concern regarding expression of the truncated PRRT2 constructs in the Nav1.2 stable cell line, particularly PRRT2(1-266), which shows little effect on slow inactivation of Nav1.2 channels. In the revision, we will include expression controls for each truncation construct in the Nav1.2-expressing cells to rule out lack of expression as an explanation for the observed functional differences.

      Reviewer #2 (Public review):

      Summary:

      As a member of DspB subfamily, PRRT2 is primarily expressed in the nervous system and has been associated with various paroxysmal neurological disorders. Previous studies have shown that PRRT2 directly interacts with Nav1.2 and Nav1.6, modulating channel properties and neuronal excitability.

      In this study, Lu et al. reported that PRRT2 is a physiological regulator of Nav channel slow inactivation, promoting the development of Nav slow inactivation and impeding the recovery from slow inactivation. This effect can be replicated by the C-terminal region (256-346) of PRRT2, and is highly conserved across species from zebrafish, mouse, to human PRRT2. TRARG1 and TMEM233, the other two DspB family members, showed similar effects on Nav1.2 slow inactivation. Co-IP data confirms the interaction between Nav channels and PRRT2. Prrt2-mutant mice, which lack PRRT2 expression, require lower stimulation thresholds for evoking after-discharges when compared to WT mice.

      Strengths:

      (1) This study is well designed, and data support the conclusion that PRRT2 is a potent regulator of slow inactivation of Nav channels.

      (2) This study reveals similar effects on Nav1.2 slow inactivation by PRRT2, TMEM233, and TRARG1, indicating a common regulation of Nav channels by DspB family members (Supplemental Figure 2). A recent study has shown that TMEM233 is essential for ExTxA (a plant toxin)-mediated inhibition on fast inactivation of Nav channels; and PRRT2 and TRARG1 could replicate this effect (Jami S, et al. Nat Commun 2023). It is possible that all three DspB members regulate Nav channel properties through the same mechanism, and exploring molecules that target PRRT2/TRARG1/TMEM233 might be a novel strategy for developing new treatments of DspB-related neurological diseases.

      Weaknesses:

      (1) Previously, the authors have reported that PRRT2 reduces Nav1.2 current density and alters biophysical properties of both Nav1.2 and Nav1.6 channels, including enhanced steady-state inactivation, slower recovery, and stronger use-dependent inhibition (Lu B, et al. Cell Rep 2021, Fig 3 & S5). All those changes are expected to alter neuronal excitability and should be discussed.

      We agree that PRRT2 has been reported to exert multiple effects on Nav channels which are all expected to influence neuronal excitability (Fruscione et al., 2018; Lu et al., 2021; Valente et al., 2023). In the revised manuscript, we will expand the Discussion to integrate these prior findings and to clarify how these PRRT2-dependent changes may interact with (and potentially converge on) modulation of slow inactivation to shape neuronal excitability.

      (2) In this study, the fast inactivation kinetics was examined by a single stimulus at 0 mV, which may not be sufficient for the conclusion. Inactivation kinetics at more voltage potentials should be added.

      We thank the reviewer for this suggestion. In the revision, we will extend our analysis of Nav1.2 fast-inactivation kinetics across a range of test potentials (e.g., -20, -10, 0, +10 and +20 mV) in the presence and absence of PRRT2.

      (3) It is a little surprising that there is no difference in Nav1.2 current density in axon-blebs between WT and Prrt2-mutant mice (Figure 7B). PRRT2 significantly shifts steady-state slow inactivation curve to hyperpolarizing direction, at -70 mV, nearly 70% of Nav1.2 channels are inactivated by slow inactivation in cells expressing PRRT2 when compared to less than 10% in cells expressing GFP (Figure supplement 1B); with a holding potential of -70 mV, I would expect that most of Nav channels are inactivated in axon-blebs from WT mice but not in axon-blebs from Prrt2-mutant mice, and therefore sodium current density should be different in Figure 7B, which was not. Any explanation?

      We appreciate the reviewer for raising this point. In our axonal bleb recordings, although the holding potential was -70 mV, sodium current density was measured after a hyperpolarizing pre-pulse (-110 mV) to relieve inactivation immediately prior to the test depolarization (as described in the Methods). Thus, the current density measurement in Figure 7B reflects the maximal available current following this recovery step, rather than the steady-state availability at -70 mV. In the revision, we will state this explicitly in the Results and/or figure legend to avoid confusion.

      (4) Besides Nav channels, PRRT2 has been shown to act on Cav2.1 channels as well as molecules involved in neurotransmitter release, which may also contribute to abnormal neuronal activity in Prrt2-mutant mice. These should be mentioned when discussing PRRT2's role in neuronal resilience.

      We agree with the reviewer. In the revised manuscript, we will broaden the Discussion to acknowledge PRRT2 functions beyond Nav channels, including reported roles in Cav2.1 regulation and neurotransmitter release. We will frame the in vivo phenotypes in Prrt2-mutant mice as likely arising from convergent mechanisms—altered intrinsic excitability together with changes in synaptic transmission.

      Reviewer #3 (Public review):

      This paper reveals that the neuronal protein PRRT2, previously known for its association with paroxysmal dyskinesia and infantile seizures, modulates the slow inactivation of voltage-gated sodium ion (Nav) channels, a gating process that limits excitability during prolonged activity. Using electrophysiology, molecular biology, and mouse models, the authors show that PRRT2 accelerates entry of Nav channels into the slow-inactivated state and slows their recovery, effectively dampening excessive excitability. The effect seems evolutionarily conserved, requires the C-terminal region of PRRT2, and is recapitulated in cortical neurons, where PRRT2 deficiency leads to hyper-responsiveness and reduced cortical resilience in vivo. These findings extend the functional repertoire of PRRT2, identifying it as a physiological brake on neuronal excitability. The work provides a mechanistic link between PRRT2 mutations and episodic neurological phenotypes.

      Comments:

      (1) The precise structural interface and the molecular basis of gating modulation remain inferred rather than demonstrated.

      We thank the reviewer for this comment. In the revision, we will make it explicit that our structural modeling are based on prediction rather than evidential. We will also expand the Limitations section to highlight that direct structural and biochemical mapping of the PRRT2-Nav interface (e.g., through targeted mutagenesis, crosslinking, and/or structural determination) will be required to define the binding interface and establish the molecular basis of gating modulation.

      (2) The in vivo phenotype reflects a complex circuit outcome and does not isolate slow-inactivation defects per se.

      We agree with the reviewer. In the revision, we will refine the Discussion to avoid over-attributing the in vivo phenotype to slow-inactivation defects alone and to explicitly state that impaired slow inactivation in Prrt2-mutant mice represents one plausible contributing mechanism to reduced cortical resilience, alongside other PRRT2-dependent process.

      (3) Expression of PRRT2 in muscle or heart is low, so the cross-isoform claims are likely of limited physiological significance.

      We thank the review for your comment about physiological relevance. In the revised manuscript, we will clarify that our Nav isoform panel was designed to assess mechanistic generality at the channel level rather than to imply broad in vivo relevance across tissues. We will also expand the Discussion to emphasize that any therapeutic strategy involving PRRT2 delivery should consider its consistent effect on slow inactivation across multiple Nav isoforms.

      (4) The mechanistic separation between the trafficking effect of PRRT2 and its gating effects is not clearly resolved.

      We appreciate the reviewer for raising this important point. In the revision, we will expand the Discussion to clarify why we interpret the effect of PRRT2 on slow inactivation as a gating modulation rather than a secondary consequence of altered channel abundance or localization. First, our slow inactivation measurements are expressed as the fraction of available channels after depolarization conditioning relative to baseline availability within the same cell (post-/pre-conditioning), which minimizes confounding by differences in initial surface expression. Second, the slow inactivation of Nav channel occurs on a rapid, activity-dependent timescale (seconds), whereas remarkable changes in trafficking and surface abundance generally develop over longer intervals (minutes to hours).

      (5) Additional studies with Nav1.6 should be carried out.

      We thank the reviewer’s suggestion. We will include Nav1.6 slow inactivation experiments in the revised manuscript.

    1. Author response:

      eLife Assessment

      This important study fills a major geographic and temporal gap in understanding Paleocene mammal evolution in Asia and proposes an intriguing "brawn before bite" hypothesis grounded in diverse analytical approaches. However, the findings are incomplete because limitations in sampling design - such as the use of worn or damaged teeth, the pooling of different tooth positions, and the lack of independence among teeth from the same individuals - introduce uncertainties that weaken support for the reported disparity patterns. The taxonomic focus on predominantly herbivorous clades also narrows the ecological scope of the results. Clarifying methodological choices, expanding the ecological context, and tempering evolutionary interpretations would substantially strengthen the study.

      We thank Dr. Rasmann for the constructive evaluation of our manuscript. Considering the reviewers’ comments, we plan to implement revisions to our study focusing on (1) expansion of the fossil sample description, including a detailed account of the process of excluding extremely worn or damaged teeth from all analyses, (2) expanded reporting of the analyses done on individual tooth positions, and tempering the interpretation of the pooled samples in light of the issues raised by reviewers, (3) providing a more comprehensive introduction that includes an overview of the Paleocene mammal faunas in south China, which unevenly samples certain clades whereas others are extremely rare, and why the current available fossil samples would not permit a whole-fauna analysis to be adequately conducted across the three land mammal age time bins of the Paleocene in China. We believe these revisions would substantially strengthen the study’s robustness and impact for understanding the ecomorphological evolution of the earliest abundant placental mammals during the Paleocene in Asia.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This work provides valuable new insights into the Paleocene Asian mammal recovery and diversification dynamics during the first ten million years post-dinosaur extinction. Studies that have examined the mammalian recovery and diversification post-dinosaur extinction have primarily focused on the North American mammal fossil record, and it's unclear if patterns documented in North America are characteristic of global patterns. This study examines dietary metrics of Paleocene Asian mammals and found that there is a body size disparity increase before dietary niche expansion and that dietary metrics track climatic and paleobotanical trends of Asia during the first 10 million years after the dinosaur extinction.

      Strengths:

      The Asian Paleocene mammal fossil record is greatly understudied, and this work begins to fill important gaps. In particular, the use of interdisciplinary data (i.e., climatic and paleobotanical) is really interesting in conjunction with observed dietary metric trends.

      Weaknesses:

      While this work has the potential to be exciting and contribute greatly to our understanding of mammalian evolution during the first 10 million years post-dinosaur extinction, the major weakness is in the dental topographic analysis (DTA) dataset.

      There are several specimens in Figure 1 that have broken cusps, deep wear facets, and general abrasion. Thus, any values generated from DTA are not accurate and cannot be used to support their claims. Furthermore, the authors analyze all tooth positions at once, which makes this study seem comprehensive (200 individual teeth), but it's unclear what sort of noise this introduces to the study. Typically, DTA studies will analyze a singular tooth position (e.g., Pampush et al. 2018 Biol. J. Linn. Soc.), allowing for more meaningful comparisons and an understanding of what value differences mean. Even so, the dataset consists of only 48 specimens. This means that even if all the specimens were pristinely preserved and generated DTA values could be trusted, it's still only 48 specimens (representing 4 different clades) to capture patterns across 10 million years. For example, the authors note that their results show an increase in OPCR and DNE values from the middle to the late Paleocene in pantodonts. However, if a singular tooth position is analyzed, such as the lower second molar, the middle and late Paleocene partitions are only represented by a singular specimen each. With a sample size this small, it's unlikely that the authors are capturing real trends, which makes the claims of this study highly questionable.

      We thank Reviewer 1 for their careful review of our manuscript. A major external limitation of the application of DTA to fossil samples is the availability of specimens. Whereas a typical study design using extant or geologically younger/more abundant fossil species would preferably sample much larger quantities of teeth from each treatment group (time bins, in our case), the rarity of well-preserved Paleocene mammalian dentitions in Asia necessitates the analysis of small samples in order to make observations regarding major trends in a region and time period otherwise impossible to study (see Chow et al. 1977). That said, we plan to clarify methodological details in response to the reviewer’s comments, including a more comprehensive explanation of our criteria for exclusion of broken tooth crowns from the analyses. We also plan to expand our results reporting on individual tooth position analysis, potentially including resampling and/or simulation analyses to assess the effect of small and uneven samples on our interpretation of results. Lastly, we plan to revise the discussion and conclusion accordingly, including more explicit distinction between well-supported findings that emerge from various planned sensitivity analyses, versus those that are more speculative and tentative in nature.

      Chow, M., Zhang, Y., Wang, B., and Ding, S. (1977). Paleocene mammalian fauna from the Nanxiong Basin, Guangdong Province. Paleontol. Sin. New Ser. C 20, 1–100.

      Reviewer #2 (Public review):

      Summary:

      This study uses dental traits of a large sample of Chinese mammals to track evolutionary patterns through the Paleocene. It presents and argues for a 'brawn before bite' hypothesis - mammals increased in body size disparity before evolving more specialized or adapted dentitions. The study makes use of an impressive array of analyses, including dental topographic, finite element, and integration analyses, which help to provide a unique insight into mammalian evolutionary patterns.

      Strengths:

      This paper helps to fill in a major gap in our knowledge of Paleocene mammal patterns in Asia, which is especially important because of the diversification of placentals at that time. The total sample of teeth is impressive and required considerable effort for scanning and analyzing. And there is a wealth of results for DTA, FEA, and integration analyses. Further, some of the results are especially interesting, such as the novel 'brawn before bite' hypothesis and the possible link between shifts in dental traits and arid environments in the Late Paleocene. Overall, I enjoyed reading the paper, and I think the results will be of interest to a broad audience.

      Weaknesses:

      I have four major concerns with the study, especially related to the sampling of teeth and taxa, that I discuss in more detail below. Due to these issues, I believe that the study is incomplete in its support of the 'brawn before bite' hypothesis. Although my concerns are significant, many of them can be addressed with some simple updates/revisions to analyses or text, and I try to provide constructive advice throughout my review.

      (1) If I understand correctly, teeth of different tooth positions (e.g., premolars and molars), and those from the same specimen, are lumped into the same analyses. And unless I missed it, no justification is given for these methodological choices (besides testing for differences in proportions of tooth positions per time bin; L902). I think this creates some major statistical concerns. For example, DTA values for premolars and molars aren't directly comparable (I don't think?) because they have different functions (e.g., greater grinding function for molars). My recommendation is to perform different disparity-through-time analyses for each tooth position, assuming the sample sizes are big enough per time bin. Or, if the authors maintain their current methods/results, they should provide justification in the main text for that choice.

      We thank Reviewer 2 for raising several issues worthy of clarification. Separate analyses for individual tooth positions were performed but not emphasized in the first version of the study. In our revised version we plan to highlight the nuances of the results from premolar versus molar partition analyses.

      Also, I think lumping teeth from the same specimen into your analyses creates a major statistical concern because the observations aren't independent. In other words, the teeth of the same individual should have relatively similar DTA values, which can greatly bias your results. This is essentially the same issue as phylogenetic non-independence, but taken to a much greater extreme.

      It seems like it'd be much more appropriate to perform specimen-level analyses (e.g., Wilson 2013) or species-level analyses (e.g., Grossnickle & Newham 2016) and report those results in the main text. If the authors believe that their methods are justified, then they should explain this in the text.

      We plan to emphasize individual tooth position analyses in our revisions, and provide a stronger justification for our current treatment of multiple teeth from the same individual specimens as independent samples. We recognize the statistical nonindependence raised by Reviewer 2, but we would point out that from an ecomorphological perspective, it is unclear to us that the heterodont dentition of these early Cenozoic placental mammals should represent a single ecological signal (and thus warrant using only a single tooth position as representative of an individual’s DTA values). We plan to closely examine the nature of nonindependence in the DTA data within individuals, to assess a balanced approach to maximize information content from the relatively small and rare fossil samples used, while minimizing signal nonindependence across the dentition.

      (2) Maybe I misunderstood, but it sounds like the sampling is almost exclusively clades that are primarily herbivorous/omnivorous (Pantodonta, Arctostylopida, Anagalida, and maybe Tillodonta), which means that the full ecomorphological diversity of the time bins is not being sampled (e.g., insectivores aren't fully sampled). Similarly, the authors say that they "focused sampling" on those major clades and "Additional data were collected on other clades ... opportunistically" (L628). If they favored sampling of specific clades, then doesn't that also bias their results?

      If the study is primarily focused on a few herbivorous clades, then the Introduction should be reframed to reflect this. You could explain that you're specifically tracking herbivore patterns after the K-Pg.

      We plan to revise the introduction section to more accurately reflect the emphasis on those clades. However, we would note that conventional dietary ecomorphology categories used to characterize later branching placental mammals are likely to be less informative when applied to their Paleocene counterparts. Although there are dental morphological traits that began to characterize major placental clades during the Paleocene, distinctive dietary ecologies have not been demonstrated for most of the clade representatives studied. Thus, insectivory was probably not restricted to “Insectivora”, nor carnivory to early Carnivmorpha or “Creodonta”, each of which represented less than 5% of the taxonomic richness during the Paleocene in China (Wang et al. 2007).

      Wang, Y., Meng, J., Ni, X., and Li, C. (2007). Major events of Paleogene mammal radiation in China. Geol. J. 42, 415–430.

      (3) There are a lot of topics lacking background information, which makes the paper challenging to read for non-experts. Maybe the authors are hindered by a short word limit. But if they can expand their main text, then I strongly recommend the following:

      (a) The authors should discuss diets. Much of the data are diet correlates (DTA values), but diets are almost never mentioned, except in the Methods. For example, the authors say: "An overall shift towards increased dental topographic trait magnitudes ..." (L137). Does that mean there was a shift toward increased herbivory? If so, why not mention the dietary shift? And if most of the sampled taxa are herbivores (see above comment), then shouldn't herbivory be a focal point of the paper?

      We plan to revise the text to make clearer connections between DTA and dietary inferences, and at the same time advise caution in making one-to-one linkages between them. Broadly speaking, dental indices such as DTA are phenotypic traits, and as in other phenotypic traits, the strength of structure-function relationships needs to be explicitly established before dietary ecological inferences can be confidently made. There is, to date, no consistent connection between dental topology and tooth use proxies and biomechanical traits in extant non-herbivorous species (e.g., DeSantis et al. 2017, Tseng and DeSantis 2024), and in our analyses, FEA and DTA generally did not show strong correlations to each other. Thus, we plan to continue to exercise care in interpreting DTA data as dietary data.

      DeSantis LRG, Tseng ZJ, Liu J, Hurst A, Schubert BW, Jiangzuo Q. Assessing niche conservatism using a multiproxy approach: dietary ecology of extinct and extant spotted hyenas. Paleobiology. 2017;43(2):286-303. doi:10.1017/pab.2016.45

      Tseng ZJ, DeSantis LR. Relationship between tooth macrowear and jaw morphofunctional traits in representative hypercarnivores. PeerJ. 2024 Nov 11;12:e18435.

      (b) The authors should expand on "we used dentitions as ecological indicators" (L75). For non-experts, how/why are dentitions linked to ecology? And, again, why not mention diet? A strong link between tooth shape and diet is a critical assumption here (and one I'm sure that all mammalogists agree with), but the authors don't provide justification (at least in the Introduction) for that assumption. Many relevant papers cited later in the Methods could be cited in the Introduction (e.g., Evans et al. 2007).

      Thank you for this suggestion. We plan to expand the introduction section to better contextualize the methodological basis for the work presented.

      (c) Include a better introduction of the sample, such as explicitly stating that your sample only includes placentals (assuming that's the case) and is focused on three major clades. Are non-placentals like multituberculates or stem placentals/eutherians found at Chinese Paleocene fossil localities and not sampled in the study, or are they absent in the sampled area?

      We thank Reviewer 2 for raising this important point worthy of clarification. Multituberculates are completely absent from the first two land mammal ages in the Paleocene of Asia, and non-placentals are rare in general (Wang et al. 2007). We plan to provide more context for the taxonomic sampling choices made in the study.

      Wang, Y., Meng, J., Ni, X., and Li, C. (2007). Major events of Paleogene mammal radiation in China. Geol. J. 42, 415–430.

      (d) The way in which "integration" is being used should be defined. That is a loaded term which has been defined in different ways. I also recommend providing more explanation on the integration analyses and what the results mean.

      If the authors don't have space to expand the main text, then they should at least expand on the topics in the supplement, with appropriate citations to the supplement in the main text.

      We plan to clarify our usage of “integration” to enable readers to accurately interpret what we mean by it.

      (4) Finally, I'm not convinced that the results fully support the 'brawn before bite' hypothesis. I like the hypothesis. However, the 'brawn before ...' part of the hypothesis assumes that body size disparity (L63) increased first, and I don't think that pattern is ever shown. First, body size disparity is never reported or plotted (at least that I could find) - the authors just show the violin plots of the body sizes (Figures 1B, S6A). Second, the authors don't show evidence of an actual increase in body size disparity. Instead, they seem to assume that there was a rapid diversification in the earliest Paleocene, and thus the early Paleocene bin has already "reached maximum saturation" (L148). But what if the body size disparity in the latest Cretaceous was the same as that in the Paleocene? (Although that's unlikely, note that papers like Clauset & Redner 2009 and Grossnickle & Newham 2016 found evidence of greater body size disparity in the latest Cretaceous than is commonly recognized.) Similarly, what if body size disparity increased rapidly in the Eocene? Wouldn't that suggest a 'BITE before brawn' hypothesis? So, without showing when an increase in body size diversity occurred, I don't think that the authors can make a strong argument for 'brawn before [insert any trait]".

      Although it's probably well beyond the scope of the study to add Cretaceous or Eocene data, the authors could at least review literature on body size patterns during those times to provide greater evidence for an earliest Paleocene increase in size disparity.

      We plan to provide a broader discussion and any supporting evidence from the Cretaceous and Eocene to either make a stronger case for “brawn before bite”, or to refine what we mean by brawn/size/size disparity.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This Review Article explores the intricate relationship between humans and Mycobacterium tuberculosis (Mtb), providing an additional perspective on TB disease. Specifically, this review focuses on the utilization of systems-level approaches to study TB, while highlighting challenges in the frameworks used to identify the relevant immunologic signals that may explain the clinical spectrum of disease. The work could be further enhanced by better defining key terms that anchor the review, such as "unified mechanism" and "immunological route." This review will be of interest to immunologists as well as those interested in evolution and host-pathogen interactions.

      We thank the editors for reviewing our article and for the primarily positive comments. We accept that better definition and terminology will improve the clarity of the message, and so have changed the wording as suggested above in the revised manuscript.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This is an interesting and useful review highlighting the complex pathways through which pulmonary colonisation or infection with Mycobacterium tuberculosis (Mtb) may progress to develop symptomatic disease and transmit the pathogen. I found the section on immune correlates associated with individuals who have clearly been exposed to and reacted to Mtb but did not develop latent infections particularly valuable. However, several aspects would benefit from clarification.

      Strengths:

      The main strengths lie in the arguments presented for a multiplicity of immune pathways to TB disease.

      Weaknesses:

      The main weaknesses lie in clarity, particularly in the precise meanings of the three figures.

      We accept this point, and have completely changed figure 2, and have expanded the legends for figure 1 and 3 to maximise clarity.

      I accept that there is a 'goldilocks zone' that underpins the majority of TB cases we see and predominantly reflects different patterns of immune response, but the analogies used need to be more clearly thought through.

      We are glad the reviewer agrees with the fundamental argument of different patterns of immunity, and have revised the manuscript throughout where we feel the analogies could be clarified.

      Reviewer #2 (Public review):

      Summary:

      This is a thought-provoking perspective by Reichmann et al, outlining supportive evidence that Mycobacterium tuberculosis co-evolved with its host Homo Sapiens to both increase susceptibility to infection and reduce rates of fatal disease through decreased virulence. TB is an ancient disease where two modes of virulence are likely to have evolved through different stages of human evolution: one before the Neolithic Demographic Transition, where humans lived in sparse hunter-gatherer communities, which likely selected for prolonged Mtb infection with reduced virulence to allow for transmission across sparse populations. Conversely, following the agricultural and industrial revolutions, Mtb virulence is likely to have evolved to attack a higher number of susceptible individuals. These different disease modalities highlight the central idea that there are different immunological routes to TB disease, which converge on a disease phenotype characterized by high bacterial load and destruction of the extracellular matrix. The writing is very clear and provides a lot of supportive evidence from population studies and the recent clinical trials of novel TB vaccines, like M72 and H56. However, there are areas to support the thesis that have been described only in broad strokes, including the impact of host and Mtb genetic heterogeneity on this selection, and the alternative model that there are likely different TB diseases (as opposed to different routes to the same disease), as described by several groups advancing the concept of heterogeneous TB endotypes. I expand on specific points below.

      Strengths:

      The idea that Mtb evolved to both increase transmission (and possible commensalism with humans) with low rates of reactivation is intriguing. The heterogeneous TB phenotypes in the collaborative cross model (PMID: 35112666) support this idea, where some genetic backgrounds can tolerate a high bacterial load with minimal pathology, while others show signs of pathogenesis with low bacterial loads. This supports the idea that the underlying host state, driven by a number of factors like genetics and nutrition, is likely to explain whether someone will co-exist with Mtb without pathology, or progress to disease. I particularly enjoyed the discussion of the protective advantages provided by Mtb infection, which may have rewired the human immune system to provide protection against heterologous pathogens- this is supported by recent studies showing that Mtb infection provides moderate protection against SARS-CoV-2 (PMID: 35325013, and 37720210), and may have applied to other viruses that are likely to have played a more significant role in the past in the natural selection of Homo Sapiens.

      We thank the reviewer for their positive comments, and also for pointing out work that we have overlooked citing previously. We now discuss and cite the work above as suggested

      Modeling from Marcel Behr and colleagues (PMID: 31649096) indeed suggests that there are at least TB clinical phenotypes that likely mirror the two distinct phases of Mtb co-evolution with humans. Most of the TB disease progression occurs rapidly (within 1-2 years of exposure), and the rest are slow cases of reactivation over time. I enjoyed the discussion of the difference between the types of immune hits needed to progress to disease in the two scenarios, where you may need severe immune hits for rapid progression, a phenotype that likely evolved after the Neolithic transition to larger human populations. On the other hand, a series of milder immune events leading to reactivation after a long period of asymptomatic infection likely mirrors slow progression in the hunter-gatherer communities, to allow for prolonged transmission in scarce populations. Perhaps a clearer analysis of these models would be helpful for the reader.

      We agree that we did not present these concepts in as much detail as we should, and so we now discuss this more on lines 81 – 83 and 184 - 187)

      Weaknesses:

      The discussion of genetic heterogeneity is limited and only discusses evidence from MSMD studies. Genetics is an important angle to consider in the co-evolution of Mtb and humans. There is a large body of literature on both host and Mtb genetic associations with TB disease. The very fact that host variants in one population do not necessarily cross-validate across populations is evidence in support of population-specific adaptations. Specific Mtb lineages are likely to have co-evolved with distinct human populations. A key reference is missing (PMID: 23995134), which shows that different lineages co-evolved with human migrations. Also, meta-analyses of human GWAS studies to define variants associated with TB are very relevant to the topic of co-evolution (e.g., PMID: 38224499). eQTL studies can also highlight genetic variants associated with regulating key immune genes involved in the response to TB. The authors do mention that Mtb itself is relatively clonal with ~2K SNPs marking Mtb variation, much of which has likely evolved under the selection pressure of modern antibiotics. However, some of this limited universe of variants can still explain co-adaptations between distinct Mtb lineages and different human populations, as shown recently in the co-evolution of lineage 2 with a variant common in Peruvians (PMID: 39613754).

      We thank the reviewer for these comments and agree we failed to cite and discuss the work from Sebastian Gagneux’s group on co-migration, which we now discuss. We include a new paragraph discussing co-evolution as suggested on lines 145 – 155 and 218 -220 , citing the work proposed, which we agree enhances the arguments about co-evolution.

      Although the examples of anti-TNF and anti-PD1 treatments are relevant as drivers of TB in limited clinical contexts, the bigger picture is that they highlight major distinct disease endotypes. These restricted examples show that TB can be driven by immune deficiency (as in the case of anti-TNF, HIV, and malnutrition) or hyperactivation (as in the case of anti-PD1 treatment), but there are still certainly many other routes leading to immune suppression or hyperactivation. Considering the idea of hyper-activation as a TB driver, the apparent higher rate of recurrence in the H56 trial referenced in the review is likely due to immune hyperactivation, especially in the context of residual bacteria in the lung. These different TB manifestations (immune suppression vs immune hyperactivation) mirror TB endotypes described by DiNardo et al (PMID: 35169026) from analysis of extensive transcriptomic data, which indicate that it's not merely different routes leading to the same final endpoint of clinical disease, but rather multiple different disease endpoints. A similar scenario is shown in the transcriptomic signatures underlying disease progression in BCG-vaccinated infants, where two distinct clusters mirrored the hyperactivation and immune suppression phenotypes (PMID: 27183822). A discussion of how to think about translating the extensive information from system biology into treatment stratification approaches, or adjunct host-directed therapies, would be helpful.

      We agree with the points made and that the two publications above further enhance the paper. We have added discussion of the different disease endpoints on line 65 - 67, the evidence regarding immune herpeactivation versus suppression in the vaccination study on lines 162 - 164, and expanded on the translational implications on lines 349 – 352.

      Reviewer #3 (Public review):

      Summary:

      This perspective article by Reichmann et al. highlights the importance of moving beyond the search for a single, unified immune mechanism to explain host-Mtb interactions. Drawing from studies in immune profiling, host and bacterial genetics, the authors emphasize inconsistencies in the literature and argue for broader, more integrative models. Overall, the article is thought-provoking and well-articulated, raising a concept that is worth further exploration in the TB field.

      Strengths:

      Timely and relevant in the context of the rapidly expanding multi-omics datasets that provide unprecedented insights into host-Mtb interactions.

      Weaknesses (Minor):

      Clarity on the notion of a "unified mechanism". It remains unclear whether prior studies explicitly proposed a single unifying immunological model. While inconsistencies in findings exist, they do not necessarily demonstrate that earlier work was uniformly "single-minded". Moreover, heterogeneity in TB has been recognized previously (PMIDs: 19855401, 28736436), which the authors could acknowledge.

      We accept this point and have toned down the language, acknowledging that we are expanding on an argument that others have made, whilst focusing on the implications for the systems immunology era, and cite the previous work as suggested.

      Evolutionary timeline and industrial-era framing. The evolutionary model is outdated. Ancient DNA studies place the Mtb's most recent common ancestor at ~6,000 years BP (PMIDs: 25141181; 25848958). The Industrial Revolution is cited as a driver of TB expansion, but this remains speculative without bacterial-genomics evidence and should be framed as a hypothesis. Additionally, the claim that Mtb genomes have been conserved only since the Industrial Revolution (lines 165-167) is inaccurate; conservation extends back to the MRCA (PMID: 31448322).

      Our understanding is that the evolutionary timeline is not fully resolved, with conflicting evidence proposing different dates. The ancient DNA studies giving a timeline of 6,000 years seem to oppose the evidence of evidence of Mtb infection of humans in the middle east 10,000 years ago, and other estimates suggesting 70,000 years. Therefore, we have cited the work above and added a sentence highlighting that different studies propose different timelines. We would propose the industrial revolution created the ideal societal conditions for the expansion of TB, and this would seem widely accepted in the field, but have added a proviso as suggested. We did not intent to claim that Mtb genomes have been conserved since the industrial revolution, the point we were making is that despite rapid expansion within human populations, it has still remained conserved. We therefore have revised our discussion of the conservation of the Mtb genomes on lines and 72 – 74, 81 – 83 and 185 – 190.

      Trained immunity and TB infection. The treatment of trained immunity is incomplete. While BCG vaccination is known to induce trained immunity (ref 59), revaccination does not provide sustained protection (ref 8), and importantly, Mtb infection itself can also impart trained immunity (PMID: 33125891). Including these nuances would strengthen the discussion.

      We have refined this section. We did cite PMID: 33125891 in the original submission but have changed the wording to emphasise the point on line …

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Abstract

      Line 30: What is an immunological route? Suggest

      ”...host-pathogen interaction, with diverse immunological processes leading to TB disease (10%) or stable lifelong association or elimination. We suggest these alternate relationships result from the prolonged co-evolution of the pathogen with humans and may even confer a survival advantage in the 90% of exposures that do not progress to disease.”

      Thank you, we have reworded the abstract along the lines suggested above, but not identically to allow for other reviewer comments.

      Introduction

      Ln 43: It is misleading to suggest that the study of TB was the leading influence in establishing the Koch's postulates framework. Many other infections were involved, and Jacob Henle, one of Koch's teachers, is credited with the first clear formulation (see Evans AS. 1976 THE YALE JOURNAL OF BIOLOGY AND MEDICIN PMID: 782050).

      We have downplayed the language, stating that TB “contributed” to the formulation if Koch’s postulated.

      Ln 46: While the review rightly emphasises intracellular infection in macrophages, the importance and abundance of extracellular bacilli should not be ignored, particularly in transmission and in cavities.

      We agree, and have added text on the importance of extracellular bacteria and transmission.

      Ln: 56: This is misleading as primary disease prevention is implied, whereas the vaccine was given to individuals presumed to be already infected (TST or IGRA positive). Suggest ..."reduces by 50% progression to overt TB disease when given to those with immunological evidence of latent infection.

      Thank you, edit made as suggested

      Ln 62: Not sure why it is urgent. Suggest "high priority".

      Wording changed as suggested.

      Figure 1 needs clarification. The colour scale appears to signify the strength or vigour of the immune response so that disease is associated with high (orange/red) or low (green/blue) activity. The arrows seem to imply either a sequence or a route map when all we really have is an association with a plausible mechanistic link. They might also be taken to imply a hierarchy that is not appropriate. I'm not sure that the X-rays and arrows add anything, and the rectangle provides the key information on its own. Clarify please.

      We have clarified the figure legend. We feel the X-rays give the clinical context, and so have kept them, and now state in the legend that this is highlighting that there are diverse pathways leading to active disease to try to emphasise the point the figure is illustrating.

      Ln 149-157: I agree that the current dogma is that overt pulmonary disease is required to spread Mtb and fuel disease prevalence. It is vitally important to distinguish the spread of the organism from the occurrence of disease (which does not, of itself, spread). However, both epidemiological (e.g. Ryckman TS, et al. 2022Proc Natl Acad Sci U S A:10.1073/pnas.2211045119) and recent mechanistic (Dinkele R, et al. 2024iScience:10.1016/j.isci.2024.110731, Patterson B, et al. 2024Proc Natl Acad Sci U S A:10. E1073/pnas.2314813121, Warner DF, et al. 2025Nat Rev Microbiol:10.1038/s41579-025-01201-x) studies indicate the importance of asymptomatic infections, and those associated with sputum positivity have recently been recognised by WHO. I think it will be important to acknowledge the importance of this aspect and consider how immune responses may or may not contribute. I regard the view that Mtb is an obligate pathogen, dependent on overt pTB for transmission, as needing to be reviewed.

      We agree that we did not give sufficient emphasis to the emerging evidence on asymptomatic infections, and that this may play an important part in transmission in high incidence settings. We now include a discussion on this, and citation of the papers above, on lines 168 – 170.

      Ln 159: The terms colonise and colonisation are used, without a clear definition, several times. My view is that both refer to the establishment and replication of an organism on or within a host without associated damage. Where there is associated damage, this is often mediated by immune responses. In this header, I think "establishment in humanity" would be appropriate.

      We agree with this point and have changed the header as suggested, and clarified our meaning when we use the term colonisation, which the reviewer correctly interprets.

      Ln 181-: I strongly support the view that Mtb has contributed to human selection, even to the suggestion that humanity is adapted to maintain a long-term relationship with Mtb

      Thank you, and we have expanded on this evidence as suggested by other reviewers.

      Ln 189: improved.

      Apologies, typo corrected.

      Figure 2: I was also confused by this. The x-axis does not make sense, as a single property should increase. Moreover, does incidence refer to incidence in individuals with that specific balance of resistance and susceptibility, or contribution to overall global incidence - I suspect the latter (also, prevalence would make more sense). At the same time, the legend implies that those with high resistance to colonisation will be infrequent in the population, suggesting that the Y axis should be labelled "frequency in human population". Finally, I can't see what single label could apply to the X axis. While the implication that the majority of global infections reflect a balance between the resistance and susceptibilities is indicated, a frequency distribution does not seem an appropriate representation.

      The reviewer is correct that the X axis is aiming to represent two variables, which is not logical, and so we have completely changed this figure to a simple one that we hope makes the point clearly and have amended the legend appropriately. We are aiming to highlight the selective pressures of Mtb on the human population over millennia.

      Ln 244: Immunological failure - I agree with the statement but again find the figure (3) unhelpful. Do we start or end in the middle? Is the disease the outside - if so, why are different locations implied? The notion of a maze has some value, but the bacteria should start and finish in the same place by different routes.

      We are attempting to illustrate the concept that escape from host immunological control can occur through different mechanisms. As this comment was just from one reviewer, we have left the figure unchanged but have expanded the legend to try to make the point that this is just a conceptual illustration of multiple routes to disease.

      Ln 262 onward: I broadly agree with the points made about omic technologies, but would wish to see major emphasis on clear phenotyping of cases. There is something of a contradiction in the review between the emphasis on the multiplicity of immunological processes leading ultimately to disease and the recommendation to analyse via omics, which, in their most widely applied format, bundle these complexities into analyses of the humoral and cellular samples available in blood. Admittedly, the authors point out opportunities for 3-dimensional and single-cell analyses, but it is difficult to see where these end without extrapolation ad infinitum.

      We totally agree that clear phenotyping of infection is critical, and expand on this further on lines 307 - 309.

      Reviewer #2 (Recommendations for the authors):

      I suggest expanding on the genetic determinants of Mtb/host co-evolution.

      Thank you, we have now expanded on these sections as suggested.

      Reviewer #3 (Recommendations for the authors):

      We are in an era of exploding large-scale datasets from multi-omics profiling of Mtb and host interactions, offering an unprecedented lens to understand the complexity of the host immune response to Mtb-a pathogen that has infected human populations for thousands of years. The guiding philosophy for how to interpret this tremendous volume of data and what models can be built from it will be critical. In this context, the perspective article by Reichmann et al. raises an interesting concept: to "avoid unified immune mechanisms" when attempting to understand the immunology underpinning host-Mtb interactions. To support their arguments, the authors review studies and provide evidence from immune profiling, host and bacterial genetics, and showcase several inconsistencies. Overall, this perspective article is well articulated, and the concept is worthwhile for further exploration. A few comments for consideration:

      Clarity on the notion of a "unified mechanism". Was there ever a single, clearly proposed unified immunological mechanism? For example, in lines 64-65, the authors criticize that almost all investigations into immune responses to Mtb are based on the premise that a unifying disease mechanism exists. However, after reading the article, it was not clear to me how previous studies attempted to unify the model or what that unifying mechanism was. While inconsistencies in findings certainly exist, they do not necessarily indicate that prior work was guided by a unified framework. I agree that interpreting and exploring data from a broader perspective is valuable, but I am not fully convinced that previous studies were uniformly "single-minded". In fact, the concept of heterogeneity in TB has been previously discussed (e.g., PMIDs: 19855401, 28736436).

      We accept this point, and that we have overstated the argument and not acknowledged previous work sufficiently. We now downplay the language and cite the work as proposed.

      However, we would propose that essentially all published studies imply that single mechanisms underly development of disease. The authors are not aware of any manuscript that concludes “Therefore, xxxx pathway is one of several that can lead to TB disease”, instead they state “Therefore, xxxx pathway leads to TB disease”. The implication of this language is that the mechanism described occurs in all patients, whilst in fact it likely only is involved in a subset. We have toned down the language and expand on this concept on line 268 – 270.

      Evolutionary timeline and industrial-era framing. The evolutionary model needs updating. The manuscript cites a "70,000-year" origin for Mtb, but ancient-DNA studies place the most recent common ancestor at ~6,000 years BP (PMIDs: 25141181; 25848958). The Industrial Revolution is invoked multiple times as a driver of TB expansion, yet the magnitude of its contribution remains debated and, to my knowledge, lacks direct bacterial-genomics evidence for causal attribution; this should be framed as a hypothesis rather than a conclusion. In addition, the statement in lines 165-167 is inaccurate: at the genome level, Mtb has remained highly conserved since its most recent common ancestor-not specifically since the Industrial Revolution (PMID: 31448322).

      We accept these points and have made the suggested amendments, as outlined in the public responses. Our understanding is that the evidence about the most common ancestor is controversial; if the divergence of human populations occurred concurrently with Mtb, then this must have been significantly earlier than 6,000 years ago, and so there are conflicting arguments in this domain.

      Trained immunity and TB infection. The discussion of trained immunity could be expanded. Reference 59 suggests the induction of innate immune training, but reference 8 reports that revaccination does not confer protection against sustained TB infection, indicating that at least "re"-vaccination may not enhance protection. Furthermore, while BCG is often highlighted as a prototypical inducer of trained immunity, real-world infection occurs through Mtb itself. Importantly, a later study demonstrated that Mtb infection can also impart trained immunity (PMID: 33125891). Integrating these findings would provide a more nuanced view of how both vaccination and infection shape innate immune training in the TB context.

      We thank the reviewer for these suggestions and have edited the relevant section to include these studies.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public reviews:

      Reviewer #1 (Public review):

      In this important study, the authors characterized the transformation of neural representations of olfactory stimuli from the primary sensory cortex to multisensory regions in the medial temporal lobe and investigated how they were affected by non-associative learning. The authors used high-density silicon probe recordings from five different cortical regions while familiar vs. novel odors were presented to a head-restrained mouse. This is a timely study because unlike other sensory systems (e.g., vision), the progressive transformation of olfactory information is still poorly understood. The authors report that both odor identity and experience are encoded by all of these five cortical areas but nonetheless some themes emerge. Single neuron tuning of odor identity is broad in the sensory cortices but becomes narrowly tuned in hippocampal regions. Furthermore, while experience affects neuronal response magnitudes in early sensory cortices, it changes the proportion of active neurons in hippocampal regions. Thus, this study is an important step forward in the ongoing quest to understand how olfactory information is progressively transformed along the olfactory pathway.

      The study is well-executed. The direct comparison of neuronal representations from five different brain regions is impressive. Conclusions are based on single neuronal level as well as population level decoding analyses. Among all the reported results, one stands out for being remarkably robust. The authors show that the anterior olfactory nucleus (AON), which receives direct input from the olfactory bulb output neurons, was far superior at decoding odor identity as well as novelty compared to all the other brain regions. This is perhaps surprising because the other primary sensory region - the piriform cortex - has been thought to be the canonical site for representing odor identity. A vast majority of studies have focused on aPCx, but direct comparisons between odor coding in the AON and aPCx are rare. The experimental design of this current study allowed the authors to do so and the AON was found to convincingly outperform aPCx. Although this result goes against the canonical model, it is consistent with a few recent studies including one that predicted this outcome based on anatomical and functional comparisons between the AON-projecting tufted cells vs. the aPCx-projecting mitral cells in the olfactory bulb (Chae, Banerjee et. al. 2022). Future experiments are needed to probe the circuit mechanisms that generate this important difference between the two primary olfactory cortices as well as their potential causal roles in odor identification.

      The authors were also interested in how familiarity vs. novelty affects neuronal representation across all these brain regions. One weakness of this study is that neuronal responses were not measured during the process of habituation. Neuronal responses were measured after four days of daily exposure to a few odors (familiar) and then some other novel odors were introduced. This creates a confound because the novel vs. familiar stimuli are different odorants and that itself can lead to drastic differences in evoked neural responses. Although the authors try to rule out this confound by doing a clever decoding and Euclidian distance analysis, an alternate more straightforward strategy would have been to measure neuronal activity for each odorant during the process of habituation.

      Reviewer #2 (Public review):

      This manuscript investigates how olfactory representations are transformed along the cortico-hippocampal pathway in mice during a non-associative learning paradigm involving novel and familiar odors. By recording single-unit activity in several key brain regions (AON, aPCx, LEC, CA1, and SUB), the authors aim to elucidate how stimulus identity and experience are encoded and how these representations change across the pathway.

      The study addresses an important question in sensory neuroscience regarding the interplay between sensory processing and signaling novelty/familiarity. It provides insights into how the brain processes and retains sensory experiences, suggesting that the earlier stations in the olfactory pathway, the AON aPCx, play a central role in detecting novelty and encoding odor, while areas deeper into the pathway (LEC, CA1 & Sub) are more sparse and encodes odor identity but not novelty/familiarity. However, there are several concerns related to methodology, data interpretation, and the strength of the conclusions drawn.

      Strengths:

      The authors combine the use of modern tools to obtain high-density recordings from large populations of neurons at different stages of the olfactory system (although mostly one region at a time) with elegant data analyses to study an important and interesting question.

      Weaknesses:

      (1) The first and biggest problem I have with this paper is that it is very confusing, and the results seem to be all over the place. In some parts, it seems like the AON and aPCx are more sensitive to novelty; in others, it seems the other way around. I find their metrics confusing and unconvincing. For example, the example cells in Figure 1C show an AON neuron with a very low spontaneous firing rate and a CA1 with a much higher firing rate, but the opposite is true in Figure 2A. So, what are we to make of Figure 2C that shows the difference in firing rates between novel vs. familiar odors measured as a difference in spikes/sec. This seems nearly meaningless. The authors could have used a difference in Z-scored responses to normalize different baseline activity levels. (This is just one example of a problem with the methodology.)

      We appreciate the reviewer’s concerns regarding clarity and methodology. It is less clear why all neurons in a given brain area should have similar firing rates. Anatomically defined brain areas typically comprise of multiple cell types, which can have diverse baseline firing rates. Since we computed absolute firing rate differences per neuron (i.e., novel vs. familiar odor responses within the same neuron), baseline differences across neurons do not have a major impact.

      The suggestion to use Z-scores instead of absolute firing rate differences is well taken. However, Z-scoring assumes that the underlying data are normally distributed, which is not the case in our dataset. Specifically, when analyzing odor-evoked firing rates on a per-neuron basis, only 4% of neurons exhibit a normal distribution. In cases of skewed distributions, Z-scoring can distort the data by exaggerating small variations, leading to misleading conclusions. We acknowledge that different analysis methods exist, we believe that our chosen approach best reflects the properties of the dataset and avoids potential misinterpretations introduced by inappropriate normalization techniques.

      (2) There are a lot of high-level data analyses (e.g., decoding, analyzing decoding errors, calculating mutual information, calculating distances in state space, etc.) but very little neural data (except for Figure 2C, and see my comment above about how this is flawed). So, if responses to novel vs. familiar odors are different in the AON and aPCx, how are they different? Why is decoding accuracy better for novel odors in CA1 but better for familiar odors in SUB (Figure 3A)? The authors identify a small subset of neurons that have unusually high weights in the SVM analyses that contribute to decoding novelty, but they don't tell us which neurons these are and how they are responding differently to novel vs. familiar odors.

      We performed additional analyses to address the reviewer’s feedback (Figures 2C-E and lines 118-132) and added more single-neuron data (Figures 1, S3 and S4).

      (3) The authors call AON and aPCx "primary sensory cortices" and LEC, CA1, and Sub "multisensory areas". This is a straw man argument. For example, we now know that PCx encodes multimodal signals (Poo et al. 2021, Federman et al., 2024; Kehl et al., 2024), and LEC receives direct OB inputs, which has traditionally been the criterion for being considered a "primary olfactory cortical area". So, this terminology is outdated and wrong, and although it suits the authors' needs here in drawing distinctions, it is simplistic and not helpful moving forward.

      We appreciate the reviewer’s concern regarding the classification of brain regions as “primary sensory” versus “multisensory.” Of note, the cited studies (Poo et al., 2021; Federman et al., 2024; Kehl et al., 2024) focus on posterior PCx (pPCx), while our recordings were conducted in very anterior section of anterior PCx. The aPCx and pPCx have distinct patterns of connectivity, both anatomically and functionally. To the best of our knowledge, there is no evidence for multimodal responses in aPCx, whereas there is for LEC, CA1 and SUB. Furthermore, our distinction is not based on a connectivity argument, as the reviewer suggests, but on differences in the α-Poisson ratio (Figure 1E and F).

      To avoid confusion due to definitions of what constitutes a “primary sensory” region, we adopted a more neutral description throughout the manuscript.

      (4) Why not simply report z-scored firing rates for all neurons as a function of trial number? (e.g., Jacobson & Friedrich, 2018). Figure 2C is not sufficient.

      Regarding z-scores, please see response to 1). We further added a figure showing responses of all neurons to novel stimuli (using ROC instead of z-scoring, as described previously (e.g. Cohen et al. Nature 2012). We added the following figure to the supplementary for the completeness of the analysis (S2E).

      For example, in the Discussion, they say, "novel stimuli caused larger increases in firing rates than familiar stimuli" (L. 270), but what does this mean?

      This means that on average, the population of neurons exhibit higher firing rates in response to novel odors compared to familiar ones.

      Odors typically increase the firing in some neurons and suppress firing in others. Where does the delta come from? Is this because novel odors more strongly activate neurons that increase their firing or because familiar odors more strongly suppress neurons?

      We thank the reviewer for this valuable feedback and extended the characterization of firing rate properties, including a separate analysis of neurons i) significantly excited by odorants, ii) significantly inhibited by odorants and iii) not responsive to odorants. We added the analysis and corresponding discussion to the main manuscript (Figures 2C-E and lines 118-132)

      (5) Lines 122-124 - If cells in AON and aPCx responded the same way to novel and familiar odors, then we would say that they only encode for odor and not at all for experience. So, I don't understand why the authors say these areas code for a "mixed representation of chemical identity and experience." "On the other hand," if LEC, CA1, and SUB are odor selective and only encode novel odors, then these areas, not AON and aPCx, are the jointly encoding chemical identity and experience. Also, I do not understand why, here, they say that AON and PCx respond to both while LEC, CA1, and SUB were selective for novel stimuli, but the authors then go on to argue that novelty is encoded in the AON and PCx, but not in the LEC, CA1, and SUB.

      We appreciate the reviewer’s request for clarification. Throughout the brain areas we studied, odorant identity and experience can be decoded. However, the way information is represented is different between regions. We acknowledge that that “mixed” representation is a misleading term and removed it from the manuscript.

      In AON and aPCx, neurons significantly respond to both novel and familiar odors. However, the magnitude of their responses to novel and familiar odors is sufficiently distinct to allow for decoding of odor experience (i.e., whether an odor is novel or familiar). Moreover, novelty engages more neurons in encoding the stimulus (Figure 2D). In neural space, the position of an odor’s representation in AON and aPCx shifts depending on whether it is novel or familiar, meaning that experience modifies the neural representation of odor identity. This suggests that in these regions the two representations are intertwined.

      In contrast, some neurons in LEC, CA1, and SUB exhibit responses to novel odors, but few neurons respond to familiar odors at all. This suggests a more selective encoding of novelty.

      (6) Lines 132-140 - As presented in the text and the figure, this section is poorly written and confusing. Their use of the word "shuffled" is a major source of this confusion, because this typically is the control that produces outcomes at the chance level. More importantly, they did the wrong analysis here. The better and, I think, the only way to do this analysis correctly is to train on some of the odors and test on an untrained odor (i.e., what Bernardi et al., 2021 called "cross-condition generalization performance"; CCGP).

      We appreciate the feedback and thank the reviewer for the recommendation to implement cross-condition generalization performance (CCGP) as used in Bernardi et al., 2020. We acknowledge that the term "shuffled" may have caused confusion, as it typically refers to control analyses producing chance-level outcomes. In our case, by "shuffling" we shuffled the identity of novel and familiar odors to assess how much the decoder relies on odor identity when distinguishing novelty. This test provided insight into how novelty-based structure exists within neural activity beyond random grouping but does not directly assess generalization.

      As suggested, we used CCGP to measure how well novelty-related representations generalize across different odors. Our findings show that in AON and aPCx, novelty-related information is indeed highly generalizable, supporting the idea that these regions encode novelty in a less odor-selective manner (Figure 2K).

      Reviewer #3 (Public review):

      In this manuscript, the authors investigate how odor-evoked neural activity is modulated by experience within the olfactory-hippocampal network. The authors perform extracellular recordings in the anterior olfactory nucleus (AON), the anterior piriform (aPCx) and lateral entorhinal cortex (LEC), the hippocampus (CA1), and the subiculum (SUB), in naïve mice and in mice repeatedly exposed to the same odorants. They determine the response properties of individual neurons and use population decoding analyses to assess the effect of experience on odor information coding across these regions.

      The authors' findings show that odor identity is represented in all recorded areas, but that the response magnitude and selectivity of neurons are differentially modulated by experience across the olfactory-hippocampal pathway.

      Overall, this work represents a valuable multi-region data set of odor-evoked neural activity. However, limitations in the interpretability of odor experience of the behavioral paradigm, and limitations in experimental design and analysis, restrict the conclusions that can be drawn from this study.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Some suggestions, in no particular order, to further improve the manuscript:

      (1) The example neuronal responses for CA1 and SUB in Figure 1 are not very inspiring. To my eyes, the odor period response is not that different from the baseline period. In general, a thorough characterization of firing rate properties during the odor period between the different brain regions would be informative.

      We thank the reviewer for this valuable feedback. We have replaced the example neurons from CA1 and SUB in Figure 1C. We further extended the characterization of firing rate properties, including a separate analysis of neurons i) significantly excited by odorants, ii) significantly inhibited by odorants and iii) not responsive to odorants. We added the analysis and corresponding discussion to the main manuscript (Figures 2C-E and lines 118-132)

      (2) For the summary in Figure 1, why not show neuronal responses as z-scored firing rates as opposed to auROC?

      We chose to use auROC instead of z-scored firing rates due to the non-normality of the dataset, which can distort results when using z-scores. Specifically, z-scoring can exaggerate small deviations in neurons with low responsiveness, potentially leading to misleading conclusions. auROC provides a more robust measure of response change that is less sensitive to these distortions because it does not assume any specific distribution. This approach has been used previously (e.g. Cohen et al. 2012, Nature).

      (3) To study novelty, the authors presented odorants that were not used during four days of habituation. But this design makes it hard to dissociate odor identity from novelty. Why not track the response of the same odorants during the habituation process itself?

      We respectfully disagree with the argument that using different stimuli as novel and familiar constitutes a confound in our analysis. In our study, we used multiple different, structurally dissimilar single molecule chemicals which were randomly assigned to novel and familiar categories in each animal. If individual stimuli did cause “drastic differences in evoked neural responses”, these would be evenly distributed between novel and familiar stimuli. It is therefore extremely unlikely that the clear differences we observed between novel and familiar conditions and between brain areas can be attributed to the contribution of individual stimuli, in particular given our analyses was performed at the population level. In fact, we observed that responses between novel and familiar conditions were qualitatively very similar in the short time window after odor onset (Figure 1G and H).

      Importantly, the goal of this study was to investigate the impact of long-term habituation over more than 4 days, rather than short term habituation during one behavioral session. However, tracking the activity of large numbers of neurons across multiple days presents a significant technical challenge, due to the difficulty of identifying stable single-unit recordings over extended periods of time with sufficient certainty. Tools that facilitate tracking have recently been developed (e.g. Yuan AX et al., Elife. 2024) and it will be interesting to apply them to our dataset in the future.

      (4) Since novel odors lead to greater sniffing and sniffing strongly influences firing rates in the olfactory system, the authors decided to focus on a 400 ms window with similar sniffing rates for both novel vs. familiar odors. Although I understand the rationale for this choice, I worry that this is too restrictive, and it may not capture the full extent of the phenomenology.

      Could the authors model the effect of sniffing on firing rates of individual neurons from the data, and then check whether the odor response for novel context can be fully explained just by increased sniffing or not?

      It is an interesting suggestion to extend the window of analysis and observe how responses evolve with sniffing (and other behavioral reactions). To address this, we added an additional figure to the supplementary material, showing the mean responses of all neurons to novel stimuli during the entire odor presentation window (Fig. S1B).

      As suggested, we further created a Generalized Linear Model (GLM) for the entire 2s odor stimulation period, incorporating sniffing and novelty as independent variables. As expected, sniffing had a dominant impact on firing rate in all brain areas. A smaller proportion of neurons was modulated by novelty or by the interaction between novelty x breathing, suggesting the entrainment of neural activity by sniffing during the response to novel odors. These results support our decision to focus the analysis on the early 400ms window in order to dissociate the effects of novelty and behavioral responses. Taken together, our results suggest that odorant responses are modulated by novelty early during odorant processing, whereas at later stages sniffing becomes the predominant factor driving firing (Figure S2C-D).

      (5) The authors conclude that aPCx has a subset of neurons dedicated to familiar odors based on the distribution of SVM weights in Figure 3D. To me, this is the weakest conclusion of the paper because although significant, the effect size is paltry; the central tendencies are hardly different for the two conditions in aPCx. Could the authors show the PSTHs of some of these neurons to make this point more convincing?

      We appreciate the reviewer’s concern regarding the effect size. To strengthen our conclusion, we now include PSTHs of representative neurons in the least 10% and best 10% of neuronal population based on the SVM analysis (Figures S3 and S4). We hope this provides more clarity and support for the interpretation that there is a subset of neurons in aPCx that show greater sensitivity to familiar odors, despite the relatively modest central tendency differences.

      In the revised manuscript, we discuss the effect size more explicitly in the text to provide context for its significance (lines 193 - 195).

      Reviewer #2 (Recommendations for the authors):

      (1) The authors only talk about "responsive" neurons. Does this include neurons whose activity increases significantly (activated) and neurons whose activity decreases (suppressed)?

      Yes, the term "responsive" refers to neurons whose activity either increases significantly (excited) or decreases (inhibited) in response to the odor stimuli. We performed additional analyses to characterize responses separately for the different groups (Figure 2C-E and lines 118-132).

      (2) Line 54 - The Schoonover paper doesn't show that cells lose their responses to odors, but rather that the population of cells that respond to odors changes with time. That is, population responses don't become more sparse

      The fact that “the population of cells that respond to odors changes with time”, implies that some neurons lose their responsiveness (e.g. unit 2 in Figure 1 of Schoonover et al., 2021), while others become responsive (e.g. unit 1 in Figure 1 of Schoonover et al., 2021). Frequent responses reduce drift rate (Figure 4 of Schoonover et al., 2021), thus fewer neurons loose or gain responsiveness. We have revised the manuscript to clarify this.

      (3) Line 104 - "Recurrent" is incorrectly used here. I think the authors mean "repeated" or something more like that.

      Thank you for pointing this out. We replaced "recurrent" with "repeated".

      (4) Figure 3D - What is the scale bar here?

      We apologize for the accidental omission. The scale bar was be added to Figure 3D in the revised version of the manuscript.

      (5) Line 377 - They say they lowered their electrodes to "200 um/s per second." This must be incorrect. Is this just a typo, or is it really 200 um/s, because that's really fast?

      Thank you for pointing this out. It was 20 to 60 um/s, the change has been made in the manuscript.

      (6) Line 431: The authors say they used auROC to calculate changes in firing rates (which I think is only shown in Figure 1D). Note that auROC measures the discriminability of two distributions, not the strength or change in the strength of response.

      Indeed we used auROC to measure the discriminability of firing between baseline and during stimulus response. We have corrected the wording in the methods.

      (7) Figure 1B: The anatomical locations of the five areas they recorded from are straightforward, and this figure is not hugely helpful. However, the reader would benefit tremendously by including an experimental schematic. As is, we needed to scour the text and methods sections to understand exactly what they did when.

      We thank the reviewer for this suggestion. We included an experimental schematic in the supplementary material.

      (8) Figure 1F(left): This plot is much less useful without showing a pre-odor window, even if only times after the odor onset were used for calculation alpha

      We appreciate this concern, however the goal of Figure 1F is to illustrate the meaning of the alpha value itself. We chose not to include a pre-odor window comparison to avoid confusing the reader.

      (9) Figure 2A: What are the bar plots above the raster plots? Are these firing rates? Are the bars overlaid or stacked? Where is the y-axis scale bar?

      The bar plots above the raster plots represent a histogram of the spike count/trials over time, with a bin width of 50 ms. These bars are overlaid on the raster plot. We will include a y-axis scale bar in the revised figure to clarify the presentation.

      (10) Figure 4G: This makes no sense. First, the Y axis is supposed to measure standard deviation, but the axis label is spikes/s. Second, if responses in the AON are much less reliable than responses in "deeper" areas, why is odor decoding in AON so much better than in the other areas?

      We acknowledge the error in the axis label, and we will correct it to indicate the correct units. AON has a larger response variability but also larger responses magnitudes, which can explain the higher decoding accuracy.

      (11) From the model and text, one predicts that the lifetime sparseness increases along the pathway. The authors should use this metric as well/instead of "odor selectivity" because of problems with arbitrary thresholding.

      We acknowledge that lifetime sparseness, often computed using lifetime kurtosis, can be an informative measure of selectivity. However, we believe it has limitations that make it less suitable for our analysis. One key issue is that lifetime sparseness does not account for the stability of responses across multiple presentations of the same stimulus. In contrast, our odor selectivity measure incorporates trial-to-trial variability by considering responses over 10 trials and assessing significance using a Wilcoxon test compared to baseline. While the choice of a p-value threshold (e.g., 0.05) is somewhat arbitrary, it is a widely accepted statistical convention. Additionally, lifetime sparseness does not account for excitatory and inhibitory responses. For example, if a neuron X is strongly inhibited by odor A, strongly excited by odor B, and unresponsive to odors C and D, lifetime sparseness would classify it as highly selective for odor B, without capturing its inhibitory selectivity for odor A. The lifetime sparseness will be higher than if X was simply unresponsive for A.

      Our odor selectivity measure addresses this by considering both excitation and inhibition as potential responses. Thus, while lifetime sparseness could provide a useful complementary perspective in another type of dataset, it does not fully capture the dynamics of odor selectivity here.

      Author response 1.

      Lifetime Kurtosis distribution per region.

      Reviewer #3 (Recommendations for the authors):

      Main points:

      (1) The authors use a non-associative learning paradigm - repeated odor exposure - to test how experience modulates odor responses along the olfactory-hippocampal pathway. While repeated odor exposure clearly modulates odor-evoked neural activity, the relevance of this modulation and its differential effect across different brain areas are difficult to assess in the absence of any behavioral read-outs.

      Our experimental paradigm involves a robust, reliable behavioral readout of non-associative learning. Novel olfactory stimuli evoke a well-characterized orienting reaction, which includes a multitude of physiological reactions, including exploratory sniffing, facial movements and pupil dilation (Modirshanechi et al., Trends Neuroscience 2023). In our study, we focused on exploration sniffing.

      Compared to associative learning, non-associative learning might have received less attention. However, it is critically important because it forms the foundation for how organisms adapt to their environment through experience without forming associations. This is highlighted by the fact that non-instrumental stimuli can be remembered in large number (Standing, 1973) and with remarkable detail (Brady et al., 2008). While non-associative learning can thus create vast, implicit memory of stimuli in the environment, it is unclear how stimulus representations reflect this memory. Our study contributes to answering this question. We describe the impact of experience on olfactory sensory representations and reveal a transformation of representations from olfactory cortical to hippocampal structures. Our findings also indicate that sensory responses to familiar stimuli persist within sensory cortical and hippocampal regions, even after spontaneous orienting behaviors habituated. Further studies involving experimental manipulation techniques are needed to elucidate the causal mechanisms underlying the formation of stimulus memory during non-associative learning.

      (2) The authors discuss the olfactory-hippocampal pathway as a transition from primary sensory (AON, aPCx) to associative areas (LEC, CA1, SUB). While this is reasonable, given the known circuit connectivity, other interpretations are possible. For example, AON, aPCx, and LEC receive direct inputs from the olfactory bulb ('primary cortex'), while CA1 and SUB do not; AON receives direct top-down inputs from CA1 ('associative cortex'), while aPCx does not. In fact, the data presented in this manuscript does not appear to support a consistent, smooth transformation from sensory to associative, as implied by the authors (e.g. Figure 4A, F, and G).

      Thank you for this insightful comment. Indeed, there are complexities in the circuitry, and the relationships between different areas are not linear. We believe that AON and aPCx are distinctly different from LEC, CA1 and SUB, as the latter areas have been shown to integrate multimodal sensory information. To avoid confusion due to definitions of what constitutes a “primary sensory” region, we adopted a more neutral description throughout the manuscript. We also removed the term “gradual” to describe the transition of neural representations from olfactory cortical to hippocampal areas.

      (3) The analysis of odor-evoked responses is focused on a 400 ms window to exclude differences in sniffing behavior. This window spans 200 ms before and after the first inhalation after odor onset. Inhalation onset initiates neural odor responses - why do the authors include neural data before inhalation onset?

      The reason to include a brief time window prior to odor onset is to account for what is often called “partical” sniffs. In our experimental setup, odor delivery is not triggered by the animal’s inhalation. Therefore, it can happen that an animal has just begun to inhale when the stimulus is delivered. In this case, the animal is exposed to odorant molecules prior to the first complete inhalation after odor onset. We acknowledge that this limits the temporal resolution of our measurements, but it does not affect the comparison of sensory representations between different brain areas.

      It would also be interesting to explore the effect of sniffing behavior (see point 2) on odor-evoked neural activity.

      Thank you for your comment, we performed additional analysis including a GLM to address this question (Figure S2C-D).

      Minor points:

      (4) Figure 2A represents raster plots for 2 neurons per area - it is unclear how to distinguish between the 2 neurons in the plots.

      Figure 2A shows one example neuron per brain area. Each neurons has two raster plot which indicate responses to either a novel (orange) or a familiar stimulus (blue). We have revised the figure caption for clarity.

      (5) Overall, axes should be kept consistent and labeled in more detail. For example, Figure 2H and I are difficult to compare, given that the y-axis changes and that decoding accuracies are difficult to estimate without additional marks on the y-axis.

      Axes are indeed different, because chance level decoding accuracy is different between those two figures. The decoding between novel and familiar odors has a chance level of 0.5, while chance level decoding odors is 0.1 (there are 10 odors to decode the identity from).

      (6) Some parts of the discussion seem only loosely related to the data presented in this manuscript. For example, the statement that 'AON rather than aPCx should be considered as the primary sensory cortex in olfaction' seems out of context. Similarly, it would be helpful to provide data on the stability of subpopulations of neurons tuned to familiar odors, rather than simply speculate that they could be stable. The authors could summarize more speculative statements in an 'Ideas and Speculation' subsection.

      Thank you for your comment. We appreciate your perspective on our hypotheses. We have revised the discussion accordingly. Specifically, we removed the discussion of stable subpopulations, since we have not performed longitudinal tracking in this study.

      (7) The authors should try to reference relevant published work more comprehensively.

      Thank you for your comment. We attempted to include relevant published work without exceeding the limit for references but might have overseen important contributions. We apologize to our colleagues, whose relevant work might not have been cited.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The main contributions of this paper are: (1) a replication of the surprising prior finding that information about peripherally-presented stimuli can be decoded from foveal V1 (Williams et al 2008), (2) a new demonstration of cross-decoding between stimuli presented in the periphery and stimuli presented at the fovea, (3) a demonstration that the information present in the fovea is based on shape not semantic category, and (4) a demonstration that the strength of foveal information about peripheral targets is correlated with the univariate response in the same block in IPS.

      Strengths:

      The design and methods appear sound, and finding (2) above is new, and importantly constrains our understanding of this surprising phenomenon. The basic effect investigated here is so surprising that even though it has been replicated several times since it was first reported in 2008, it is useful to replicate it again.

      We thank the reviewer for their summary. While we agree with many points, we would like to respectfully push back on the notion that this work is a replication of Williams et al. (2008). What our findings share with those of Williams is a report of surprising decoding at the fovea without foveal stimulation. Beyond this similarity, we treat these as related but clearly separate findings, for the following reasons:

      (1) Foveal feedback, as shown by Williams et al. (2008) and others during fixation, was only observed during a shape discrimination task, specific to the presented stimulus. Control experiments without such a task (or a color-related task) did not show effects of foveal feedback. In contrast, in the present study, the participants’ task was merely to perform saccades towards stimuli, independently of target features. We thus show that foveal feedback can occur independently of a task related to stimulus features. This dissociation demonstrates that our study must be tapping into something different than reported by Williams.

      (2) In a related study, Kroell and Rolfs (2022, 2025) demonstrated a connection between foveal feedback and saccade preparation, including the temporal details of the onset of this effect before saccade execution, highlighting the close link of this effect to saccade preparation. Here we used a very similar behavioral task to capture this saccade-related effect in neural recordings and investigate how early it occurs and what its nature is. Thus, there is a clear motivation for this study in the context of eye movement preparation that is separate from the previous work by Williams.

      (3) Lastly, decoding in the experimental task was positively associated with activity in FEF and IPS, areas that have been reliably linked to saccade preparation. We have now also performed an additional analysis (see our response to Specific point 2 of Reviewer 2) showing that decoding in the control condition did not show the same association, further supporting the link of foveal feedback to saccade preparation. 

      Despite our emphasis on these critical differences in studies, covert peripheral attention, as required by the task in Williams et al., and saccade preparation in natural vision, as in our study, are tightly coupled processes. Indeed, the task in Williams et al. would, during natural vision, likely involve an eye movement to the peripheral target. While speculative, a parsimonious and ecologically valid explanation is that both ours and earlier studies involve eye movement preparation, for which execution is suppressed, however, in studies enforcing fixation (e.g., Williams et al., 2008). We now discuss this idea of a shared underlying mechanism more extensively in the revised manuscript (pg 8 ln 228-240). 

      Weaknesses:

      (1) The paper, including in the title ("Feedback of peripheral saccade targets to early foveal cortex") seems to assume that the feedback to foveal cortex occurs in conjunction with saccade preparation. However, participants in the original Williams et al (2008) paper never made saccades to the peripheral stimuli. So, saccade preparation is not necessary for this effect to occur. Some acknowledgement and discussion of this prior evidence against the interpretation of the effect as due to saccade preparation would be useful. (e.g., one might argue that saccade preparation is automatic when attending to peripheral stimuli.)

      We agree that the effects Williams et al. showed were not sufficiently discussed in the first version of this manuscript. To more clearly engage with these findings we now introduce saccade related foveal feedback (foveal prediction) and foveal feedback during fixation separately in the introduction (pg 2 ln 46-59).

      We further added another section in the discussion called “Foveal feedback during saccade preparation” in which we discuss how our findings are related to Williams et al. and how they differ (pg 8 ln 211-240). 

      As described in our previous response, we believe that our findings go beyond those described by Williams et al. (2008) and others in significant ways. However, during natural vision, the paradigm used by Williams et al. (2008) would likely be solved using an eye movement. Thus, while participants in Williams et al. (2008) did not execute saccades, it appears plausible that they have prepared saccades. Given the fact that covert peripheral attention and saccade preparation are tightly coupled processes (Kowler et al., 1995, Vis Res; Deubel & Schneider, 1996, Vis Res; Montagnini & Castet, 2007, J Vis; Rolfs & Carrasco, 2012, J Neurosci; Rolfs et al., 2011, Nat Neurosci), their results are parsimoniously explained by saccade preparation (but not execution) to a behaviorally relevant target.

      (2) The most important new finding from this paper is the cross-decodability between stimuli presented in the fovea and stimuli presented in the periphery. This finding should be related to the prior behavioral finding (Yu & Shim, 2016) that when a foveal foil stimulus identical to a peripheral target is presented 150 ms after the onset of the peripheral target, visual discrimination of the peripheral target is improved, and this congruency effect occurred even though participants did not consciously perceive the foveal stimulus (Yu, Q., & Shim, W. M., 2016). Modulating foveal representation can influence visual discrimination in the periphery (Journal of Vision, 16(3), 15-15).

      We thank the reviewer for highlighting this highly relevant reference. In the revised version of the manuscript, we now put more emphasis on the finding of cross-decodability (pg 2 ln 60-61). We now also discuss Yu et al.’s finding, which support our conclusion that foveal feedback and direct stimulus presentation share representational formats in early visual areas (pg 9 ln 277-279).

      (3) The prior literature should be laid out more clearly. For example, most readers will not realize that the basic effect of decodability of peripherally-presented stimuli in the fovea was first reported in 2008, and that that original paper already showed that the effect cannot arise from spillover effects from peripheral retinotopic cortex because it was not present in a retinotopic location between the cortical locus corresponding to the peripheral target and the fovea. (For example, this claim on lines 56-57 is not correct: "it remains unknown 1) whether information is fed back all the way to early visual areas".) What is needed is a clear presentation of the prior findings in one place in the introduction to the paper, followed by an articulation and motivation of the new questions addressed in this paper. If I were writing the paper, I would focus on the cross-decodability between foveal and peripheral stimuli, as I think that is the most revealing finding.

      We agree that the structure of the introduction did not sufficiently place our work in the context of prior literature. We have now expanded upon our Introduction section to discuss past studies of saccade- and fixation-related foveal feedback (pg 2 ln 49-59), laying out how this effect has been studied previously. We also removed the claim that "it remains unknown 1) whether information is fed back all the way to early visual areas", where our intention was to specifically focus on foveal prediction. We realize that this was not clear and hence removed this section. Instead, we now place a stronger focus on the cross-decodability finding (pg 2 ln 60-61).

      Reviewer #2 (Public review):

      Summary:

      This study investigated whether the identity of a peripheral saccade target object is predictively fed back to the foveal retinotopic cortex during saccade preparation, a critical prediction of the foveal prediction hypothesis proposed by Kroell & Rolfs (2022). To achieve this, the authors leveraged a gaze-contingent fMRI paradigm, where the peripheral saccade target was removed before the eyes landed near it, and used multivariate decoding analysis to quantify identity information in the foveal cortex. The results showed that the identity of the saccade target object can be decoded based on foveal cortex activity, despite the fovea never directly viewing the object, and that the foveal feedback representation was similar to passive viewing and not explained by spillover effects. Additionally, exploratory analysis suggested IPS as a candidate region mediating such foveal decodability. Overall, these findings provide neural evidence for the foveal cortex processing the features of the saccade target object, potentially supporting the maintenance of perceptual stability across saccadic eye movements.

      Strengths:

      This study is well-motivated by previous theoretical findings (Kroell & Rolfs, 2022), aiming to provide neural evidence for a potential neural mechanism of trans-saccadic perceptual stability. The question is important, and the gaze-contingent fMRI paradigm is a solid methodological choice for the research goal. The use of stimuli allowing orthogonal decoding of stimulus category vs stimulus shape is a nice strength, and the resulting distinctions in decoded information by brain region are clean. The results will be of interest to readers in the field, and they fill in some untested questions regarding pre-saccadic remapping and foveal feedback.

      We thank the reviewer for the positive assessment of our study.

      Weaknesses:

      The conclusions feel a bit over-reaching; some strong theoretical claims are not fully supported, and the framing of prior literature is currently too narrow. A critical weakness lies in the inability to test a distinction between these findings (claiming to demonstrate that "feedback during saccade preparation must underlie this effect") and foveal feedback previously found during passive fixation (Williams et al., 2008). Discussions (and perhaps control analysis/experiments) about how these findings are specific to the saccade target and the temporal constraints on these effects are lacking. The relationship between the concepts of foveal prediction, foveal feedback, and predictive remapping needs more thorough treatment. The choice to use only 4 stimuli is justified in the manuscript, but remains an important limitation. The IPS results are intriguing but could be strengthened by additional control analysis. Finally, the manuscript claims the study was pre-registered ("detailing the hypotheses, methodology, and planned analyses prior to data collection"), but on the OSF link provided, there is just a brief summary paragraph, and the website says "there have been no completed registrations of this project".

      We thank the reviewer for these helpful considerations. We agree that some of the claims were not sufficiently supported by the evidence, and in the revised manuscript, we added nuance to those claims (pg 8 ln 211-240). Furthermore, we now address more directly the distinction between foveal feedback during fixation and foveal feedback (foveal prediction) during saccade preparation. In particular, we now describe the literature about these two effects separately in the introduction (pg 2 ln 46-59), and we have added a new section in the discussion (“Foveal feedback during saccade preparation”) that more thoroughly explains why a passive fixation condition would have been unlikely to produce the same results we find (pg 8 ln 211-227). We also adapted the section about “Saccadic remapping or foveal prediction”, clearly delineating foveal prediction from feature remapping and predictive updating of attention pointers. As recommended by the reviewer, we conducted the parametric modulation analyses on the control condition, strengthening the claim that our findings are saccade-related. These results were added as Supplementary Figure 2 and are discussed in (pg 7 ln 190-191) and (pg 8 ln 224-227). 

      Lastly, we would like to apologize about a mistake we made with the pre-registration. We realized that the pre-registration had indeed not been submitted. We have now done so without changing the pre-registration itself, which can be seen from the recent activity of the preregistration (screenshot attached in the end). After consulting an open science expert at the University of Leipzig, we added a note of this mistake to the methods section of the revised manuscript (pg 10 ln 326-332). We could remove reference to this preregistration altogether, but would keep it at the discretion of the editor. 

      Specifics:

      (1) In the eccentricity-dependent decoding results (Figure 2B), are there any statistical tests to support the results being a U-shaped curve? The dip isn't especially pronounced. Is 4 degrees lower than the further ones? Are there alternative methods of quantifying this (e.g., fitting it to a linear and quadratic function)?

      We statistically tested the U-shaped relationship using a weighted quadratic regression, which showed significant positive curvature for decoding between fovea and periphery in all early visual areas (V1: t(27) = 3.98, p = 0.008, V2: t(27) = 3.03, p = 0.02, V3: t(27)= 2.776, p = 0.025, one-sided). We now report these results in the revised manuscript (pg 5 ln 137-138).

      (2) In the parametric modulation analysis, the evidence for IPS being the only region showing stronger fovea vs peripheral beta values was weak, especially given the exploratory nature of this analysis. The raw beta value can reflect other things, such as global brain fluctuations or signal-to-noise ratio. I would also want to see the results of the same analysis performed on the control condition decoding results.

      We appreciate the reviewer’s suggestion and repeated the same parametric modulation analysis on the control condition to assess the influence of potential confounds on the overall beta values (Supplementary Figure 2). The results show a negative association between foveal decoding and FEF and IPS (likely because eye movements in the control condition lead to less foveal presentation of the stimulus) and a positive association with LO. Peripheral decoding was not associated with significant changes in any of the ROIs, indicating that global brain fluctuations alone are not responsible for the effects reported in the experimental condition. The results of this analysis thus show a specific positive association of IPS activity with the experimental condition, not the control condition, which is in line with the idea that the foveal feedback effect reported in this study may be related to saccade preparation.

      (3) Many of the claims feel overstated. There is an emphasis throughout the manuscript (including claims in the abstract) that these findings demonstrate foveal prediction, specifically that "image-specific feedback during saccade preparation must underlie this effect." To my understanding, one of the key aspects of the foveal prediction phenomenon that ties it closely to trans-saccadic stability is its specificity to the saccade target but not to other objects in the environment. However, it is not clear to what degree the observed findings are specific to saccade preparation and the peripheral saccade target. Should the observers be asked to make a saccade to another fixation location, or simply maintain passive fixation, will foveal retinotopic cortex similarly contain the object's identity information? Without these control conditions, the results are consistent with foveal prediction, but do not definitively demonstrate that as the cause, so claims need to be toned down.

      We fully agree with the reviewer and toned down claims about foveal prediction. We engage with the questions raised by the reviewer more thoroughly in the new discussion section “Foveal feedback during saccade preparation”.

      In addition, we agree that another condition in which subjects make a saccade towards a different location would have been a great addition that we also considered, but due to concerns with statistical power did not add. While including such a condition exceeds the scope of the current study, we included this limitation in the Discussion section (pg 10 ln 316) and hope that future studies will address this question.

      (4) Another critical aspect is the temporal locus of the feedback signal. In the paradigm, the authors ensured that the saccade target object was never foveated via the gaze-contingent procedure and a conservative data exclusion criterion, thus enabling the test of feedback signals to foveal retinotopic cortex. However, due to the temporal sluggishness of fMRI BOLD signals, it is unclear when the feedback signal arrives at the foveal retinotopic cortex. In other words, it is possible that the feedback signal arrives after the eyes land at the saccade target location. This possibility is also bolstered by Chambers et al. (2013)'s TMS study, where they found that TMS to the foveal cortex at 350-400 ms SOA interrupts the peripheral discrimination task. The authors should qualify their claims of the results occurring "during saccade preparation" (e.g., pg 1 ln 22) throughout the manuscript, and discuss the importance of temporal dynamics of the effect in supporting stability across saccades.

      We fully agree that the sluggishness of the fMRI signal presents an important challenge in investigating foveal feedback. We have now included this limitation in the discussion (pg 10 ln 306-318). We also clarify that our argument connects to previous studies investigating the temporal dynamics of foveal feedback using similar tasks (pg 10 ln 313-316). Specifically, in their psychophysical work, Kroell and Rolfs (2022) and (2025) showed that foveal feedback occurs before saccade execution with a peak around 80 ms before the eye movement. 

      (5) Relatedly, the claims that result in this paradigm reflect "activity exclusively related to predictive feedback" and "must originate from predictive rather than direct visual processes" (e.g., lines 60-65 and throughout) need to be toned down. The experimental design nicely rules out direct visual foveal stimulation, but predictive feedback is not the only alternative to that. The activation could also reflect mental imagery, visual working memory, attention, etc. Importantly, the experiment uses a block design, where the same exact image is presented multiple times over the block, and the activation is taken for the block as a whole. Thus, while at no point was the image presented at the fovea, there could still be more going on than temporally-specific and saccade-specific predictive feedback.

      We agree that those claims could have misled the reader. Our intention was to state that the activation originates from feedback rather than direct foveal stimulation because of the nature of the design. We have now clarified these statements (pg 2 ln 65) and also included a discussion of other effects including imagery and working memory in the limitations section (pg 10 ln 306-313).

      (6) The authors should avoid using the terms foveal feedback and foveal prediction interchangeably. To me, foveal feedback refers to the findings of Williams et al. (2008), where participants maintained passive fixation and discriminated objects in the periphery (see also Fan et al., 2016), whereas foveal prediction refers to the neural mechanism hypothesized by Kroell & Rolfs (2022), occurring before a saccade to the target object and contains task irrelevant feature information.

      We agree, and we have now adopted a clearer distinction between these terms, referring to foveal prediction only when discussing the distinct predictive nature of the effect discovered by Kroell and Rolfs (2022). Otherwise we referred to this effect as foveal feedback.

      (7) More broadly, the treatment of how foveal prediction relates to saccadic remapping is overly simplistic. The authors seem to be taking the perspective that remapping is an attentional phenomenon marked by remapping of only attentional/spatial pointers, but this is not the classic or widely accepted definition of remapping. Within the field of saccadic remapping, it is an ongoing debate whether (/how/where/when) information about stimulus content is remapped alongside spatial location (and also whether the attentional pointer concept is even neurophysiologically viable). This relationship between saccadic remapping and foveal prediction needs clarification and deeper treatment, in both the introduction and discussion.

      We thank the reviewer for their remarks. We reformulated the discussion section on “Saccadic remapping or foveal prediction” to include the nuances about spatial and feature remapping laid out in the reviewer’s comment (pg 8-9 ln 241-269). We also put a stronger focus on the special role the fovea seems to be playing regarding the feedback of visual features (pg 8-9 ln 265-269).

      (8) As part of this enhanced discussion, the findings should be better integrated with prior studies. E.g., there is some evidence for predictive remapping inducing integration of non-spatial features (some by the authors themselves; Harrison et al., 2013; Szinte et al., 2015). How do these findings relate to the observed results? Can the results simply be a special case of non-spatial feature integration between the currently attended and remapped location (fovea)? How are the results different from neurophysiological evidence for facilitation of the saccade target object's feature across the visual field (Burrow et al., 2014)? How might the results be reconciled with a prior fMRI study that failed to find decoding of stimulus content in remapped responses (Lescroart et al, 2016)? Might this reflect a difference between peripheral-to-peripheral vs peripheral-to-foveal remapping? A recent study by Chiu & Golomb (2025) provided supporting evidence for peripheral-to-fovea remapping (but not peripheral-to-peripheral remapping) of object-location binding (though in the post-saccadic time window), and suggested foveal prediction as the underlying mechanism.

      We thank the reviewer for raising these intriguing questions. We now address them in the revised discussion. We argue that the findings by Harrison et al., 2013 and Szinte et al., 2015 of presaccadic integration of features across two peripheral locations can be explained by presaccadic updating of spatial attention pointers rather than remapping of feature information (pg 8 ln 248-253). The lack of evidence for periphery-to-periphery remapping (Lescroart et al, 2016) and the recent study by Chiu & Golomb (2025) showing object-location binding from periphery to fovea nicely align with our characterization of foveal processing as unique in predicting feature information of upcoming stimuli (pg 8-9 ln 265-269). Finally, we argue that the global (i.e., space-invariant) selection task-irrelevant saccadic target features (Burrows et al., 2014) is well-established at the neural level, but does not suffice to explain the spatially specific nature of foveal prediction (pg 8 ln 220-224). We now include these studies in the revised discussion section.

      Reviewer #3 (Public review):

      Summary:

      In this paper, the authors used fMRI to determine whether peripherally viewed objects could be decoded from the foveal cortex, even when the objects themselves were never viewed foveally. Specifically, they investigated whether pre-saccadic target attributes (shape, semantic category) could be decoded from the foveal cortex. They found that object shape, but not semantic category, could be decoded, providing evidence that foveal feedback relies on low-mid-level information. The authors claim that this provides evidence for a mechanism underlying visual stability and object recognition across saccades.

      Strengths:

      I think this is another nice demonstration that peripheral information can be decoded from / is processed in the foveal cortex - the methods seem appropriate, and the experiments and analyses are carefully conducted, and the main results seem convincing. The paper itself was very clear and well-written.

      We thank the reviewer for this positive evaluation of our work. As discussed in our response to Reviewer 1, we now elaborate on the differences between previous work showing decoding of peripheral information from foveal cortex from the effect shown here. While there are important similarities between these findings, foveal prediction in our study occurs in a saccade condition and in the absence of a task that is specific to stimulus features. 

      Weaknesses:

      There are a couple of reasons why I think the main theoretical conclusions drawn from the study might not be supported, and why a more thorough investigation might be needed to draw these conclusions.

      (1) The authors used a blocked design, with each object being shown repeatedly in the same block. This meant that the stimulus was entirely predictable on each block, which weakens the authors' claims about this being a predictive mechanism that facilitates object recognition - if the stimulus is 100% predictable, there is no aspect of recognition or discrimination actually being tested. I think to strengthen these claims, an experiment would need to have unpredictable stimuli, and potentially combine behavioural reports with decoding to see whether this mechanism can be linked to facilitating object recognition across saccades.

      We appreciate the reviewer’s point and would like to highlight that it was not our intention to claim a behavioral effect on object recognition. We believe that an ambiguous formulation in the original abstract may have been interpreted this way, and we thus removed this reference. We also speculated in our Discussion that a potential reason for foveal prediction could be a headstart in peripheral object recognition and in the revised manuscript more clearly highlight that this is a  potential future direction only.

      (2)  Given that foveal feedback has been found in previous studies that don't incorporate saccades, how is this a mechanism that might specifically contribute to stability across saccades, rather than just being a general mechanism that aids the processing/discrimination of peripherally-viewed stimuli? I don't think this paper addresses this point, which would seem to be crucial to differentiate the results from those of previous studies.

      We fully agree that this point had not been sufficiently addressed in the previous version of the manuscript. As described in our responses to similar comments from reviewers 1 and 2, we included an additional section in the Discussion (“Foveal feedback during saccade preparation”) to more clearly delineate the present study from previous findings of foveal feedback. Previous studies (Williams et al., 2008) only found foveal feedback during narrow discrimination tasks related to spatial features of the target stimulus, not during color-discrimination or fixation-only tasks, concluding that the observed effect must be related to the discrimination behavior. In contrast, we found foveal feedback (as evidenced by decoding of target features) during a saccade condition that was independent of the target features, suggesting a different role of foveal feedback than hypothesized by Williams et al. (2008).

      Recommendations for the authors:  

      Reviewer #2 (Recommendations for the authors):

      (A) Minor comments:

      (1)  The task should be clarified earlier in the manuscript.

      We now characterise the task in the abstract and clarified its description in the third paragraph, right after introducing the main literature.

      (2) Is there actually only 0.5 seconds between saccades? This feels very short/rushed.

      The inter-trial-interval was 0.5 seconds, though effectively it varied because the target only appeared once participants fixated on the fixation dot. Note that this pacing is slower than the rate of saccades in natural vision (about 3 to 4 saccades per second).Participants did not report this paradigm as rushed.

      (3) Typo on pg2 ln64 (whooe).

      Fixed.

      (4)  Can the authors also show individual data points for Figures 3 and 4?

      We added individual data points for Figures 4 and S2

      (5) The MNI coordinates on Figure 4A seem to be incorrect.

      We took out those coordinates.

      (6) Pg4 ln126 and pg6 ln194, why cite Williams et al. (2008)?

      We included this reference here to acknowledge that Williams et al. raised the same issues. We added a “cf.” before this reference to clarify this.

      (7) Pg7 ln207 Fabius et al. (2020) showed slow post-saccadic feature remapping, rather than predictive remapping of spatial attention.

      We have corrected this mistake.

      (8) The OSF link is valid, but I couldn't find a pre-registration.

      The issue with the OSF link has been resolved. The pre-registration had been set up but not published. We now published it without changing the original pre-registration (see the screenshot attached).

      (9) I couldn't access the OpenNeuro repository.

      The issue with the OpenNeuro link has been resolved.

      (B) Additional references you may wish to include:

      (1) Burrows, B. E., Zirnsak, M., Akhlaghpour, H., Wang, M., & Moore, T.  (2014). Global selection of saccadic target features by neurons in area v4. Journal of Neuroscience.

      (2) Chambers, C. D., Allen, C. P., Maizey, L., & Williams, M. A. (2013). Is delayed foveal feedback critical for extra-foveal perception?. Cortex.

      (3) Chiu, T. Y., & Golomb, J. D. (2025). The influence of saccade target status on the reference frame of object-location binding. Journal of Experimental Psychology. General.

      (4) Harrison, W. J., Retell, J. D., Remington, R. W., & Mattingley, J. B. (2013). Visual crowding at a distance during predictive remapping. Current Biology.

      (5) Lescroart, M. D., Kanwisher, N., & Golomb, J. D. (2016). No evidence for automatic remapping of stimulus features or location found with fMRI. Frontiers in Systems Neuroscience.

      (6) Moran, C., Johnson, P. A., Hogendoorn, H., & Landau, A. N. (2025). The representation of stimulus features during stable fixation and active vision. Journal of Neuroscience.

      (7) Szinte, M., Jonikaitis, D., Rolfs, M., Cavanagh, P., & Deubel, H. (2016). Presaccadic motion integration between current and future retinotopic locations of attended objects. Journal of Neurophysiology.

      We thank the reviewer for pointing out these references. We have included them in the revised version of the manuscript.

      Reviewer #3 (Recommendations for the authors):

      I just have a few minor points where I think some clarifications could be made.

      (1) Line 64 - "whooe" should be "whoose" I think.

      Fixed.

      (2) Around line 53 - you might consider citing this review on foveal feedback - https://doi.org/10.1167/jov.20.12.2

      We included the reference (pg 2 ln 55).

      (3) Line 129 - you mention a u-shaped relationship for decoding - I wasn't quite sure of the significance/relevance of this relationship - it would be helpful to expand on this / clarify what this means.

      We have expanded this section and added statistical tests of the u-shaped relationship in decoding using a weighted quadratic regression. We found significant positive curvature in all early visual areas between fovea and periphery (V1: t(27) = 3.98, p = 0.008, V2: t(27) = 3.03, p = 0.02, V3: t(27)= 2.776, p = 0.025). These findings support a u-shaped relationship. We now report these results in the revised manuscript (pg 5 ln 137-138).

      (4) Figure 1 - it would be helpful to indicate how long the target was viewed in the "stim on" panels - I assume it was for the saccade latency, but it would be good to include those values in the main text.

      We included that detail in the text (pg 3 ln 96-97).

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #1

      (1) Related to comment 3, related to the spatial communication section, either provide a clearer worked example or adjust the framing to avoid implying a more developed capability than is shown.

      We appreciate the reviewer’s feedback regarding the framing of the spatial communication section. We have removed this section from the revised version.

      (2) Related to comment 4 about resolution, consider including explicit numerical estimates of spatial resolution (e.g., median patch diameter in micrometers) for at least one dataset to help users understand practical mapping granularity.

      We appreciate the suggestion. We have added explicit numerical estimates of spatial resolution to clarify our mappings. Specifically, we now (i) define “patch” precisely and (ii) report the median patch diameter (in µm) for representative datasets:

      10x Visium (mouse cortex): spot diameter = 55 µm; center-to-center spacing = 100 µm.

      Slide-seqV2 (mouse brain): bead diameter ≈ 10 µm. When we optionally coarse-grain to 5×5 bead tiles for robustness, the effective patch diameter is ~50 µm

    1. Author response:

      The following is the authors’ response to the current reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study examines whether changes in pupil size index prediction-error-related updating during associative learning, formalised as information gain via Kullback-Leibler (KL) divergence. Across two independent tasks, pupil responses scaled with KL divergence shortly after feedback, with the timing and direction of the response varying by task. Overall, the work supports the view that pupil size reflects information-theoretic processes in a context-dependent manner.

      Strengths:

      This study provides a novel and convincing contribution by linking pupil dilation to informationtheoretic measures, such as KL divergence, supporting Zénon's hypothesis that pupil responses reflect information gain during learning. The robust methodology, including two independent datasets with distinct task structures, enhances the reliability and generalisability of the findings. By carefully analysing early and late time windows, the authors capture the timing and direction of prediction-error-related responses, oPering new insights into the temporal dynamics of model updating. The use of an ideal-learner framework to quantify prediction errors, surprise, and uncertainty provides a principled account of the computational processes underlying pupil responses. The work also highlights the critical role of task context in shaping the direction and magnitude of these ePects, revealing the adaptability of predictive processing mechanisms. Importantly, the conclusions are supported by rigorous control analyses and preprocessing sanity checks, as well as convergent results from frequentist and Bayesian linear mixed-ePects modelling approaches.

      Weaknesses:

      Some aspects of directionality remain context-dependent, and on current evidence cannot be attributed specifically to whether average uncertainty increases or decreases across trials. DiPerences between the two tasks (e.g., sensory modality and learning regime) limit direct comparisons of ePect direction and make mechanistic attribution cautious. In addition, subjective factors such as confidence were not measured and could influence both predictionerror signals and pupil responses. Importantly, the authors explicitly acknowledge these limitations, and the manuscript clearly frames them as areas for future work rather than settled conclusions.

      Reviewer #2 (Public review):

      Summary:

      The authors investigate whether pupil dilation reflects information gain during associative learning, formalised as Kullback-Leibler divergence within an ideal observer framework. They examine pupil responses in a late time window after feedback and compare these to informationtheoretic estimates (information gain, surprise, and entropy) derived from two diPerent tasks with contrasting uncertainty dynamics.

      Strength:

      The exploration of task evoked pupil dynamics beyond the immediate response/feedback period and then associating them with model estimates was interesting and inspiring. This oPered a new perspective on the relationship between pupil dilation and information processing.

      Weakness:

      However, the interpretability of the findings remains constrained by the fundamental diPerences between the two tasks (stimulus modality, feedback type, and learning structure), which confound the claimed context-dependent ePects. The later time-window pupil ePects, although intriguing, are small in magnitude and may reflect residual noise or task-specific arousal fluctuations rather than distinct information-processing signals. Thus, while the study oPers valuable methodological insight and contributes to ongoing debates about the role of the pupil in cognitive inference, its conclusions about the functional significance of late pupil responses should be treated with caution.

      Reviewer #3 (Public review):

      Summary:

      Thank you for inviting me to review this manuscript entitled "Pupil dilation oPers a time-window on prediction error" by Colizoli and colleagues. The study examines prediction errors, information gain (Kullback-Leibler [KL] divergence), and uncertainty (entropy) from an information-theory perspective using two experimental tasks and pupillometry. The authors aim to test a theoretical proposal by Zénon (2019) that the pupil response reflects information gain (KL divergence). The conclusion of this work is that (post-feedback) pupil dilation in response to information gain is context dependent.

      Strengths:

      Use of an established Bayesian model to compute KL divergence and entropy.

      Pupillometry data preprocessing and multiple robustness checks.

      Weaknesses:

      Operationalization of prediction errors based on frequency, accuracy, and their interaction:

      The authors rely on a more model-agnostic definition of the prediction error in terms of stimulus frequency ("unsigned prediction error"), accuracy, and their interaction ("signed prediction error"). While I see the point, I would argue that this approach provides a simple approximation of the prediction error, but that a model-based approach would be more appropriate.

      Model validation:

      My impression is that the ideal learner model should work well in this case. However, the authors don't directly compare model behavior to participant behavior ("posterior predictive checks") to validate the model. Therefore, it is currently unclear if the model-derived terms like KL divergence and entropy provide reasonable estimates for the participant data.

      Lack of a clear conclusion:

      The authors conclude that this study shows for the first time that (post-feedback) pupil dilation in response to information gain is context dependent. However, the study does not oPer a unifying explanation for such context dependence. The discussion is quite detailed with respect to taskspecific ePects, but fails to provide an overarching perspective on the context-dependent nature of pupil signatures of information gain. This seems to be partly due to the strong diPerences between the experimental tasks.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I highly appreciate the care and detail in the authors' response and thank them for the ePort invested in revising the manuscript. They addressed the core concerns to a high standard, and the manuscript has substantially improved in methodological rigour (through additional controls/sanity checks and complementary mixed-ePects analyses) and in clarity of interpretation (by explicitly acknowledging context-dependence and tempering stronger claims). The present version reads clearly and is much strengthened overall. I only have a few minor points below:

      Minor suggestions:

      Abstract:

      In the abstract KL is introduced as abbreviation, but at first occurence it should be written out as "Kullback-Leibler (KL)" for readers not familiar with it.

      We thank the reviewer for catching this error. It has been correct in the version of record.

      Methods:

      I appreciate the additional bayesian LME analysis. I only had a few things that I thought were missing from knowing the parameters: 1) what was the target acceptance rate (default of .95?), 2) which family was used to model the response distribution: (default) "gaussian" or robust "student-t"? Depending on the data a student-t would be preferred, but since the author's checked the fit & the results corroborate the correlation analysis, using the default would also be fine! Just add the information for completeness.

      Thank you for bringing this to our attention. We have now noted that default parameters were used in all cases unless otherwise mentioned. 

      Thank you once again for your time and consideration.

      Reviewer #2 (Recommendations for the authors):

      Thanks to the authors' ePort on revision. I am happy with this new version of manuscript.

      Thank you once again for your time and consideration.

      Reviewer #3 (Recommendations for the authors):

      (1) Regarding comments #3 and #6 (first round) on model validation and posterior predictive checks, the authors replied that since their model is not a "generative" one, they can't perform posterior predictive checks. Crucially, in eq. 2, the authors present the p{tilde}^j_k variable denoting the learned probability of event k on trial j. I don't see why this can't be exploited for simulations. In my opinion, one could (and should) generate predictions based on this variable. The simplest implementation would translate the probability into a categorical choice (w/o fitting any free parameter). Based on this, they could assess whether the model and data are comparable.

      We thank the reviewer for this clarification. The reviewer suggests using the probability distributions at each trial to predict which event should be chosen on each trial. More specifically, the event(s) with the highest probability on trial j could be used to generate a prediction for the choice of the participant on trial j. We agree that this would indeed be an interesting analysis. However, the response options of each task are limited to two-alternatives. In the cue-target task, four events are modeled (representing all possible cue-target conditions) while the participants’ response options are only “left” and “right”. Similarly, in the letter-color task, 36 events are modeled while the participants’ response options are “match” and “no-match”. In other words, we do not know which event (either four or 36, for the two tasks) the participant would have indicated on each trial. As an approximation to this fine-grained analysis, we investigated the relationship between the information-theoretic variables separately for error and correct trials. Our rationale was that we would have more insight into how the model fits depended on the participants’ actual behavior as compared with the ideal learner model.

      (2) I recommend providing a plot of the linear mixed model analysis of the pupil data. Currently, results are only presented in the text and tables, but a figure would be much more useful.

      We thank the reviewer for the suggestion to add a plot of the linear mixed model results. We appreciate the value of visualizing model estimates; however, we feel that the current presentation in the text and tables clearly conveys the relevant findings. For this reason, and to avoid further lengthening the manuscript, we prefer to retain the current format.

      (3) I would consider only presenting the linear mixed ePects for the pupil data in the main results, and the correlation results in the supplement. It is currently quite long.

      We thank the reviewer for this recommendation. We agree that the results section is detailed; however, we consider the correlation analyses to be integral to the interpretation of the pupil data and therefore prefer to keep them in the main text rather than move them to the supplement.


      The following is the authors’ response to the original reviews

      eLife Assessment

      This important study seeks to examine the relationship between pupil size and information gain, showing opposite effects dependent upon whether the average uncertainty increases or decreases across trials. Given the broad implications for learning and perception, the findings will be of broad interest to researchers in cognitive neuroscience, decision-making, and computational modelling. Nevertheless, the evidence in support of the particular conclusion is at present incomplete - the conclusions would be strengthened if the authors could both clarify the differences between model-updating and prediction error in their account and clarify the patterns in the data.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study investigates whether pupil dilation reflects prediction error signals during associative learning, defined formally by Kullback-Leibler (KL) divergence, an information-theoretic measure of information gain. Two independent tasks with different entropy dynamics (decreasing and increasing uncertainty) were analyzed: the cue-target 2AFC task and the lettercolor 2AFC task. Results revealed that pupil responses scaled with KL divergence shortly after feedback onset, but the direction of this relationship depended on whether uncertainty (entropy) increased or decreased across trials. Furthermore, signed prediction errors (interaction between frequency and accuracy) emerged at different time windows across tasks, suggesting taskspecific temporal components of model updating. Overall, the findings highlight that pupil dilation reflects information-theoretic processes in a complex, context-dependent manner.

      Strengths:

      This study provides a novel and convincing contribution by linking pupil dilation to informationtheoretic measures, such as KL divergence, supporting Zénon's hypothesis that pupil responses reflect information gained during learning. The robust methodology, including two independent datasets with distinct entropy dynamics, enhances the reliability and generalisability of the findings. By carefully analysing early and late time windows, the authors capture the temporal dynamics of prediction error signals, offering new insights into the timing of model updates. The use of an ideal learner model to quantify prediction errors, surprise, and entropy provides a principled framework for understanding the computational processes underlying pupil responses. Furthermore, the study highlights the critical role of task context - specifically increasing versus decreasing entropy - in shaping the directionality and magnitude of these effects, revealing the adaptability of predictive processing mechanisms.

      Weaknesses:

      While this study offers important insights, several limitations remain. The two tasks differ significantly in design (e.g., sensory modality and learning type), complicating direct comparisons and limiting the interpretation of differences in pupil dynamics. Importantly, the apparent context-dependent reversal between pupil constriction and dilation in response to feedback raises concerns about how these opposing effects might confound the observed correlations with KL divergence. 

      We agree with the reviewer’s concerns and acknowledge that the speculation concerning the directional effect of entropy across trials can not be fully substantiated by the current study. As the reviewer points out, the directional relationship between pupil dilation and information gain must be due to other factors, for instance, the sensory modality, learning type, or the reversal between pupil constriction and dilation across the two tasks. Also, we would like to note that ongoing experiments in our lab already contradict our original speculation. In line with the reviewer’s point, we noted these differences in the section on “Limitations and future research” in the Discussion. To better align the manuscript with the above mentioned points, we have made several changes in the Abstract, Introduction and Discussion summarized below: 

      We have removed the following text from the Abstract and Introduction: “…, specifically related to increasing or decreasing average uncertainty (entropy) across trials.”

      We have edited the following text in the Introduction (changes in italics) (p. 5):

      “We analyzed two independent datasets featuring distinct associative learning paradigms, one characterized by increasing entropy and the other by decreasing entropy as the tasks progressed. By examining these different tasks, we aimed to identify commonalities (if any) in the results across varying contexts. Additionally, the contrasting directions of entropy in the two tasks enabled us to disentangle the correlation between stimulus-pair frequency and information gain in the postfeedback pupil response.

      We have removed the following text from the Discussion:

      “…and information gain in fact seems to be driven by increased uncertainty.”

      “We speculate that this difference in the direction of scaling between information gain and the pupil response may depend on whether entropy was increasing or decreasing across trials.” 

      “…which could explain the opposite direction of the relationship between pupil dilation and information gain”

      “… and seems to relate to the direction of the entropy as learning progresses (i.e., either increasing or decreasing average uncertainty).” 

      We have edited the following texts in the Discussion (changes in italics):

      “For the first time, we show that the direction of the relationship between postfeedback pupil dilation and information gain (defined as KL divergence) was context dependent.” (p. 29):

      Finally, we have added the following correction to the Discussion (p. 30):

      “Although it is tempting to speculate that the direction of the relationship between pupil dilation and information gain may be due to either increasing or decreasing entropy as the task progressed, we must refrain from this conclusion. We note that the two tasks differ substantially in terms of design with other confounding variables and therefore cannot be directly compared to one another. We expand on these limitations in the section below (see Limitations and future research).”

      Finally, subjective factors such as participants' confidence and internal belief states were not measured, despite their potential influence on prediction errors and pupil responses.

      Thank you for the thoughtful comment. We agree with the reviewer that subjective factors, such as participants' confidence, can be important in understanding prediction errors and pupil responses. As per the reviewer’s point, we have included the following limitation in the Discussion (p. 33): 

      “Finally, while we acknowledge the potential relevance of subjective factors, such as the participants’ overt confidence reports, in understanding prediction errors and pupil responses, the current study focused on the more objective, model-driven measure of information-theoretic variables. This approach aligns with our use of the ideal learner model, which estimates information-theoretic variables while being agnostic about the observer's subjective experience itself. Future research is needed to explore the relationship between information-gain signals in pupil dilation and the observer’s reported experience of or awareness about confidence in their decisions.” 

      Reviewer #2 (Public review):

      Summary:

      The authors proposed that variability in post-feedback pupillary responses during the associative learning tasks can be explained by information gain, which is measured as KL divergence. They analysed pupil responses in a later time window (2.5s-3s after feedback onset) and correlated them with information-theory-based estimates from an ideal learner model (i.e., information gain-KL divergence, surprise-subjective probability, and entropy-average uncertainty) in two different associative decision-making tasks.

      Strength:

      The exploration of task-evoked pupil dynamics beyond the immediate response/feedback period and then associating them with model estimates was interesting and inspiring. This offered a new perspective on the relationship between pupil dilation and information processing.

      Weakness:

      However, disentangling these later effects from noise needs caution. Noise in pupillometry can arise from variations in stimuli and task engagement, as well as artefacts from earlier pupil dynamics. The increasing variance in the time series of pupillary responses (e.g., as shown in Figure 2D) highlights this concern.

      It's also unclear what this complicated association between information gain and pupil dynamics actually means. The complexity of the two different tasks reported made the interpretation more difficult in the present manuscript.

      We share the reviewer’s concerns. To make this point come across more clearly, we have added the following text to the Introduction (p. 5):

      “The current study was motivated by Zenon’s hypothesis concerning the relationship between pupil dilation and information gain, particularly in light of the varying sources of signal and noise introduced by task context and pupil dynamics. By demonstrating how task context can influence which signals are reflected in pupil dilation, and highlighting the importance of considering their temporal dynamics, we aim to promote a more nuanced and model-driven approach to cognitive research using pupillometry.”

      Reviewer #3 (Public review):

      Summary:

      This study examines prediction errors, information gain (Kullback-Leibler [KL] divergence), and uncertainty (entropy) from an information-theory perspective using two experimental tasks and pupillometry. The authors aim to test a theoretical proposal by Zénon (2019) that the pupil response reflects information gain (KL divergence). In particular, the study defines the prediction error in terms of KL divergence and speculates that changes in pupil size associated with KL divergence depend on entropy. Moreover, the authors examine the temporal characteristics of pupil correlates of prediction errors, which differed considerably across previous studies that employed different experimental paradigms. In my opinion, the study does not achieve these aims due to several methodological and theoretical issues.

      Strengths:

      (1)  Use of an established Bayesian model to compute KL divergence and entropy.

      (2)  Pupillometry data preprocessing, including deconvolution.

      Weaknesses:

      (1) Definition of the prediction error in terms of KL divergence:

      I'm concerned about the authors' theoretical assumption that the prediction error is defined in terms of KL divergence. The authors primarily refer to a review article by Zénon (2019): "Eye pupil signals information gain". It is my understanding that Zénon argues that KL divergence quantifies the update of a belief, not the prediction error: "In short, updates of the brain's internal model, quantified formally as the Kullback-Leibler (KL) divergence between prior and posterior beliefs, would be the common denominator to all these instances of pupillary dilation to cognition." (Zénon, 2019).

      From my perspective, the update differs from the prediction error. Prediction error refers to the difference between outcome and expectation, while update refers to the difference between the prior and the posterior. The prediction error can drive the update, but the update is typically smaller, for example, because the prediction error is weighted by the learning rate to compute the update. My interpretation of Zénon (2019) is that they explicitly argue that KL divergence defines the update in terms of the described difference between prior and posterior, not the prediction error.

      The authors also cite a few other papers, including Friston (2010), where I also could not find a definition of the prediction error in terms of KL divergence. For example [KL divergence:] "A non-commutative measure of the non-negative difference between two probability distributions." Similarly, Friston (2010) states: Bayesian Surprise - "A measure of salience based on the Kullback-Leibler divergence between the recognition density (which encodes posterior beliefs) and the prior density. It measures the information that can be recognized in the data." Finally, also in O'Reilly (2013), KL divergence is used to define the update of the internal model, not the prediction error.

      The authors seem to mix up this common definition of the model update in terms of KL divergence and their definition of prediction error along the same lines. For example, on page 4: "KL divergence is a measure of the difference between two probability distributions. In the context of predictive processing, KL divergence can be used to quantify the mismatch between the probability distributions corresponding to the brain's expectations about incoming sensory input and the actual sensory input received, in other words, the prediction error (Friston, 2010; Spratling, 2017)."

      Similarly (page 23): "In the current study, we investigated whether the pupil's response to decision outcome (i.e., feedback) in the context of associative learning reflects a prediction error as defined by KL divergence."

      This is problematic because the results might actually have limited implications for the authors' main perspective (i.e., that the pupil encodes prediction errors) and could be better interpreted in terms of model updating. In my opinion, there are two potential ways to deal with this issue:

      (a) Cite work that unambiguously supports the perspective that it is reasonable to define the prediction error in terms of KL divergence and that this has a link to pupillometry. In this case, it would be necessary to clearly explain the definition of the prediction error in terms of KL divergence and dissociate it from the definition in terms of model updating.

      (b) If there is no prior work supporting the authors' current perspective on the prediction error, it might be necessary to revise the entire paper substantially and focus on the definition in terms of model updating.

      We thank the reviewer for pointy out these inconsistencies in the manuscript and appreciate their suggestions for improvement. We take approach (a) recommended by the reviewer, and provide our reasoning as to why prediction error signals in pupil dilation are expected to correlate with information gain (defined as the KL divergence between posterior and prior belief distributions). This can be found in a new section in the introduction, copied here for convenience (p. 3-4):

      “We reasoned that the link between prediction error signals and information gain in pupil dilation is through precision-weighting. Precision refers to the amount of uncertainty (inverse variance) of both the prior belief and sensory input in the prediction error signals [6,64–67]. More precise prediction errors receive more weighting, and therefore, have greater influence on model updating processes. The precisionweighting of prediction error signals may provide a mechanism for distinguishing between known and unknown sources of uncertainty, related to the inherent stochastic nature of a signal versus insufficient information of the part of the observer, respectively [65,67,68]. In Bayesian frameworks, information gain is fundamentally linked to prediction error, modulated by precision [65,66,69–75]. In non-hierarchical Bayesian models, information gain can be derived as a function of prediction errors and the precision of the prior and likelihood distributions, a relationship that can be approximately linear [70]. In hierarchical Bayesian inference, the update in beliefs (posterior mean changes) at each level is proportional to the precision-weighted prediction error; this update encodes the information gained from new observations [65,66,69,71,72]. Neuromodulatory arousal systems are well-situated to act as precision-weighting mechanisms in line with predictive processing frameworks [76,77]. Empirical evidence suggests that neuromodulatory systems broadcast precisionweighted prediction errors to cortical regions [11,59,66,78]. Therefore, the hypothesis that feedback-locked pupil dilation reflects a prediction error signal is similarly in line with Zenon’s main claim that pupil dilation generally reflects information gain, through precision-weighting of the prediction error. We expected a prediction error signal in pupil dilation to be proportional to the information gain.”

      We have referenced previous work that has linked prediction error and information gain directly (p. 4): “The KL divergence between posterior and prior belief distributions has been previously considered to be a proxy of (precision-weighted) prediction errors [68,72].”

      We have taken the following steps to remedy this error of equating “prediction error” directly with the information gain.

      First, we have replaced “KL divergence” with “information gain” whenever possible throughout the manuscript for greater clarity. 

      Second, we have edited the section in the introduction defining information gain substantially (p. 4): 

      “Information gain can be operationalized within information theory as the KullbackLeibler (KL) divergence between the posterior and prior belief distributions of a Bayesian observer, representing a formalized quantity that is used to update internal models [29,79,80]. Itti and Baldi (2005)81 termed the KL divergence between posterior and prior belief distributions as “Bayesian surprise” and showed a link to the allocation of attention. The KL divergence between posterior and prior belief distributions has been previously considered to be a proxy of (precision-weighted) prediction errors[68,72]. According to Zénon’s hypothesis, if pupil dilation reflects information gain during the observation of an outcome event, such as feedback on decision accuracy, then pupil size will be expected to increase in proportion to how much novel sensory evidence is used to update current beliefs [29,63]. ” 

      Finally, we have made several minor textual edits to the Abstract and main text wherever possible to further clarify the proposed relationship between prediction errors and information gain.

      (2) Operationalization of prediction errors based on frequency, accuracy, and their interaction:

      The authors also rely on a more model-agnostic definition of the prediction error in terms of stimulus frequency ("unsigned prediction error"), accuracy, and their interaction ("signed prediction error"). While I see the point here, I would argue that this approach offers a simple approximation to the prediction error, but it is possible that factors like difficulty and effort can influence the pupil signal at the same time, which the current approach does not take into account. I recommend computing prediction errors (defined in terms of the difference between outcome and expectation) based on a simple reinforcement-learning model and analyzing the data using a pupillometry regression model in which nuisance regressors are controlled, and results are corrected for multiple comparisons.

      We agree with the reviewer’s suggestion that alternatively modeling the data in a reinforcement learning paradigm would be fruitful. We adopted the ideal learner model as we were primarily focused on Information Theory, stemming from our aim to test Zenon’s hypothesis that information gain drives pupil dilation. However, we agree with the reviewer that it is worthwhile to pursue different modeling approaches in future work. We have now included a complementary linear mixed model analysis in which we controlled for the effects of the information-theoretic variables on one another, while also including the nuisance regressors of pre-feedback baseline pupil dilation and reaction times (explained in more detail below in our response to your point #4). Results including correction for multiple comparisons was reported for all pupil time course data as detailed in Methods section 2.5. 

      (3) The link between model-based (KL divergence) and model-agnostic (frequency- and accuracy-based) prediction errors:

      I was expecting a validation analysis showing that KL divergence and model-agnostic prediction errors are correlated (in the behavioral data). This would be useful to validate the theoretical assumptions empirically.

      The model limitations and the operalization of prediction error in terms of post-feedback processing do not seem to allow for a comparison of information gain and model-agnostic prediction errors in the behavioral data for the following reasons. First, the simple ideal learner model used here is not a generative model, and therefore, cannot replicate or simulate the participants responses (see also our response to your point #6 “model validation” below). Second, the behavioral dependent variables obtained are accuracy and reaction times, which both occur before feedback presentation. While accuracy and reaction times can serve as a marker of the participant’s (statistical) confidence/uncertainty following the decision interval, these behavioral measures cannot provide access to post-feedback information processing. The pupil dilation is of interest to us because the peripheral arousal system is able to provide a marker of post-feedback processing. Through the analysis presented in Figure 3, we indeed aimed to make the comparison of the model-based information gain to the model-agnostic prediction errors via the proxy variable of post-feedback pupil dilation instead of behavioral variables. To bridge the gap between the “behaviorally agnostic” model parameters and the actual performance of the participants, we examined the relationship between the model-based information gain and the post-feedback pupil dilation separately for error and correct trials as shown in Figure 3D-F & Figure 3J-L. We hope this addresses the reviewers concern and apologize in case we did not understand the reviewers suggestion here.

      (4) Model-based analyses of pupil data:

      I'm concerned about the authors' model-based analyses of the pupil data. The current approach is to simply compute a correlation for each model term separately (i.e., KL divergence, surprise, entropy). While the authors do show low correlations between these terms, single correlational analyses do not allow them to control for additional variables like outcome valence, prediction error (defined in terms of the difference between outcome and expectation), and additional nuisance variables like reaction time, as well as x and y coordinates of gaze.

      Moreover, including entropy and KL divergence in the same regression model could, at least within each task, provide some insights into whether the pupil response to KL divergence depends on entropy. This could be achieved by including an interaction term between KL divergence and entropy in the model.

      In line with the reviewer’s suggestions, we have included a complementary linear mixed model analysis in which we controlled for the effects of the information-theoretic variables on one another, while also including the nuisance regressors of pre-feedback baseline pupil dilation and reaction times. We compared the performance of two models on the post-feedback pupil dilation in each time window of interest: Modle 1 had no interaction between information gain and entropy and Model 2 included an interaction term as suggested. We did not include the x- and y- coordinates of gaze in the mixed linear model analysis, as there are multiple values of these coordinates per trial. Furthermore, regressing out the x and y- coordinates of gaze can potentially remove signal of interest in the pupil dilation data in addition to the gaze-related confounds and we did not measure absolute pupil size (Mathôt, Melmi & Castet, 2015; Hayes & Petrov, 2015). We present more sanity checks on the pre-processing pipeline as recommended by Reviewer 1.  

      This new analysis resulted in several additions to the Methods (see Section 2.5) and Results. In sum, we found that including an interaction term for information gain and entropy did not lead to better model fits, but sometimes lead to significantly worse fits. Overall, the results of the linear mixed model corroborated the “simple” correlation analysis across the pupil time course while accounting for the relationship to the pre-feedback baseline pupil and preceeding reaction time differences. There was only one difference to note between the correlation and linear mixed modeling analyses: for the error trials in the cue-target 2AFC task, including entropy in the model accounted for the variance previously explained by surprise.

      (5) Major differences between experimental tasks:

      More generally, I'm not convinced that the authors' conclusion that the pupil response to KL divergence depends on entropy is sufficiently supported by the current design. The two tasks differ on different levels (stimuli, contingencies, when learning takes place), not just in terms of entropy. In my opinion, it would be necessary to rely on a common task with two conditions that differ primarily in terms of entropy while controlling for other potentially confounding factors. I'm afraid that seemingly minor task details can dramatically change pupil responses. The positive/negative difference in the correlation with KL divergence that the authors interpret to be driven by entropy may depend on another potentially confounding factor currently not controlled.

      We agree with the reviewer’s concerns and acknowledge that the speculation concerning the directional effect of entropy across trials can not be fully substantiated by the currect study. We note that Review #1 had a similar concern. Our response to Reviewer #1 addresses this concern of Reviewer #3 as well. To better align the manuscript with the above mentioned points, we have made several changes that are detailed in our response to Reviewer #1’s public review (above). 

      (6) Model validation:

      My impression is that the ideal learner model should work well in this case. However, the authors don't directly compare model behavior to participant behavior ("posterior predictive checks") to validate the model. Therefore, it is currently unclear if the model-derived terms like KL divergence and entropy provide reasonable estimates for the participant data.

      Based on our understanding, posterior predictive checks are used to assess the goodness of fit between generated (or simulated) data and observed data. Given that the “simple” ideal learner model employed in the current study is not a generative model, a posterior predictive check would not apply here (Gelman, Carlin, Stern, Dunson, Vehtari, & Rubin (2013). The ideal learner model is unable to simulate or replicate the participants’ responses and behaviors such as accuracy and reaction times; it simply computes the probability of seeing each stimulus type at each trial based on the prior distribution and the exact trial order of the stimuli presented to each participant. The model’s probabilities are computed directly from a Dirichlet distribution of values that represent the number of occurences of each stimulus-pair type for each task. The information-theoretic variables are then directly computed from these probabilities using standard formulas. The exact formulas used in the ideal learner model can be found in section 2.4.

      We have now included a complementary linear mixed model analysis which also provides insight into the amount of explained variance of these information-theoretic predictors on the post-feedback pupil response, while also including the pre-feedback baseline pupil and reaction time differences (see section 3.3, Tables 3 & 4). The R<sup>2</sup> values ranged from 0.16 – 0.50 across all conditions tested.

      (7) Discussion:

      The authors interpret the directional effect of the pupil response w.r.t. KL divergence in terms of differences in entropy. However, I did not find a normative/computational explanation supporting this interpretation. Why should the pupil (or the central arousal system) respond differently to KL divergence depending on differences in entropy?

      The current suggestion (page 24) that might go in this direction is that pupil responses are driven by uncertainty (entropy) rather than learning (quoting O'Reilly et al. (2013)). However, this might be inconsistent with the authors' overarching perspective based on Zénon (2019) stating that pupil responses reflect updating, which seems to imply learning, in my opinion. To go beyond the suggestion that the relationship between KL divergence and pupil size "needs more context" than previously assumed, I would recommend a deeper discussion of the computational underpinnings of the result.

      Since we have removed the original speculative conclusion from the manuscript, we will refrain from discussing the computational underpinnings of a potential mechanism. To note as mentioned above, we have preliminary data from our own lab that contradicts our original hypothesis about the relationship between entropy and information gain on the post-feedback pupil response. 

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Apart from the points raised in the public review above, I'd like to use the opportunity here to provide a more detailed review of potential issues, questions, and queries I have:

      (1) Constriction vs. Dilation Effects:

      The study observes a context-dependent relationship between KL divergence and pupil responses, where pupil dilation and constriction appear to exhibit opposing effects. However, this phenomenon raises a critical concern: Could the initial pupil constriction to visual stimuli (e.g., in the cue-target task) confound correlations with KL divergence? This potential confound warrants further clarification or control analyses to ensure that the observed effects genuinely reflect prediction error signals and are not merely a result of low-level stimulus-driven responses.

      We agree with the reviewers concern and have added the following information to the limitations section in the Discussion (changes in italics below; p. 32-33).

      “First, the two associative learning paradigms differed in many ways and were not directly comparable. For instance, the shape of the mean pupil response function differed across the two tasks in accordance with a visual or auditory feedback stimulus (compare Supplementary Figure 3A with Supplementary Figure 3D), and it is unclear whether these overall response differences contributed to any differences obtained between task conditions within each task. We are unable to rule out whether so-called “low level” effects such as the initial constriction to visual stimuli in the cue-target 2AFC task as compared with the dilation in response auditory stimuli in letter-color 2AFC task could confound correlations with information gain. Future work should strive to disentangle how the specific aspects of the associative learning paradigms relate to prediction errors in pupil dilation by systematically manipulating design elements within each task.”

      Here, I also was curious about Supplementary Figure 1, showing 'no difference' between the two tones (indicating 'error' or 'correct'). Was this the case for FDR-corrected or uncorrected cluster statistics? Especially since the main results also showed sig. differences only for uncorrected cluster statistics (Figure 2), but were n.s. for FDR corrected. I.e. can we be sure to rule out a confound of the tones here after all?

      As per the reviewer’s suggestion, we verified that there were also no significant clusters after feedback onset before applying the correction for multiple comparisons. We have added this information to Supplemenatary section 1.2 as follows: 

      “Results showed that the auditory tone dilated pupils on average (Supplementary Figure 1C). Crucially, however, the two tones did not differ from one another in either of the time windows of interest (Supplementary Figure 1D; no significant time points after feedback onset were obtained either before or after correcting for multiple comparisons using cluster-based permutation methods; see Section 2.5.” 

      Supplementary Figure 1 is showing effects cluster-corrected for multiple comparisons using cluster-based permutation tests from the MNE software package in Python (see Methods section 2.5). We have clarified that the cluster-correction was based on permutation testing in the figure legend. 

      (2) Participant-Specific Priors:

      The ideal learner models do not account for individualised priors, assuming homogeneous learning behaviour across participants. Could incorporating participant-specific priors better reflect variability in how individuals update their beliefs during associative learning?

      We have clarified in the Methods (see section 2.4) that the ideal learner models did account for participant-specific stimuli including participant-specific priors in the letter-color 2AFC task. We have added the following texts: 

      “We also note that while the ideal learner model for the cue-target 2AFC task used a uniform (flat) prior distribution for all participants, the model parameters were based on the participant-specific cue-target counterbalancing conditions and randomized trial order.” (p. 13)

      “The prior distributions used for the letter-color 2AFC task were estimated from the randomized letter-color pairs and randomized trial order presentation in the preceding odd-ball task; this resulted in participant-specific prior distributions for the ideal learner model of the letter-color 2AFC task. The model parameters were likewise estimated from the (participant-specific) randomized trial order presented in the letter-color 2AFC task.” (p. 13)

      (3) Trial-by-Trial Variability:

      The analysis does not account for random effects or inter-trial variability using mixed-effects models. Including such models could provide a more robust statistical framework and ensure the observed relationships are not influenced by unaccounted participant- or trial-specific factors.

      We have included a complementary linear mixed model analysis in which “subject” was modeled as a random effect on the post-feedback pupil response in each time window of interest and for each task. Across all trials, the results of the linear mixed model corroborated the “simple” correlation analysis across the pupil time course while accounting for the relationship to the prefeedback baseline pupil and preceeding reaction time differences (see section 3.3, Tables 3 & 4).

      (4) Preprocessing/Analysis choices:

      Before anything else, I'd like to highlight the authors' effort in providing public code (and data) in a very readable and detailed format!

      We appreciate the compliment - thank you for taking the time to look at the data and code provided.

      I found the idea of regressing the effect of Blinks/Saccades on the pupil trace intriguing. However, I miss a complete picture here to understand how well this actually worked, especially since it seems to be performed on already interpolated data. My main points here are:

      (4.1) Why is the deconvolution performed on already interpolated data and not on 'raw' data where there are actually peaks of information to fit?

      To our understanding, at least one critical reason for interpolating the data before proceeding with the deconvolution analysis is that the raw data contain many missing values (i.e., NaNs) due to the presence of blinks. Interpolating over the missing data first ensures that there are valid numerical elements in the linear algebra equations. We refer the reviewer to the methods detailed in Knapen et al. (2016) for more details on this pre-processing method. 

      (4.2) What is the model fit (e.g. R-squared)? If this was a poor fit for the regressors in the first place, can we trust the residuals (i.e. clean pupil trace)? Is it possible to plot the same Pupil trace of Figure 1D with a) the 'raw' pupil time-series, b) after interpolation only (both of course also mean-centered for comparison), on top of the residuals after deconvolution (already presented), so we can be sure that this is not driving the effects in a 'bad' way? I'd just like to make sure that this approach did not lead to artefacts in the residuals rather than removing them.

      We thank the reviewer for this suggestion. In the Supplementary Materials, we have included a new figure (Supplementary Figure 2, copied below for convience), which illustrates the same conditions as in Figure 1D and Figure 2D, with 1) the raw data, and 2) the interpolated data before the nuisance regression. Both the raw data and interpolated data have been band-pass filtered as was done in the original pre-processing pipeline and converted to percent signal change. These figures can be compared directly to Figure 1D and Figure 2D, for the two tasks, respectively. 

      Of note is that the raw data seem to be dominated by responses to blinks (and/or saccades). Crucially, the pattern of results remains overall unchaged between the interpolated-only and fully pre-processed version of the data for both tasks. 

      In the Supplementary Materials (see Supplementary section 2), we have added the descriptives of the model fits from the deconvolution method. Model fits (R<sup>2</sup>) for the nuisance regression were generally low: cue-target 2AFC task, M = 0.03, SD = 0.02, range = [0.00, 0.07]; letter-color visual 2AFC, M = 0.08, SD = 0.04, range = [0.02, 0.16].

      Furthermore, a Pearson correlation analysis between the interpolated and fully pre-processed data within the time windows of interest for both task indicated high correspondence: 

      Cue-target 2AFC task

      Early time window: M = 0.99, SD = 0.01, range = [0.955, 1.000]

      Late time window: M = 0.99, SD = 0.01, range = [0.971, 1.000]

      Letter-color visual 2AFC

      Early time window: M = 0.95, SD = 0.04, range = [0.803, 0.998]

      Late time window: M = 0.97, SD = 0.02, range = [0.908, 0.999]

      In hindsight, including the deconvolution (nuisance regression) method may not have changed the pattern of results much. However, the decision to include this deconvolution method was not data-driven; instead, it was based on the literature establishing the importance of removing variance (up to 5 s) of these blinks and saccades from cognitive effects of interest in pupil dilation (Knapen et al., 2016). 

      (4.3) Since this should also lead to predicted time series for the nuisance-regressors, can we see a similar effect (of what is reported for the pupil dilation) based on the blink/saccade traces of a) their predicted time series based on the deconvolution, which could indicate a problem with the interpretation of the pupil dilation effects, and b) the 'raw' blink/saccade events from the eye-tracker? I understand that this is a very exhaustive analysis so I would actually just be interested here in an averaged time-course / blink&saccade frequency of the same time-window in Figure 1D to complement the PD analysis as a sanity check.

      Also included in the Supplementary Figure 2 is the data averaged as in Figure 1D and Figure 2D for the raw data and nuisance-predictor time courses (please refer to the bottom row of the sub-plots). No pattern was observed in either the raw data or the nuisance predictors as was shown in the residual time courses. 

      (4.4) How many samples were removed from the time series due to blinks/saccades in the first place? 150ms for both events in both directions is quite a long bit of time so I wonder how much 'original' information of the pupil was actually left in the time windows of interest that were used for subsequent interpretations.

      We thank the reviewer for bringing this issue to our attention. The size of the interpolation window was based on previous literature, indicating a range of 100-200 ms as acceptable (Urai et al., 2017; Knapen et al., 2016; Winn et al., 2018). The ratio of interpolated-to-original data (across the entire trial) varied greatly between participants and between trials: cue-target 2AFC task, M = 0.262, SD = 0.242, range = [0,1]; letter-color 2AFC task, M = 0.194, SD = 0.199, range = [0,1]. 

      We have now included a conservative analysis in which only trials with more than half (threshold = 60%) of original data are included in the analyses. Crucially, we still observe the same pattern of effects as when all data are considered across both tasks (compare the second to last row in the Supplementary Figure 2 to Figure 1D and Figure 2D).

      (4.5) Was the baseline correction performed on the percentage change unit?

      Yes, the baseline correction was performed on the pupil timeseries after converting to percentsignal change. We have added that information to the Methods (section 2.3).

      (4.6) What metric was used to define events in the derivative as 'peaks'? I assume some sort of threshold? How was this chosen?

      The threshold was chosen in a data-driven manner and was kept consistent across both tasks. The following details have been added to the Methods:

      “The size of the interpolation window preceding nuisance events was based on previous literature [13,39,99]. After interpolation based on data-markers and/or missing values, remaining blinks and saccades were estimated by testing the first derivative of the pupil dilation time series against a threshold rate of change. The threshold for identifying peaks in the temporal derivative is data-driven, partially based on past work[10,14,33]. The output of each participant’s pre-processing pipeline was checked visually. Once an appropriate threshold was established at the group level, it remained the same for all participants (minimum peak height of 10 units).” (p. 8 & 11).

      (5) Multicollinearity Between Variables:

      Lastly, the authors state on page 13: "Furthermore, it is expected that these explanatory variables will be correlated with one another. For this reason, we did not adopt a multiple regression approach to test the relationship between the information-theoretic variables and pupil response in a single model". However, the very purpose of multiple regression is to account for and disentangle the contributions of correlated predictors, no? I might have missed something here.

      We apologize for the ambiguity of our explanation in the Methods section. We originally sought to assess the overall relationship between the post-feedback response and information gain (primarily), but also surprise and entropy. Our reasoning was that these variables are often investigated in isolation across different experiments (i.e., only investigating Shannon surprise), and we would like to know what the pattern of results would look like when comparing a single information-theoretic variable to the pupil response (one-by-one). We assumed that including additional explanatory variables (that we expected to show some degree of collinearity with each other) in a regression model would affect variance attributed to them as compared with the one-on-one relationships observed with the pupil response (Morrissey & Ruxton 2018). We also acknowledge the value of a multiple regression approach on our data. Based on the suggestions by the reviewers we have included a complementary linear mixed model analysis in which we controlled for the effects of the information-theoretic variables on one another, while also including the nuisance regressors of pre-feedback baseline pupil dilation and reaction times.  

      This new analysis resulted in several additions to the Methods (see Section 2.5) and Results (see Tables 3 and 4). Overall, the results of the linear mixed model corroborated the “simple” correlation analysis across the pupil time course while accounting for the relationship to the prefeedback baseline pupil and preceeding reaction time differences. There was only one difference to note between the correlation and linear mixed modeling analyses: for the error trials in the cue-target 2AFC task, including entropy in the model accounted for the variance previously explained by surprise. 

      Reviewer #2 (Recommendations for the authors):

      (1) Given the inherent temporal dependencies in pupil dynamics, characterising later pupil responses as independent of earlier ones in a three-way repeated measures ANOVA may not be appropriate. A more suitable approach might involve incorporating the earlier pupil response as a covariate in the model.

      We thank the reviewer for bringing this issue to our attention. From our understanding, a repeated-measures ANOVA with factor “time window” would be appropriate in the current context for the following reasons. First, autocorrelation (closely tied to sphericity) is generally not considered a problem when only two timepoints are compared from time series data (Field, 2013; Tabachnick & Fidell, 2019). Second, the repeated-measures component of the ANOVA takes the correlated variance between time points into account in the statistical inference. Finally, as a complementary analysis, we present the results testing the interaction between the frequency and accuracy conditions across the full time courses (see Figures 1D and 2D); in these pupil time courses, any difference between the early and late time windows can be judged by the reader visually and qualitatively. 

      (2) Please clarify the correlations between KL divergence, surprise, entropy, and pupil response time series. Specifically, state whether these correlations account for the interrelationships between these information-theoretic measures. Given their strong correlations, partialing out these effects is crucial for accurate interpretation.

      As mentioned above, based on the suggestions by the reviewers we have included a complementary linear mixed model analysis in which we controlled for the effects of the information-theoretic variables on one another, while also including the nuisance regressors of pre-feedback baseline pupil dilation and reaction times.  

      This new analysis resulted in several additions to the Methods (see Section 2.5) and Results (see Tables 3 and 4). Overall, the results of the linear mixed model corroborated the “simple” correlation analysis across the pupil time course while accounting for the relationship to the prefeedback baseline pupil and preceeding reaction time differences. There was only one difference to note between the correlation and linear mixed modeling analyses: for the error trials in the cue-target 2AFC task, including entropy in the model accounted for the variance previously explained by surprise. 

      (3) The effects observed in the late time windows appear weak (e.g., Figure 2E vs. 2F, and the generally low correlation coefficients in Figure 3). Please elaborate on the reliability and potential implications of these findings.

      We have now included a complementary linear mixed model analysis which also provides insight into the amount of explained variance of these information-theoretic predictors on the post-feedback pupil response, while also including the pre-feedback baseline pupil and reaction time differences (see section 3.3, Tables 3 & 4). The R<sup>2</sup> values ranged from 0.16 – 0.50 across all conditions tested. Including the pre-feedback baseline pupil dilation as a predictor in the linear mixed model analysis consistently led to more explained variance in the post-feedback pupil response, as expected.  

      (4) In Figure 3 (C-J), please clarify how the trial-by-trial correlations were computed (averaged across trials or subjects). Also, specify how the standard error of the mean (SEM) was calculated (using the number of participants or trials).

      The trial-by-trial correlations between the pupil signal and model parameters were computed for each participant, then the coefficients were averaged across participants for statistical inference. We have added several clarifications in the text (see section 2.5 and legends of Figure 3 and Supplementary Figure 4).

      We have added “the standard error of the mean across participants” to all figure labels.

      (5) For all time axes (e.g., Figure 2D), please label the ticks at 0, 0.5, 1, 1.5, 2, 2.5, and 3 seconds. Clearly indicate the duration of the feedback on the time axes. This is particularly important for interpreting the pupil dilation responses evoked by auditory feedback.

      We have labeled the x-ticks every 0.5 seconds in all figures and indicated the duration of the auditory feedback in the letter-color decision task and as well as the stimuli presented in the control tasks in the Supplementary Materials. 

      Reviewer #3 (Recommendations for the authors):

      (1) Introduction page 3: "In information theory, information gain quantifies the reduction of uncertainty about a random variable given the knowledge of another variable. In other words, information gain measures how much knowing about one variable improves the prediction or understanding of another variable."

      (2) In my opinion, the description of information gain can be clarified. Currently, it is not very concrete and quite abstract. I would recommend explaining it in the context of belief updating.

      We have removed these unclear statements in the Introduction. We now clearly state the following:

      “Information gain can be operationalized within information theory as the KullbackLeibler (KL) divergence between the posterior and prior belief distributions of a Bayesian observer, representing a formalized quantity that is used to update internal models [29,79,80].” (p. 4)

      (3) Page 4: The inconsistencies across studies are described in extreme detail. I recommend shortening this part and summarizing the inconsistencies instead of listing all of the findings separately.

      As per the reviewer’s recommendation, we have shortened this part of the introduction to summarize the inconsistencies in a more concise manner as follows: 

      “Previous studies have shown different temporal response dynamics of prediction error signals in pupil dilation following feedback on decision outcome: While some studies suggest that the prediction error signals arise around the peak (~1 s) of the canonical impulse response function of the pupil [11,30,41,61,62,90], other studies have shown evidence that prediction error signals (also) arise considerably later with respect to feedback on choice outcome [10,25,32,41,62]. A relatively slower prediction error signal following feedback presentation may suggest deeper cognitive processing, increased cognitive load from sustained attention or ongoing uncertainty, or that the brain is integrating multiple sources of information before updating its internal model. Taken together, the literature on prediction error signals in pupil dilation following feedback on decision outcome does not converge to produce a consistent temporal signature.” (p. 5)

      We would like to note some additional minor corrections to the preprint:

      We have clarified the direction of the effect in Supplementary Figure 3 with the following: 

      “Participants who showed a larger mean difference between the 80% as compared with the 20% frequency conditions in accuracy also showed smaller differences (a larger mean difference in magnitude in the negative direction) in pupil responses between frequency conditions (see Supplementary Figure 4).”

      The y-axis labels in Supplementary Figure 3 were incorrect and have been corrected as the following: “Pupil responses (80-20%)”.

      We corrected typos, formatting and grammatical mistakes when discovered during the revision process. Some minor changes were made to improve clarity. Of course, we include a version of the manuscript with Tracked Changes as instructed for consideration.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1(Public review):

      In this manuscript, Pagano and colleagues test the idea that the protein GMCL1 functions as a substrate receptor for a Cullin RING 3 E3 ubiquitin ligase (CUL3) complex. Using a pulldown approach, they identify GMCL1 binding proteins, including the DNA damage scaffolding protein 53BP1. They then focus on the idea that GMCL1 recruits 53BP1 for CUL3-dependent ubiquitination, triggering subsequent proteasomal degradation of ubiquitinated 53BP1.

      In addition to its DNA damage signalling function, in mitosis, 53BP1 is reported to form a stopwatch complex with the deubiquitinating enzyme USP28 and the transcription factor p53 (PMID: 38547292). These 53BP1-stopwatch complexes generated in mitosis are inherited by G1 daughter cells and help promote p53-dependent cell cycle arrest independent from DNA damage (PMID: 38547292). Several studies show that knockout of 53BP1 overcomes G1 cell cycle arrest after mitotic delays caused by anti-mitotic drugs or centrosome ablation (PMID: 27432897, 27432896). In this model, it is crucial that 53BP1 remains stable in mitosis and more stopwatch complex is formed after delayed mitosis.

      Major concerns:

      Pagano and coworkers suggest that 53BP1 levels can sometimes be suppressed in mitosis if the cells overexpress GMCL1. They carry out a bioinformatic analysis of available public data for p53 wild-type cancer cell lines resistant to the anti-mitotic drug paclitaxel and related compounds. Stratifying GMCL1 into low and high expression groups reveals a weak (p = 0.05 or ns) correlation with sensitivity to taxanes. It is unclear on what basis the authors claim paclitaxel-resistant and p53 wild-type cancer cell lines bypass the mitotic surveillance/timer pathway. They have not tested this. Figure 3 is a correlation assembled from public databases but has no experimental tests. Figure 4 looks at proliferation but not cell cycle progression or the length of mitosis. The main conclusions relating to cell cycle progression and specifically the link to mitotic delays are therefore not supported by experimental data. There is no imaging of the cell cycle or cell fate after mitotic delays, or analysis of where the cells arrest in the cell cycle. Most of the cell lines used have been reported to lack a functional mitotic surveillance pathway in the recent work by Meitinger. To support these conclusions, the stability of endogenous 53BP1 under different conditions in cells known to have a functional mitotic surveillance pathway needs to be examined. A key suggestion in the work is that the level of GMCL1 expression correlates with resistance to taxanes. For the mitotic surveillance pathway, the type of drug (nocodazole, taxol, etc) used to induce a delay isn't thought to be relevant, only the length of the delay. Do GMCL1-overexpressing cells show resistance to anti-mitotics in general?

      We thank the reviewer for this insightful comment. We propose that GMCL1 promotes CUL3-dependent ubiquitination of 53BP1 during prolonged mitotic arrest, thereby facilitating its proteasome-dependent degradation. To evaluate the potential clinical relevance of this mechanism, we stratified cancer cell lines based on GMCL1 mRNA expression using publicly available datasets from DepMap (PMID: 39468210). We observed correlations between GMCL1 expression levels and taxane sensitivity that appear to reflect specific cancer type-drug combinations. To experimentally evaluate this correlation and obtain mechanistic insights, we performed knockdown experiments in hTERT-RPE1 cells, which are known to possess an intact mitotic surveillance pathway. Silencing of GMCL1 alone inhibited cell proliferation and induced apoptosis, while co-depletion of either TP53BP1 or USP28 significantly rescued these effects. These results suggest that GMCL1 modulates the stability of 53BP1 and therefore the availability of the 53BP1-USP28-p53 ternary complex in cells with a functional mitotic surveillance pathway (MSP) (new Figure 5I,J) directly linking GMCL1 to the regulation of the MSP complex. Moreover, to further support our mechanism, we assessed the effect of GMCL1 levels on cell cycle progression. Briefly, following nocodazole synchronization and release, we treated cells with EdU and performed FACS analyses at different times. Knockdown of GMCL1 alone led to a delayed cell cycle progression, but co-depletion of either TP53BP1 or USP28 restored this phenotype (new Figure 3A and new Supplementary Figure 3A-C). These results are consistent with our proliferation data and suggest that the observed effects of GMCL1 are specific to mitotic exit. Finally, overexpression of GMCL1 accelerates cell cycle progression (as assessed by FACS analyses) upon release from prolonged mitotic arrest (new Figure 3B and new Supplementary Figure 3D-E). 

      Importantly, if GMCL1 specifically degrades 53BP1 during prolonged mitotic arrests, the authors should show what happens during normal cell divisions without any delays or drug treatments. How much 53BP1 is destroyed in mitosis under those conditions? Does 53BP1 destruction depend on the length of mitosis, drug treatment, or does 53BP1 get degraded every mitosis regardless of length? Testing the contribution of key mitotic E3 ligase activities on mitotic 53BP1 stability, such as the anaphase-promoting complex/cyclosome (APC/C) is important in this regard. One previous study reported an analysis of putative APC/C KEN-box degron motifs in 53BP1 and concluded these play a role in 53BP1 stability in anaphase (PMID: 28228263).

      Physiological mitosis under unperturbed conditions is typically brief (approximately 30 minutes), making protein quantification during this window challenging. Despite this, we tried by synchronizing cells using RO-3306 and releasing them into drug-free medium to assess GMCL1 dynamics during normal mitosis. Under these conditions, GMCL1 expression was similar to that in asynchronous cells and higher than the levels upon extended mitosis. However, when we attempted to measure the half-life of proteins using cycloheximide, most cells died, likely due to the toxic effect of cycloheximide in cells subjected to co-treatment with RO-3306 or nocodazole. This is the same reasons why in Figure 2C, we assessed 53BP1 in daughter cells rather than mitotic cells. 

      There is no direct test of the proposed mechanism, and it is therefore unclear if 53BP1 is ubiquitinated by a GMCL1-CUL3 ligase in cells, and how efficient this process would be at different cell cycle stages. A key issue is the lack of experimental data explaining why the proposed mechanism would be restricted to mitosis. Indirect effects, such as loss of 53BP1 from the chromatin fraction during M phase upon GMCL1 overexpression, do not necessarily mean that 53BP1 is degraded. PLK1-dependent chromatin-cytoplasmic shuttling of 53BP1 during mitotic delays has been described previously (PMID: 38547292, 37888778). These papers are cited in the text, but the main conclusions of those papers on 53BP1 incorporation into a stopwatch complex during mitotic delays have been ignored. Are the authors sure that 53BP1 is destroyed in mitosis and not simply re-localised between chromatin and non-chromatin fractions? At the very least, these reported findings should be discussed in the text.

      To examine whether GMCL1 promotes 53BP1 ubiquitination in cells, we expressed in cells Trypsin-Resistant Tandem Ubiquitin-Binding Entity (TR-TUBE), a protein that binds polyubiquitin chains. Abundant, endogenous ubiquitinated 53BP1 co-precipitated with TR-TUBE constructs only when wild-type GMCL1 but not the E142K GMCL1 mutant, was expressed (new Figure 2D).  The PLK1-dependent incorporation of 53BP1 into the stopwatch complex and the chromatin-cytoplasmic shuttling of 53BP1 during mitotic delays is now discussed in the text. That said, compared to parental cells, 53BP1 levels in the chromatin fraction are high in two different GMCL1 KO clones in M phase arrested cells (Figure 2A-B).  This increase does not correspond to a decrease in the 53BP1 soluble fraction (Figure 2A and new Supplementary Figure 2D), suggesting decreased 53BP1 is not due to re-localization. The increased half-life of 53BP1 in daughter cells (Figure 2C), also supports this hypothesis. 

      The authors use a variety of cancer cell line models throughout their study, most of which have been reported to lack a functional mitotic surveillance pathway. U2OS and HCT116 cells do not respond normally to mitotic delays, despite being annotated as p53 WT. Other studies have used p53 wild-type hTERT RPE-1 cells to study the mitotic surveillance pathway. If the model is correct, then over-expressing GMCL1 in hTERT-RPE1 cells should suppress cell cycle arrest after mitotic delays, and GMCL1 KO should make the cells more sensitive to delays. These experiments are needed to provide an adequate test of the proposed model.

      We greatly appreciate the reviewer’s suggestion regarding overexpression of GMCL1 in hTERT-RPE1 cells. To address this, we generated stable RPE1 cells expressing V5-tagged GMCL1 and conducted EdU incorporation assays following nocodazole synchronization and release. Overexpression of GMCL1 enhanced cell cycle progression compared to control cells (new Figure 3B and new Supplementary Figure 3D-E) after mitotic arrest, consistent with our model. We, therefore, propose that GMCL1 controls 53BP1 stability to suppress p53-dependent cell cycle arrest.

      We also want to point out that while some papers suggest that HCT116 and U2OS cells do not have an intact mitotic surveillance pathway, others have shown that the MSP is indeed functioning in HCT116 cells and can be triggered with variable efficiency in U2OS cells (PMID: 38547292). This is likely due to high heterogeneity and extensive clonal diversity of cancer cell lines grown in different labs. Please see examples in PMIDs: 3620713, 30089904, and 30778230. In particular, PMID: 30089904 shows that this heterogeneity correlates with considerably different drug responses. 

      To conclude, while the authors propose a potentially interesting model on how GMCL1 overexpression could regulate 53BP1 stability to limit p53-dependent cell cycle arrest, it is unclear what triggers this pathway or when it is relevant. 53BP1 is known to function in DNA damage signalling, and GMCL1 might be relevant in that context. The manuscript contains the initial description of GMCL1-53BP1 interaction but lacks a proper analysis of the function of this interaction and is therefore a preliminary report.

      We hope that the new experiments, along with the clarifications provided in this response letter and revised manuscript, offer the reviewer increased confidence in the robustness and validity of our proposed model.

      Reviewer #2 (Public review):

      This study investigates the role of GMCL1 in regulating the mitotic surveillance pathway (MSP), a protective mechanism that activates p53 following prolonged mitosis. The authors identify a physical interaction between 53BP1 and GMCL1, but not with GMCL2. They propose that the ubiquitin ligase complex CRL3-GMCL1 targets 53BP1 for degradation during mitosis, thereby preventing the formation of the "mitotic stopwatch" complex (53BP1-USP28-p53) and subsequent p53 activation. The authors show that high GMCL1 expression correlates with resistance to paclitaxel in cancer cell lines that express wild-type p53. Importantly, loss of GMCL1 restores paclitaxel sensitivity in these cells, but not in p53-deficient lines. They propose that GMCL1 overexpression enables cancer cells to bypass MSP-mediated p53 activation, promoting survival despite mitotic stress. Targeting GMCL1 may thus represent a therapeutic strategy to re-sensitize resistant tumors to taxane-based chemotherapy.

      Strengths:

      This manuscript presents potentially interesting observations. The major strength of this article is the identification of GMCL1 as a 53BP1 interaction partner. The authors identified relevant domains and showed that GMCL1 controls 53BP1 stability. The authors further show a potentially interesting link between GMCL1 status and sensitivity to Taxol.

      Weaknesses:

      However, the manuscript is significantly weakened by unsubstantiated mechanistic claims, overreliance on a non-functional model system (U2OS), and overinterpretation of correlative data. To support the conclusions of the manuscript, the authors must show that the GMCL1-dependent sensitivity to Taxol depends on the mitotic surveillance pathway.

      To demonstrate that GMCL1-dependent taxane sensitivity is mediated through the mitotic surveillance pathway (MSP), we now performed experiments using hTERT-RPE1 (RPE1) cells, a widely used, non-transformed cell line known to possess a functional MSP.  We compared RPE1 cells with knockdown of GMCL1 alone to those with simultaneous knockdown of GMCL1 and either TP53BP1 or USP28. Upon paclitaxel (Taxol) treatment, cells with GMCL1 knockdown exhibited suppressed proliferation and increased apoptosis. Notably, these phenotypes were rescued by co-depletion of TP53BP1 or USP28 (new Figure 5I,J). These results support the notion that GMCL1 contributes to MSP activity, at least in part, through its regulation of 53BP1.       

      To further strengthen our mechanistic experiments, we assessed the effect of GMCL1 levels on cell cycle progression. Following nocodazole synchronization and release, we treated cells with EdU and performed FACS analyses at different times. Knockdown of GMCL1 alone led to a delay in cell cycle progression, but co-depletion of either TP53BP1 or USP28 alleviate this phenotype (new Figure 3A and new Supplementary Figure 3A, B). These results are consistent with our proliferation data.

      Reviewer #3 (Public review):

      Summary:

      In this study, Kito et al follow up on previous work that identified Drosophila GCL as a mitotic substrate recognition subunit of a CUL3-RING ubiquitin ligase (CRL3) complex.

      Here they characterize mutants of the human ortholog of GCL, GMCL1, that disrupt the interaction with CUL3 (GMCL1E142K) and that lack the substrate interaction domain (GMCL1 BBO). Immunoprecipitation followed by mass spectrometry identified 9 proteins that interacted with wild-type FLAG-GMCL1 and GMCL1 EK but not GMCL1 BBO. These proteins included 53BP1, which plays a well-characterized role in double-strand break repair but also functions in a USP28-p53-53BP1 "mitotic stopwatch" complex that arrests the cell cycle after a substantially prolonged mitosis. Consistent with the IP-MS results, FLAG-GMCL1 immunoprecipitated 53BP1. Depletion of GMCL1 during mitotic arrest increased protein levels of 53BP1, and this could be rescued by wild-type GMCL1 but not the E142K mutant or a R433A mutant that failed to immunoprecipitate 53BP1.

      Using a publicly available dataset, the authors identified a relatively small subset of cell lines with high levels of GMCL1 mRNA that were resistant to the taxanes paclitaxel, cabazitaxel, and docetaxel. This type of analysis is confounded by the fact that paclitaxel and other microtubule poisons accumulate to substantially different levels in various cell lines (DOI: 10.1073/pnas.90.20.9552 , DOI: 10.1091/mbc.10.4.947 ), so careful follow-up experiments are required to validate results. The correlation between increased GMCL1 mRNA and taxane resistance was not observed in lung cancer cell lines. The authors propose this was because nearly half of lung cancers harbor p53 mutations, and lung cancer cell lines with wild-type but not mutant p53 showed the correlation between increased GMCL1 mRNA and taxane resistance. However, the other cancer cell types in which they report increased GMCL1 expression correlates with taxane sensitivity also have high rates of p53 mutation. Furthermore, p53 status does not predict taxane response in patients (DOI: 10.1002/1097-0142(20000815)89:4<769::aid-cncr8>3.0.co;2-6 , DOI: 10.1002/(SICI)1097-0142(19960915)78:6<1203::AID-CNCR6>3.0.CO;2-A , PMID: 10955790).

      The authors then depleted GMCL1 and reported that it increased apoptosis in two cell lines with wild-type p53 (MCF7 and U2OS) due to activation of the mitotic stopwatch. This is surprising because the mitotic stopwatch paper they cite (DOI: 10.1126/science.add9528 ) reported that U2OS cells have an inactive stopwatch and that activation of the stopwatch results in cell cycle arrest rather than apoptosis in most cell types, including MCF7. Beyond this, it has recently been shown that the level of taxanes and other microtubule poisons achieved in patient tumors is too low to induce mitotic arrest (DOI: 10.1126/scitranslmed.3007965 , DOI: 10.1126/scitranslmed.abd4811 , DOI: 10.1371/journal.pbio.3002339 ), raising concerns about the relevance of prolonged mitosis to paclitaxel response in cancer. The findings here demonstrating that GMCL1 mediates degradation of 53BP1 during mitotic arrest are solid and of interest to cell biologists, but it is unclear that these findings are relevant to paclitaxel response in patients.

      Strengths:

      This study identified 53BP1 as a target of CRL3GMCL1-mediated degradation during mitotic arrest. AlphaFold3 predictions of the binding interface, followed by mutational analysis, identified mutants of each protein (GMCL1 R433A and 53BP1 IEDI1422-1425AAAA) that disrupted their interaction. Knock-in of a FLAG tag into the C-terminus of GMCL1 in HCT116 cells, followed by FLAG immunoprecipitation, confirmed that endogenous GMCL1 interacts with endogenous CUL3 and 53BP1 during mitotic arrest.

      Weaknesses:

      The clinical relevance of the study is overinterpreted. The authors have not taken relevant data about the clinical mechanism of taxanes into account. Supraphysiologic doses of microtubule poisons cause mitotic arrest and can activate the mitotic stopwatch. However, in physiologic concentrations of clinically useful microtubule poisons, cells proceed through mitosis and divide their chromosomes on mitotic spindles that are at least transiently multipolar. Though these low concentrations may result in a brief mitotic delay, it is substantially shorter than the arrest caused by high concentrations of microtubule poisons, and the one mimicked here by 16 hours of 0.4 mg/mL nocodazole, which is not used clinically and does not induce multipolar spindles. Resistance to mitotic arrest occurs through different mechanisms than resistance to multipolar spindles. No evidence is presented in the current version of the manuscript that GMCL1 affects cellular response to clinically relevant doses of paclitaxel.

      We agree that it would be an overstatement to claim that GMCL1 and p53 regulates paclitaxel sensitivity in cancer patients in a clinical context. The correlations we observed were based on publicly available cancer cell lines from datasets catalogued in CCLE and DepMap, which do not fully account for clinical heterogeneity and patient-specific factors. In response to this important point, we have revised the text accordingly. 

      In the experiments shown in former Figure 4A-H (now Figure 5A-H) and in those shown in the new Figure 5I-J, we used 100 nM paclitaxel to test the hypothesis that low GMCL1 levels sensitizes cancer cells in a p53-dependent manner. Here, paclitaxel was chosen to mimic the conditions reported in the PRISM dataset (PMID: 32613204), which compiles the proliferation inhibitory activity of 4,518 compounds tested across 578 cancer cell lines. Consistent with our cell cycle findings, the paclitaxel sensitivity caused by GMCL1 depletion was reverted by silencing 53BP1 or USP28 (new Figure 5I-J), again supporting the involvement of the stopwatch complex. We are unsure about how to model the “physiologic concentrations of clinically useful microtubule poisons” in cell-based studies. A recent review notes that “The time above a threshold paclitaxel plasma concentration (0.05 mmol/L) is important for the efficacy and toxicity of the drug” (PMID: 28612269).  Two other reviews mention that the clinically relevant concentration of paclitaxel is considered to be plasma levels between 0.05–0.1 μmol/L (approximately 50–100 nM) and that in clinical dosing, typical patient plasma concentrations after paclitaxel infusion range from 80–280 nM, with corresponding intratumoral concentrations between 1.1–9.0 μM, due to drug accumulation in tumor tissue (PMIDs: 24670687 and  29703818).  We have now emphasized in the revised text the rationale for using 100 nM paclitaxel in our experiments.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      General comments on the Figures:

      (1) Western blots lack molecular weight markers on most panels and are often over-exposed and over-contrasted, rendering them hard to interpret.

      We have now included molecular weight markers in all Western blot panels. We have also reprocessed the images to avoid overexposure and excessive contrast, ensuring that the bands are clearly visible and interpretable.

      (2) Input and IP samples do not show percentage loading, so it is hard to interpret relative enrichments.

      In the revised figures, we have indicated what % of the input was loaded.

      (3) The authors change between cell line models for their experiments, and this is not clear in the figures. These are important details for interpreting the data, as many of the cell lines used are not functional for the mitotic surveillance pathway.

      In the revised manuscript, we have clearly indicated the specific cell lines used in each experiment in the figure legends. Additionally, to address concerns regarding the mitotic surveillance pathway, we have included new experiments using hTERT-RPE1 cells, which have been reported to possess a functional mitotic surveillance pathway (MSP) (Figure 4I-J).

      (4) No n-numbers are provided in the figure legends. Are the Western blots provided done once, or are they reproducible? Many of the blots would benefit from quantification and presentation via graphs to test for reproducible changes to 53BP1 levels under the different conditions.

      As now indicated in the methods section, we have conducted each Western blot no less than three times, yielding results that exhibit a high degree of reproducibility. A representative Western blot has been selected for each figure. We did not include densiometric quantification of immunoblots, given that the semi-quantitative nature of this technique would lead to an overinterpretation of our data; unfortunately, this is a limitation of the technique. In fact, eLife and other similar scientific journals do not adhere to the practice of quantifying Western blots. One exception to this norm is for protein half-life studies, which is done to measure the kinetics of decay rates and their internal comparisons. Accordingly, the experiments in Figure 2C were quantified.

      (5) Graphs displayed in the supplementary figures are blacked out, and individual data points cannot be visualised. All graphs should have individual data points clearly visible.

      We revised the quantified graphs and replaced them with scatter plots to clearly display individual data points, showing sample distribution.

      Additional experiments with specific comments on Figures:

      (1) Figure 1C-D: the relative amount of 53BP1 co-precipitating with FLAG-tagged GMCL1 WT appears very different between the two experiments. If the idea is that MLN4924 (Cullin neddylation inhibitor) makes the interaction easier to capture, then this should be explained in the text, and ideally shown on the same gel/blot -/+ MLN4924.

      We now present the samples treated with and without MLN4924 on the same gel/blot to allow direct comparison (new Figure 1D) and clarified this point in the text.

      (2) Figure 1E: The figure legend states that GMCL1 was immunoprecipitated, but the Figure looks as though FLAG-tagged 53BP1 was the bait protein being immunoprecipitated? Can the authors clarify?

      We thank the reviewer for pointing out the discrepancy between the figure and the figure legend in Figure 1E. The immunoprecipitation was indeed performed using FLAG-tagged 53BP1, and we have now rectified the figure legend accordingly. 

      (3) Figure 1F: Rather than parental cell lysate, the better control would be to IP FLAG from another FLAG-tagged expressing cell line, to rule out non-specific binding with the FLAG tag at the non-overexpressed level. 

      Figure 1F shows interaction at the endogenous level. The specificity of binding with overexpressed proteins is shown in Figures 1C and 1D.

      The USP28 blot is over-exposed and makes it hard to see any changes in electrophoretic mobility - it looks as though there is a change between the parental and the KI cell line? It is surprising that USP28 would co-IP with GMCL1 (presumably because USP28 is bound to 53BP1) if the function of GMCL1-53BP1 interaction is to promote 53BP1 degradation. Can the authors reconcile this? Crucially, if the authors claim that the 53BP1-GMCL1 interaction is specific to prolonged mitosis, then this experiment should be repeated and performed with asynchronous, normal-length mitosis, and prolonged mitosis conditions. This is vital for supporting the claim that this interaction only occurs during prolonged mitoses and does not occur in every mitosis regardless of length.

      This is a good point. Unfortunately, many of the protein-protein interactions occur post lysis. Therefore, we could not observe differences in asynchronous vs. mitotic cells.

      (4) Figure S1F: Label on blot should be CUL3 not CUI3.

      We thank the reviewer for pointing this out and we have corrected the typo.

      (5) Figure 2A: The authors suggest an increase in chromatin-bound 53BP1 in GMCL1 KO U2OS cells, specifically in M phase. Again, is this time in mitosis dependent, or would this be evident in every mitosis, regardless of length? Such an experiment would benefit from repetition and quantification to test whether the observed effect is reproducibly consistent. If the authors' model is correct, simply treating U2OS WT mitotic cells with MG132 during the mitotic arrest and performing the same fractionation should bring 53BP1 levels up to that seen in GMCL1 KO cells under the same conditions.

      The reviewer’s suggestion to assess 53BP1 accumulation in wild-type U2OS cells treated with MG132 during mitotic arrest is indeed highly relevant. However, treatment with MG132 during prolonged mitosis consistently led to significant cell death, making it technically challenging to evaluate 53BP1 levels under these conditions.

      (6) Figure 2B: The authors restore GMCL1 expression in the KO U2OS cells using WT and 2 distinct mutant cDNAs. However, the expression of these constructs is not equivalent, and thus their effects cannot be directly compared. It is also surprising that GMCL1 is much higher in M phase samples in this experiment (shouldn't it be destroyed?), when no such behaviour has been observed in the other figures.

      There is no evidence in our study or others that GMCL1 should be destroyed in M phase.  We show that the R433A mutant is expressed at a level very similar to the WT protein, yet it doesn’t promote the degradation of 53BP1. It is true that the E142K is expressed less in mitotic cells whereas is the most expressed in asynchronous cells. For some reason, this mutant has an inverse behavior compared to the WT, limiting the interpretation of this result. We now mention this in the text. 

      (7) Figure 2C: The CHX experiment would benefit from inclusion of a control protein known to have a short half-life (e.g. c-myc, p53). Is GMCL1 known to have a relatively short half-life? It looks as though GMCL1 disappears after 1 h CHX treatment (although hard to definitively tell in the absence of molecular weight markers). 53BP1 appears to continue declining in the absence of GMCL1, which is surprising if p53BP1 degradation requires GMCL1. How can the authors reconcile this?

      As a control for the CHX chase experiments, we included p21, whose protein levels decreased in a CHX-dependent. GMCL1 itself also appeared to undergo degradation upon CHX treatment, but it doesn’t disappear completely.

      (8) Supplemental Figure 2:

      Transcription is largely inhibited in M phase, so the p53 target gene transcripts present in M phase are inherited from the preceding G2 phase. The qPCR's thus need a reference sample to compare against. I.e., was p21/PUMA/NOXA mRNA already low in G2 in the GMCL1 KO + WT cells before they entered mitosis? Or is the mRNA stability affected during M phase specifically? Is this effect on the mRNA dependent on the time in mitosis?

      It is well established that transcription is not entirely shut down during mitosis, particularly for a subset of genes involved in cell cycle regulation. For example, p21, PUMA, NOXA, and p53 mRNAs have been shown to remain actively transcribed during mitosis (see Table S5 in PMID: 28912132). However, we currently lack direct evidence that p53 activation during mitosis, specifically through the mitotic surveillance pathway, drives the transcription of p21, PUMA, or NOXA mRNAs during M phase. In the absence of such mechanistic data, we opted to exclude these analyses from the final figures.

      Panel B: blots are too over-exposed to see differences in p53 stability under the different conditions. Mitotic samples should be included to show how these differ from the G1 samples.

      The background of all blot images has been adjusted to ensure clarity and consistency.

      Panel D: The authors show no significant difference in the cell cycle profiles of the GMCL1 KO and reconstituted cells compared to parental U2OS cells. This should also be performed in the G1 daughter cells following a prolonged mitosis, to test the effect of the different GMCL1 constructs on G1 cell cycle arrest. U2OS cells have been reported not to have a functional mitotic surveillance pathway (Meitinger et al, Science, 2024), so U2OS cells are perhaps not a good model for testing this.

      We performed cell cycle profiling using EdU incorporation in hTERT-RPE1 cells, which possess a functional MSP, to evaluate cell cycle progression in daughter cells following prolonged mitosis. We observed that GMCL1 knockdown alone leads to G1-phase arrest. In contrast, co-depletion of GMCL1 with either 53BP1 or USP28 bypasses this arrest, indicating that GMCL1 regulates cell cycle progression in an MSP-dependent manner. Please see also the answer to the public review above. 

      (9) Figure 3:

      The authors show expression data for GMCL1 in the different cancer cell lines. This should be validated for a subset of cancer cell lines at the GMCL1 protein level, and cross-correlated to their MSP/mitotic timer status. Does GMCL1 depletion or knockout in p53 wild-type cancer cell lines overexpressing GMCL1 protein restore mitotic surveillance function?

      We were unable to assess GMCL1 protein levels using publicly available proteomics datasets, as GMCL1 expression was not detected. In p53 wild-type hTERT-RPE1 cells, GMCL1 knockdown impaired the mitotic surveillance pathway, as evidenced by G1-phase arrest following prolonged mitosis (new Figure 3A and new Supplementary Figure 3A, B). This arrest was rescued by co-depletion of either TP53BP1 or USP28, indicating that GMCL1 acts upstream of the MSP.

      (10) Figure 4:

      The authors show siRNA experiments depleting GMCL1 and testing the effects of GMCL1 loss on cell viability and apoptosis induction. This is performed in different cell line backgrounds. However, there is no demonstration that any of the observed effects are due to a lack of GMCL1 activity on 53BP1. These experiments need to be repeated in 53BP1 co-depleted cells to test for rescue. Without this, the interpretation is purely correlative.

      We assessed the effects of GMCL1 knockdown, alone or in combination with TP53BP1 or USP28 knockdown, on cell viability and apoptosis in hTERT-RPE1 cells using siRNA. Knockdown of GMCL1 alone led to a significant reduction in cell viability and an increase in apoptosis. However, co-depletion of GMCL1 with either TP53BP1 or USP28 restored both cell viability and apoptosis levels to those observed in control cells (new Figure 5I,J).

      (11) Text comments:

      Line 257: HeLa cells supress p53 through the E6 viral protein and are not "mutant" for p53.

      The authors should cite early work by Uetake and Sluder describing the effects of spindle poisons on the mitotic surveillance pathway.

      We appreciate the reviewer’s comments – We have now made the necessary corrections.

      Reviewer #2 (Recommendations for the authors):

      Major Points:

      (1) Unsubstantiated Mechanistic Claims:

      In Figures 3 and 4, the authors show correlations between GMCL1 expression and sensitivity to Taxol. However, they fail to demonstrate that the mitotic stopwatch is mechanistically involved. To support this conclusion, the authors must test whether deletion of 53BP1, USP28, or disruption of their interaction rescues Taxol sensitivity in GMCL1-depleted cells. Since 53BP1 also plays a role in DNA damage response, such rescue experiments are necessary to distinguish between mitotic surveillance-specific and broader stress-response effects. Deletion of USP28 would be particularly informative.

      We sought to experimentally determine whether GMCL1 is involved in regulating the mitotic stopwatch. Knockdown of GMCL1 alone resulted in reduced cell proliferation and increased apoptosis. In contrast, co-depletion of GMCL1 with either TP53BP1 or USP28 restored both proliferation and apoptosis levels to those observed in control cells (new Figure 5I, J). To further strengthen our mechanistic experiments, we assessed the effect of GMCL1 levels on cell cycle progression. We conducted EdU incorporation assays following nocodazole synchronization and release. Knockdown of GMCL1 alone led to a delay in G1 progression, whereas co-depletion of either TP53BP1 or USP28 rescued normal cell cycle progression (new Figure 3A and new Supplementary Figure 3A, B). These results are consistent with our proliferation data and suggest that GMCL1 functions upstream of the ternary complex, likely by regulating 53BP1 protein levels.

      (2) Model System Limitations (U2OS Cells):

      The use of U2OS cells is highly problematic for investigating the mitotic surveillance pathway. U2OS cells lack a functional mitotic stopwatch and do not arrest following prolonged mitosis in a 53BP1/USP28-dependent manner (PMID: 38547292). Therefore, conclusions drawn from this model system about the function of the mitotic surveillance pathway are not substantiated. Key experiments should be repeated in a cell line with an intact pathway, such as RPE1.

      We now performed all key experiments also hTERT-RPE1 cells (see above). We also would like to point out that while some papers suggest that HCT116 and U2OS cells do not have an intact mitotic surveillance pathway, others have showed that the MSP is indeed functioning in HCT116 cells and can be triggered with variable efficiency in U2OS cells (PMID: 38547292).  This is likely due to high heterogeneity and extensive clonal diversity of cancer cell lines grown in different labs. Please see examples in PMIDs: 3620713, 30089904, and 30778230. In particular, PMID: 30089904 shows that this heterogeneity correlates with considerably different drug responses. 

      (3) Misinterpretation of p53 Activity Timing:

      The manuscript states that "GMCL1 KO cells led to decreased mRNA levels of p21 and NOXA during mitosis" (line 194). However, it is well established that the mitotic surveillance pathway activates p53 in the G1 phase following prolonged mitosis-not during mitosis itself (PMID: 38547292). Therefore, the observed changes in mRNA levels during mitosis are unlikely to be relevant to this pathway.

      We currently lack direct evidence that p53 activated during mitosis through the mitotic surveillance pathway directly influences the transcription of p21, PUMA, or NOXA mRNAs during M phase. Therefore, we have chosen to exclude these data from the final figures.

      (4) Incorrect Interpretation of 53BP1 Chromatin Binding:

      The authors claim that 53BP1 remains associated with chromatin during mitosis, which contradicts established literature. It is known that 53BP1 is released from chromatin during mitosis via mitosis-specific phosphorylation (PMID: 24703952), and this is supported by more recent findings (PMID: 38547292). A likely explanation for the discrepancy may be contamination of mitotic fractions with interphase cells. The chromatin fraction data in Figure 2C must be interpreted with caution.

      Our method to synchronize in M phase is rather stringent (see Supplementary Figure 3D as an example). The literature indicates that the bulk of 53BP1 is released from chromatin during mitosis. Yet, even in the two publications mentioned by the reviewer, there is a difference in the observable amount of 53BP1 bound to chromatin (compare Figure 2B in PMID: 38547292 and Figure 5A in PMID: 24703952). The difference is likely due to the different biochemical approaches used to purify chromatin bound proteins (salt and detergent concentrations, sonication, etc.). Using our fractionation approach, we can reliably separate the soluble fraction (containing also the nucleoplasmic fraction) and chromatin associated proteins as indicated by the controls such as a-Tubulin and Histon H3.  We have now mentioned these limitations when comparing different fractionation methods in our discussion section.

      (5) Inadequate Citation of Foundational Literature:

      The literature on the mitotic surveillance pathway is relatively limited, and it is essential that the authors provide a comprehensive and accurate account of its development. The foundational work by the Sluder lab (PMID: 20832310), demonstrating a p53-dependent arrest following prolonged mitosis, must be cited. Furthermore, the three key 2016 papers (PMID: 27432896, 27432897, 27432896) that identified the involvement of USP28 and 53BP1 in this pathway are critical and should be cited as the basis of the mitotic surveillance pathway.

      In contrast, the manuscript currently emphasizes publications that either contribute minimally or have been contradicted by prior and subsequent work. For example: PMID: 31699974, which proposes Ser15 phosphorylation of p53 as critical, has been contradicted by multiple groups (e.g., Holland, Oegema, and Tsou labs).

      PMID: 37888778, which suggests that 53BP1 must be released from kinetochores, is inconsistent with findings that indicate kinetochore localization is not relevant.

      The authors should thoroughly revise the Introduction to reflect what this reviewer would describe as a more accurate and scholarly approach to the literature.

      We have substantially revised both the Introduction and Discussion sections to incorporate important references kindly suggested by the reviewer.

      Minor Points:

      (1) Overexposed Western Blots:

      The Western blots throughout the manuscript are heavily overexposed and saturated, obscuring differences in protein levels and hindering data interpretation. The authors should provide properly exposed blots with quantification where appropriate.

      We have provided Western blot images with appropriate exposure levels and included quantification where appropriate (i.e., to measure the kinetics of decay rates as in Figure 2C). For all the other immunoblots, we did not include densiometric quantification, given that the semi-quantitative nature of this technique would lead to overinterpretation of our data. This is, unfortunately, a limitation of the technique. In fact, eLife and other similar scientific journals do not adhere to the practice of quantifying Western blot analyses. 

      (2) Missing information in the graphs in Figure 2C and 4; S2? How many repeats? What are the asterisks?

      Panels referenced above have been repeated several times, and further details are now provided in the figure legends.

      Reviewer #3 (Recommendations for the authors):

      (1)   The claim that GMCL1 modulates paclitaxel sensitivity in cancer should be toned down

      .

      We agree that it would be an overstatement to claim that GMCL1 regulates paclitaxel sensitivity in cancer patients in a clinical context. The correlations we observed were based on publicly available, cell line–based datasets, which do not fully account for clinical heterogeneity and patient-specific factors. In response to this important point, we have revised our statements and corresponding text accordingly. We now placed greater emphasis on our molecular and cell biology studies.

      (2) Additional experiments in low, physiologically relevant concentrations of paclitaxel would be interesting. It is possible that these concentrations activate the mitotic stopwatch in a portion of cells, in addition to inducing cell death due to chromosome loss, activation of an immune response, and chromothripsis. Results should be interpreted in the context of this complexity.

      Please see the response to the public review. 

      (3) It would be helpful to show that CUL3 interacts with 53BP1 only in the presence of GMCL1.

      We show that the binding of 53BP1 to GMCL1 is independent of the ability of GMCL1 to bind CUL3 (Figure 1C, D). The binding between 53BP1 and CUL3 is difficult to detect (Figure 1F) likely because it’s not direct but mediated by GMCL1.

      (4) The GMCL1 "KO" lines appear to still express a low level of GMCL1 (Figure 2A), which should be acknowledged

      We have included the GMCL1 mRNA expression data, as measured by RT-PCR, in Supplementary Figure 1G, demonstrating that GMCL1 expression was undetectable under the tested conditions.

      (5) Additional description of the methods is warranted. This is particularly true for the database analysis that forms the basis for the claim that GMCL1 overexpression causes resistance to paclitaxel and other taxanes presented in Figure 3, the methodology used to obtain M-phase cells, and the concentration and duration of taxol treatment.

      We have now extensively revised the Methods section.  

      (6) "Taxol" and "paclitaxel" are used interchangeably throughout the manuscript. Consistency would be preferable.

      We have revised the manuscript to maintain consistency in the use of the terms “Taxol” and “paclitaxel” and now refer to “paclitaxel” when discussing that individual compound; “taxanes” when referring collectively to cabazitaxel, docetaxel and paclitaxel; and “Taxol” has been removed entirely to avoid redundancy or confusion.    

      (7) It is unclear why it is claimed that GMCL1 interacts "specifically" with 53BP1 (line 176) since multiple interactors were identified in the IP-MS study

      We meant that the GMCL1 R433A mutant loses its ability to bind 53BP1, suggesting that the GMCL1-53BP1 interaction is not an artifact. We have now clarified the text. 

      (8) The bottom row in Figure S3 is misleading. Paclitaxel is not uniformly effective in every tumor of any given type, and so resistance occurs in every cancer type.

      We fully agree that cancer is highly heterogeneous and that paclitaxel efficacy varies across tumors, even within the same histological subtype. Our intension was not to suggest uniform sensitivity/resistance, but rather to provide a high-level overview using aggregated data. We acknowledge that this coarse-grained representation may unintentionally imply overly generalized conclusions. To avoid potential misinterpretation, we have removed the corresponding panel in the revised paper.

    1. Author response:

      Here we provide a provisional response addressing the public comments and outlining the revisions we are planning to make:

      (1) We will add additional baseline models to delineate the contributions of the acoustic and linguistic pathways.

      (2) We will show additional ablation analysis and other model comparison results, as suggested by the reviewers, to justify the choice of the DNN models.

      (3) We will clarify the use of the TIMIT dataset during pre-training. In fact, the TIMIT speech data (the speech corpora used in the test set) was not included or used when pre-training the acoustic or linguistic pathway. It was only used in fine-tuning the final speech synthesizer (the cosyvoice model). We will present results without this fine-tuning step, which will fully eliminate the usage of the TIMIT data during model training.

      (4) We will further analyze the phoneme confusion matrices and/or other data to evaluate the model behavior.

      (5) We will analyze the test sentences with high and low accuracies. We will also include results with partial training data (e.g. using 25%, 50%, 75% of the training set) to further evaluate the impact of the total amount of training data.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      This research group has consistently performed cutting-edge research aiming to understand the role of hormones in the control of social behaviors, specifically by utilizing the genetically-tractable teleost fish, medaka, and the current work is no exception. The overall claim they make, that estrogens modulate social behaviors in males and females is supported, with important caveats. For one, there is no evidence these estrogens are generated by "neurons" as would be assumed by their main claim that it is NEUROestrogens that drive this effect. While indeed the aromatase they have investigated is expressed solely in the brain, in most teleosts, brain aromatase is only present in glial cells (astrocytes, radial glia). The authors should change this description so as not to mislead the reader. Below I detail more specific strengths and weaknesses of this manuscript.

      We thank the reviewer for this positive evaluation of our work and for the helpful comments and suggestions. Regarding the concern that the term “neuroestrogens” may be misleading, we addressed this in the previous revision by consistently replacing it throughout the manuscript with “brain-derived estrogens” or “brain estrogens.”

      In addition, the following sentence was added to the Introduction (line 61): “In teleost brains, including those of medaka, aromatase is exclusively localized in radial glial cells, in contrast to its neuronal localization in rodent brains (Forlano et al., 2001; Diotel et al., 2010; Takeuchi and Okubo, 2013).”

      Strenghth:

      Excellent use of the medaka model to disentangle the control of social behavior by sex steroid hormones 

      The findings are strong for the most part because deficits in the mutants are restored by the molecule (estrogens) that was no longer present due to the mutation 

      Presentation of the approach and findings are clear, allowing the reader to make their own inferences and compare them with the authors' 

      Includes multiple follow-up experiments, which leads to tests of internal replication and an impactful mechanistic proposal 

      Findings are provocative not just for teleost researchers, but for other species since, as the authors point out, the data suggest mechanisms of estrogenic control of social behaviors may be evolutionary ancient 

      We thank the reviewer again for their positive evaluation of our work.

      Weakness:

      As stated in the summary, the authors are attributing the estrogen source to neurons and there isn't evidence this is the case. The impact of the findings doesn't rest on this either

      As mentioned above, we addressed this in the previous revision by replacing “neuroestrogens” with “brain-derived estrogens” or “brain estrogens” throughout the manuscript. In addition, the following sentence was added to the Introduction (line 61): “In teleost brains, including those of medaka, aromatase is exclusively localized in radial glial cells, in contrast to its neuronal localization in rodent brains (Forlano et al., 2001; Diotel et al., 2010; Takeuchi and Okubo, 2013).”

      The d4 versus d8 esr2a mutants showed different results for aggression. The meaning and implications of this finding are not discussed, leaving the reader wondering

      This comment is the same as one raised in the first review (Reviewer #1’s comment 2 on weaknesses), which we already addressed in our initial revision. For the reviewer’s convenience, we provide the response below:

      Line 300: As the reviewer correctly noted, circles were significantly reduced in mutant males of the Δ8 line, whereas no significant reduction was observed in those of the Δ4 line. However, a tendency toward reduction was evident in the Δ4 line (P = 0.1512), and both lines showed significant differences in fin displays. Based on these findings, we believe our conclusion that esr2a<sup>−/−</sup> males exhibit reduced aggression remains valid. To clarify this point and address potential reader concerns, we have revised the text as follows: “esr2a<sup>−/−</sup> males exhibited significantly fewer fin displays (P = 0.0461 and 0.0293 for Δ8 and Δ4 lines, respectively) and circles (P = 0.0446 and 0.1512 for Δ8 and Δ4 lines, respectively) than their wild-type siblings (Fig. 5L; Fig. S8E), suggesting less aggression” was edited to read “esr2a<sup>−/−</sup> males from both the Δ8 and Δ4 lines exhibited significantly fewer fin displays than their wild-type siblings (P = 0.0461 and 0.0293, respectively). Circles followed a similar pattern, with a significant reduction in the Δ8 line (P = 0.0446) and a comparable but non-significant decrease in the Δ4 line (P =0.1512) (Figure 5L, Figure 5—figure supplement 3E), showing less aggression.”

      Lack of attribution of previous published work from other research groups that would provide the proper context of the present study

      This comment is also the same as one raised in the first review (Reviewer #1’s comment 3 on weaknesses). In our previous revision, in response to this comment, we cited the relevant references (Hallgren et al., 2006; O’Connell and Hofmann, 2012; Huffman et al., 2013; Jalabert et al., 2015; Yong et al., 2017; Alward et al., 2020; Ogino et al., 2023) in the appropriate sections. We also added the following new references and revised the Introduction and Discussion accordingly:

      (2) Alward BA, Laud VA, Skalnik CJ, York RA, Juntti SA, Fernald RD. 2020. Modular genetic control of social status in a cichlid fish. Proceedings of the National Academy of Sciences of the United States of America 117:28167–28174. DOI: https://doi.org/10.1073/pnas.2008925117

      (39) O’Connell LA, Hofmann HA. 2012. Social status predicts how sex steroid receptors regulate complex behavior across levels of biological organization. Endocrinology 153:1341–1351. DOI:https://doi.org/10.1210/en.2011-1663

      (54) Yong L, Thet Z, Zhu Y. 2017. Genetic editing of the androgen receptor contributes to impaired male courtship behavior in zebrafish. Journal of Experimental Biology 220:3017–3021.DOI:https://doi.org/10.1242/jeb.161596

      There are a surprising number of citations not included; some of the ones not included argue against the authors' claims that their findings were "contrary to expectation"

      In our previous revision, we cited the relevant references (Hallgren et al., 2006; O’Connell and Hofmann, 2012; Huffman et al., 2013; Jalabert et al., 2015) in the Introduction. We also revised the text to remove phrases such as “contrary to expectation” and “unexpected.”

      The experimental design for studying aggression in males has flaws. A standard test like a residentintruder test should be used.

      Following this comment, we have attempted additional aggression assays using the resident-intruder paradigm. However, these experiments did not produce consistent or interpretable results. As noted in our previous revision, medaka naturally form shoals and exhibit weak territoriality, and even slight differences in dominance between a resident and an intruder can markedly increase variability, reducing data reliability. Therefore, we believe that the approach used in the present study provides a more suitable assessment of aggression in medaka, regardless of territorial tendencies. We will continue to explore potential refinements in future studies and respectfully ask the reviewer to evaluate the present work based on the assay used here.

      While they investigate males and females, there are fewer experiments and explanations for the female results, making it feel like a small addition or an aside

      While we did not adopt this comment in our previous revision, we have carefully reconsidered the reviewers’ feedback and have now decided to remove the female data. This change allows us to present a more focused and cohesive story centered on males. The specific revisions are outlined below:

      Abstract

      Line 25: The text “, thereby revealing a previously unappreciated mode of action of brain-derived estrogens. We additionally show that female fish lacking Cyp19a1b are less receptive to male courtship and conversely court other females, highlighting the significance of brain-derived estrogens in establishing sex-typical behaviors in both sexes.” has been revised to “. Taken together, these findings reveal a previously unappreciated mode of action of brain-derived estrogens in shaping male-typical behaviors.”

      Results

      Line 88: The text “Loss of cyp19a1b function in these fish was verified by measuring brain and peripheral levels of sex steroids. As expected, brain estradiol-17β (E2) in both male and female homozygous mutants (cyp19a1b<sup>−/−</sup>) was significantly reduced to 16% and 50%, respectively, of the levels in their wild-type (cyp19a1b<sup>+/+</sup>) siblings (P = 0.0037, males; P = 0.0092, females) (Fig. 1, A and B). In males, brain E2 in heterozygotes (cyp19a1b<sup>−/−</sup>) was also reduced to 45% of the level in wild-type siblings (P = 0.0284) (Fig. 1A), indicating a dosage effect of cyp19a1b mutation. In contrast, peripheral E2 levels were unaltered in both cyp19a1b<sup>−/−</sup> males and females (Fig. S1, C and D), consistent with the expected functioning of Cyp19a1b primarily in the brain. Strikingly, brain levels of testosterone, as opposed to E2, increased 2.2-fold in cyp19a1b<sup>−/−</sup> males relative to wild-type siblings (P = 0.0006) (Fig. 1A). Similarly, brain 11KT levels in cyp19a1b<sup>−/−</sup> males and females increased 6.2- and 1.9-fold, respectively, versus wild-type siblings (P = 0.0007, males; P = 0.0316, females) (Fig. 1, A and B). These results show that cyp19a1b-deficient fish have reduced estrogen levels coupled with increased androgen levels in the brain, confirming the loss of cyp19a1b function. They also suggest that the majority of estrogens in the male brain and half of those in the female brain are synthesized locally in the brain. In addition, peripheral 11KT levels in cyp19a1b<sup>−/−</sup> males and females increased 3.7- and 1.8-fold, respectively (P = 0.0789, males; P = 0.0118, females) (Fig. S1, C and D), indicating peripheral influence in addition to central effects.” has been revised to “Loss of cyp19a1b function in these fish was verified by measuring brain and peripheral levels of sex steroids in males. As expected, brain estradiol-17β (E2) in homozygous mutants (cyp19a1b<sup>−/−</sup>) was significantly reduced to 16% of the levels in wild-type (cyp19a1b<sup>+/+</sup>) siblings (P = 0.0037) (Figure 1A). Brain E2 in heterozygotes (cyp19a1b<sup>+/−</sup>) was also reduced to 45% of wild-type levels (P = 0.0284) (Figure 1A), indicating a dosage effect of the cyp19a1b mutation. In contrast, peripheral E2 levels were unaltered in cyp19a1b<sup>−/−</sup> males (Figure 1B), consistent with the expected functioning of Cyp19a1b primarily in the brain. Strikingly, brain testosterone levels, as opposed to E2, increased 2.2-fold in cyp19a1b<sup>−/−</sup> males relative to wild-type siblings (P = 0.0006) (Figure 1A). Similarly, brain 11KT levels increased 6.2-fold (P = 0.0007) (Figure 1A). These results indicate that cyp19a1b-deficient males have reduced estrogen coupled with elevated androgen levels in the brain, confirming the loss of cyp19a1b function. They also suggest that the majority of estrogens in the male brain are synthesized locally in the brain. Peripheral 11KT levels also increased 3.7-fold in cyp19a1b<sup>−/−</sup> males (P = 0.0789) (Figure 1B), indicating peripheral influence in addition to central effects.”

      Line 211: “expression of vt in the pNVT of cyp19a1b<sup>−/−</sup> males was significantly reduced to 18% as compared with cyp19a1b<sup>+/+</sup> males (P = 0.0040), a level comparable to that observed in females” has been revised to “expression of vt in the pNVT of cyp19a1b<sup>−/−</sup> males was significantly reduced to 18% as compared with cyp19a1b<sup>+/+</sup> males (P = 0.0040).”

      The subsection entitled “cyp19a1b-deficient females are less receptive to males and instead court other females,” which followed line 311, has been removed.

      Discussion

      The two paragraphs between lines 373 and 374, which addressed the female data, have been removed.

      Materials and methods

      Line 433: “males and females” has been changed to “males”.

      Line 457: “focal fish” has been changed to “focal male”.

      Line 458: “stimulus fish” has been changed to “stimulus female”.

      Line 458: “Fig. 6, E and F, ” has been deleted.

      Line 460: “; wild-type males in Fig. 6, A to C” has been deleted.

      Line 466: The text “The period of interaction/recording was extended to 2 hours in tests of courtship displays received from the stimulus esr2b-deficient female and in tests of mating behavior between females, because they take longer to initiate courtship (12). In tests using an esr2b-deficient female as the stimulus fish, where the latency to spawn could not be calculated because these fish were unreceptive to males and did not spawn, the sexual motivation of the focal fish was instead assessed by counting the number of courtship displays and wrapping attempts in 30 min. The number of these mating acts was also counted in tests to evaluate the receptivity of females. In tests of mating behavior between two females, the stimulus female was marked with a small notch in the caudal fin to distinguish it from the focal female.” has been revised to “In tests using an esr2b-deficient female as the stimulus fish, the latency to spawn could not be calculated because the female was unreceptive to males and did not spawn. Therefore, the sexual motivation of the focal male was assessed by counting the number of courtship displays and wrapping attempts in 30 min. To evaluate courtship displays performed by stimulus esr2bdeficient females toward focal males, the recording period was extended to 2 hours, as these females take longer to initiate courtship (Nishiike et al., 2021). In all video analyses, the researcher was blind to the fish genotype and treatment.”

      Line 499: “brains dissected from males and females of the cyp19a1b-deficient line (analysis of ara, arb, vt, gal, npba, and esr2b) and males of the esr1-, esr2a-, and esr2b-deficient lines” has been revised to “male brains from the cyp19a1b-deficient line (analysis of ara, arb, vt, and gal) and from the esr1-, esr2a-, and esr2b-deficient lines.”

      Line 504: “After color development for 15 min (gal), 40 min (npba), 2 hours (vt), or overnight (ara, arb, and esr2b)” has been revised to “After color development for 15 min (gal), 2 hours (vt), or overnight (ara and arb).”

      Line 516: “Thermo Fisher Scientific, Waltham, MA” has been changed to “Thermo Fisher Scientific” to avoid redundancy.

      Line 565: The subsection entitled “Measurement of spatial distances between fish” has been removed.

      Line 585: “6/10 cyp19a1b<sup>+/+</sup>, 3/10 cyp19a1b<sup>+/−</sup>, and 6/10 cyp19a1b<sup>−/−</sup> females were excluded in Fig. 6B;” has been deleted.

      References

      The following references have been removed:

      Capel B. 2017. Vertebrate sex determination: evolutionary plasticity of a fundamental switch. Nature Reviews Genetics 18:675–689. DOI: https://doi.org/10.1038/nrg.2017.60

      Hiraki T, Nakasone K, Hosono K, Kawabata Y, Nagahama Y, Okubo K. 2014. Neuropeptide B is femalespecifically expressed in the telencephalic and preoptic nuclei of the medaka brain. Endocrinology 155:1021–1032. DOI: https://doi.org/10.1210/en.2013-1806

      Juntti SA, Hilliard AT, Kent KR, Kumar A, Nguyen A, Jimenez MA, Loveland JL, Mourrain P, Fernald RD. 2016. A neural basis for control of cichlid female reproductive behavior by prostaglandin F2α. Current Biology 26:943–949. DOI: https://doi.org/10.1016/j.cub.2016.01.067

      Kimchi T, Xu J, Dulac C. 2007. A functional circuit underlying male sexual behaviour in the female mouse brain. Nature 448:1009–1014. DOI: https://doi.org/10.1038/nature06089

      Kobayashi M, Stacey N. 1993. Prostaglandin-induced female spawning behavior in goldfish (Carassius auratus) appears independent of ovarian influence. Hormones and Behavior 27:38–55.

      DOI:https://doi.org/10.1006/hbeh.1993.1004

      Liu H, Todd EV, Lokman PM, Lamm MS, Godwin JR, Gemmell NJ. 2017. Sexual plasticity: a fishy tale. Molecular Reproduction and Development 84:171–194. DOI: https://doi.org/10.1002/mrd.22691

      Munakata A, Kobayashi M. 2010. Endocrine control of sexual behavior in teleost fish. General and Comparative Endocrinology 165:456–468. DOI: https://doi.org/10.1016/j.ygcen.2009.04.011

      Nugent BM, Wright CL, Shetty AC, Hodes GE, Lenz KM, Mahurkar A, Russo SJ, Devine SE, McCarthy MM. 2015. Brain feminization requires active repression of masculinization via DNA methylation. Nature Neuroscience 18:690–697. DOI: https://doi.org/10.1038/nn.3988

      Shaw K, Therrien M, Lu C, Liu X, Trudeau VL. 2023. Mutation of brain aromatase disrupts spawning behavior and reproductive health in female zebrafish. Frontiers in Endocrinology 14:1225199.

      DOI:https://doi.org/10.3389/fendo.2023.1225199

      Stacey NE. 1976. Effects of indomethacin and prostaglandins on the spawning behaviour of female goldfish. Prostaglandins 12:113–126. DOI: https://doi.org/10.1016/s0090-6980(76)80010-x

      Figure 1

      Panel B, which originally showed steroid levels in female brains, has been replaced with steroid levels in the periphery of males, originally presented in Figure S1, panel C. Accordingly, the legend “(A and B) Levels of E2, testosterone, and 11KT in the brain of adult cyp19a1b<sup>+/+</sup>, cyp19a1b<sup>+/−</sup>, and cyp19a1b<sup>−/−</sup> males (A) and females (B) (n = 3 per genotype and sex).” has been revised to “(A, B) Levels of E2, testosterone, and 11KT in the brain (A) and periphery (B) of adult cyp19a1b<sup>+/+</sup>, cyp19a1b<sup>+/−</sup>, and cyp19a1b<sup>−/−</sup> males (n = 3 per genotype).”

      Figure 3

      The female data have been deleted from Figure 3. The revised Figure 3 is presented.

      The corresponding legend text has been revised as follows:

      Line 862: “males and females (n = 4 and 5 per genotype for males and females, respectively)” has been changed to “males (n = 4 per genotype)”.

      Line 864: “males and females (n = 4 except for cyp19a1b<sup>+/+</sup> males, where n = 3)” has been changed to “males (n = 3 and 4, respectively)”.

      Figure 6

      Figure 6 and its legend have been removed.

      Figure 1—figure supplement 1

      Panel C, showing male data, has been moved to Figure 1B, as described above, while panel D, showing female data, has been deleted. The corresponding legend “(C and D) Levels of E2, testosterone, and 11KT in the periphery of adult cyp19a1b<sup>+/+</sup>, cyp19a1b<sup>+/−</sup>, and cyp19a1b<sup>−/−</sup> males (C) and females (D) (n = 3 per genotype and sex). Statistical differences were assessed by Bonferroni’s post hoc test (C and D). Error bars represent SEM. *P < 0.05.” has also been removed.

      Line 804: Following this change, the figure title has been updated from “Generation of cyp19a1bdeficient medaka and evaluation of peripheral sex steroid levels” to “Generation of cyp19a1b-deficient medaka.”

      The statistics comparing "experimental to experimental" and "control to experimental" isn't appropriate 

      This comment is the same as one raised in the first review (Reviewer #1’s comment 7 on weaknesses), which we already addressed in our initial revision. For the reviewer’s convenience, we provide the response below:

      The reviewer raised concerns about the statistical analysis used for Figures 4C and 4E, suggesting that Bonferroni’s test should be used instead of Dunnett’s test. However, Dunnett’s test is commonly used to compare treatment groups to a reference group that receives no treatment, as in our study. Since we do not compare the treated groups with each other, we believe Dunnett’s test is the most appropriate choice.

      Line 576: The reviewer’s concern may have arisen from the phrase “comparisons between control and experimental groups” in the Materials and methods. We have revised it to “comparisons between untreated and E2-treated groups in Figure 4C and D” for clarity.

      Reviewer #3 (Public Review):

      Summary:

      Taking advantage of the existence in fish of two genes coding for estrogen synthase, the enzyme aromatase, one mostly expressed in the brain (Cyp19a1b) and the other mostly found in the gonads (Cyp19a1a), this study investigates the role of brain-derived estrogens in the control of sexual and aggressive behavior in medaka. The constitutive deletion of Cyp19a1b markedly reduced brain estrogen content in males and to a lesser extent in females. These effects are accompanied by reduced sexual and aggressive behavior in males and reduced preference for males in females. These effects are reversed by adult treatment with supporting a role for estrogens. The deletion of Cyp19a1b is associated with a reduced expression of the genes coding for the two androgen receptors, ara and arb, in brain regions involved in the regulation of social behavior. The analysis of the gene expression and behavior of mutants of estrogen receptors indicates that these effects are likely mediated by the activation of the esr1 and esr2a isoforms. These results provide valuable insight into the role of estrogens in social behavior in the most abundant vertebrate taxon, however the conclusion of brain-derived estrogens awaits definitive confirmation.

      We thank this reviewer for their positive evaluation of our work and comments that have improved the manuscript.

      Strength:

      Evaluation of the role of brain "specific" Cyp19a1 in male teleost fish, which as a taxon are more abundant and yet proportionally less studied that the most common birds and rodents. Therefore, evaluating the generalizability of results from higher vertebrates is important. This approach also offers great potential to study the role of brain estrogen production in females, an understudied question in all taxa.

      Results obtained from multiple mutant lines converge to show that estrogen signaling, likely synthesized in the brain drives aspects of male sexual behavior.

      The comparative discussion of the age-dependent abundance of brain aromatase in fish vs mammals and its role in organization vs activation is important beyond the study of the targeted species.  - The authors have made important corrections to tone down some of the conclusions which are more in line with the results. 

      We thank the reviewer again for their positive evaluation of our work and the revisions we have made.

      weaknesses:

      No evaluation of the mRNA and protein products of Cyp19a1b and ESR2a are presented, such that there is no proper demonstration that the mutation indeed leads to aromatase reduction. The conclusion that these effects dependent on brain derived estrogens is therefore only supported by measures of E2 with an EIA kit that is not validated. No discussion of these shortcomings is provided in the discussion thus further weakening the conclusion manuscript.

      In response to this and other comments, we have now provided direct validation that the cyp19a1b mutation in our medaka leads to loss of function. Real-time PCR analysis showed that cyp19a1b transcript levels in the brain were reduced by approximately half in cyp19a1b<sup>+/−</sup> males and were nearly absent in cyp19a1b<sup>−/−</sup> males, consistent with nonsense-mediated mRNA decay

      In addition, AlphaFold 3-based structural modeling indicated that the mutant Cyp19a1b protein lacks essential motifs, including the aromatic region and heme-binding loop, and exhibits severe conformational distortion (see figure; key structural features are annotated as follows: membrane helix (blue), aromatic region (red), and heme-binding loop (orange)). 

      Results:

      Line 101: The following text has been added: “Loss of cyp19a1b function was further confirmed by measuring cyp19a1b transcript levels in the brain and by predicting the three-dimensional structure of the mutant protein. Real-time PCR revealed that transcript levels were reduced by half in cyp19a1b<sup>+/−</sup> males and were nearly undetectable in cyp19a1b<sup>−/−</sup> males, presumably as a result of nonsense-mediated mRNA decay (Lindeboom et al., 2019) (Figure 1C). The wild-type protein, modeled by AlphaFold 3, exhibited a typical cytochrome P450 fold, including the membrane helix, aromatic region, and hemebinding loop, all arranged in the expected configuration (Figure 1—figure supplement 1C). The mutant protein, in contrast, was severely truncated, retaining only the membrane helix (Figure 1—figure supplement 1C). The absence of essential domains strongly indicates that the allele encodes a nonfunctional Cyp19a1b protein. Together, transcript and structural analyses consistently demonstrate that the mutation generated in this study causes a complete loss of cyp19a1b function.”

      Materials and methods

      Line 438: A subsection entitled “Real-time PCR” has been added. The text of this subsection is as follows: “Total RNA was isolated from the brains of cyp19a1b<sup>+/+</sup>, cyp19a1b<sup>+/−</sup>, and cyp19a1b<sup>−/−</sup> males using the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany). cDNA was synthesized with the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, MA). Real-time PCR was performed on the LightCycler 480 System II using the LightCycler 480 SYBR Green I Master (Roche Diagnostics). Melting curve analysis was conducted to verify that a single amplicon was obtained in each sample. The β-actin gene (actb; GenBank accession number NM_001104808) was used to normalize the levels of target transcripts. The primers used for real-time PCR are shown in Supplementary file 2.”

      Line 448: A subsection entitled “Protein structure prediction” has been added. The text of this subsection is as follows: “Structural predictions of Cyp19a1b proteins were conducted using AlphaFold 3 (Abramson et al., 2024). Amino acid sequences corresponding to the wild-type allele and the mutant allele generated in this study were submitted to the AlphaFold 3 prediction server. The resulting models were visualized with PyMOL (Schrödinger, New York, NY), and key structural features, including the membrane helix, aromatic region, and heme-binding loop, were annotated.”

      References

      The following two references have been added:

      Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, Bodenstein SW, Evans DA, Hung CC, O'Neill M, Reiman D, Tunyasuvunakool K, Wu Z, Žemgulytė A, Arvaniti E, Beattie C, Bertolli O, Bridgland A, Cherepanov A, Congreve M, CowenRivers AI, Cowie A, Figurnov M, Fuchs FB, Gladman H, Jain R, Khan YA, Low CMR, Perlin K, Potapenko A, Savy P, Singh S, Stecula A, Thillaisundaram A, Tong C, Yakneen S, Zhong ED, Zielinski M, Žídek A, Bapst V, Kohli P, Jaderberg M, Hassabis D, Jumper JM. 2024. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630:493–500. DOI: https://doi.org/10.1038/s41586-024-07487-w

      Lindeboom RGH, Vermeulen M, Lehner B, Supek F. 2019. The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy. Nature Genetics 51:1645–1651.DOI:https://doi.org/10.1038/s41588-019-0517-5

      Figure 1

      The real-time PCR results described above have been incorporated in Figure 1, panel C, with the corresponding legend provided below (line 788).

      (C) Brain cyp19a1b transcript levels in cyp19a1b<sup>+/+</sup>, cyp19a1b<sup>+/−</sup>, and cyp19a1b<sup>−/−</sup> males (n = 6 per genotype). Mean value for cyp19a1b<sup>+/+</sup> males was arbitrarily set to 1.

      The subsequent panels have been renumbered accordingly. The entirety of the revised Figure 1.

      Figure 1—figure supplement 1

      The AlphaFold 3-generated structural models described above have been incorporated in Figure 1— figure supplement 1, panel C, with the corresponding legend provided below (line 811).

      (C) Predicted three-dimensional structures of wild-type (left) and mutant (right) Cyp19a1b proteins. Key structural features are annotated as follows: membrane helix (blue), aromatic region (red), and heme-binding loop (orange).

      The entirety of the revised Figure 1—figure supplement 1 is presented

      The information on the primers used for real-time PCR has been included in Supplementary file 2.

      The functional deficiency of esr2a was already addressed in the previous revision. For clarity, we have reproduced the relevant information here.

      A previous study reported that female medaka lacking esr2a fail to release eggs due to oviduct atresia (Kayo et al., 2019, Sci Rep 9:8868). Similarly, in this study, some esr2a-deficient females exhibited spawning behavior but were unable to release eggs, although the sample size was limited (Δ8 line: 2/3; Δ4 line: 1/1). In contrast, this was not observed in wild-type females (Δ8 line: 0/12; Δ4 line: 0/11). These results support the effective loss of esr2a function. To incorporate this information into the manuscript, the following text has been added to the Materials and methods (line 423): “A previous study reported that esr2a-deficient female medaka cannot release eggs due to oviduct atresia (Kayo et al., 2019). Likewise, some esr2a-deficient females generated in this study, despite the limited sample size, exhibited spawning behavior but were unable to release eggs (Δ8 line: 2/3; Δ4 line: 1/1), while such failure was not observed in wild-type females (Δ8 line: 0/12; Δ4 line: 0/11). These results support the effective loss of esr2a function.”

      Most experiments are weakly powered (low sample size).

      This comment is essentially the same as one raised in the first review (Reviewer #3’s comment 7 on weaknesses). We acknowledge the reviewer’s concern that the histological analyses were weakly powered due to the limited sample size. In our earlier revision, we responded as follows:

      Histological analyses were conducted with a relatively small sample size, as our previous experience suggested that interindividual variability in the results would not be substantial. Since significant differences were detected in many analyses, further increasing the sample size was deemed unnecessary.

      The variability of the mRNA content for a same target gene between experiments (genotype comparison vs E2 treatment comparison) raises questions about the reproducibility of the data (apparent disappearance of genotype effect).

      This comment is the same as one raised in the first review (Reviewer #3’s comment 8 on weaknesses), which we already addressed in our initial revision. For the reviewer’s convenience, we provide the response below:

      As the reviewer pointed out, the overall area of ara expression is larger in Figure 2J than in Figure 2F. However, the relative area ratios of ara expression among brain nuclei are consistent between the two figures, indicating the reproducibility of the results. Thus, this difference is unlikely to affect the conclusions of this study.

      Additionally, the differences in ara expression in pPPp and arb expression in aPPp between wild-type and cyp19a1b-deficient males appear less pronounced in Figures 2J and 2K than in Figures 2F and 2H. This is likely attributable to the smaller sample size used in the experiments for Figures 2J and 2K, resulting in less distinct differences. However, as the same genotype-dependent trends are observed in both sets of figures, the conclusion that ara and arb expression is reduced in cyp19a1b-deficient male brains remains valid.

      Conclusions:

      Overall, the claims regarding role of estrogens originating in the brain on male sexual behavior is supported by converging evidence from multiple mutant lines. The role of brain-derived estrogens on gene expression in the brain is weaker as are the results in females. 

      We appreciate the reviewer’s positive evaluation of our findings on male behavior. The concern regarding the role of brain-derived estrogens in gene expression has been addressed in our rebuttal, and the female data have been removed so that the analysis now focuses on males. The specific revisions for removing the female data are described in Response to reviewer #1’s comment 6 on weaknesses.

      Recommendations For The Authors:

      Reviewer #1 (Recommendations For The Authors):

      The manuscript is improved slightly. I am thankful the authors addressed some concerns, but for several concerns the referees raised, the authors acknowledged them yet did not make corresponding changes to the manuscript or disagreed that they were issues at all without explanation. All reviewers had issues with the imbalanced focus on males versus females and the male aggression assay. Yet, they did not perform additional experiments or even make changes to the framing and scope of the manuscript. If the authors had removed the female data, they may have had a more cohesive story, but then they would still be left with inadequate behavior assays in the males. If the authors don't have the time or resources to perform the additional work, then they should have said so. However, the work would be incomplete relative to the claims. That is a key point here. If they change their scope and claims, the authors avoid overstating their findings. I want to see this work published because I believe it moves the field forward. But the authors need to be realistic in their interpretations of their data. 

      In response to this and related comments, we have removed the female data and focused the manuscript on analyses in males. The specific revisions are described in Response to reviewer #1’s comment 6 on weaknesses. Additionally, we have validated that the cyp19a1b mutation in our medaka leads to loss of function (see Response to reviewer #3’s comment 1 on weaknesses), which further strengthens the reliability of our conclusions regarding male behavior.

      I agree with the reviewer who said we need to see validation of the absence of functional cyp19a1 b in the brain. However, the results from staining for the protein and performing in situ could be quizzical. Indeed, there aren't antibodies that could distinguish between aromatase a and b, and it is not uncommon for expression of a mutated gene to be normal. One approach they could do is measure aromatase activity, but they are *sort of* doing that by measuring brain E2. It's not perfect, but we teleost folks are limited in these areas. At the very least, they should show the predicted protein structure of the mutated aromatase alleles. It could show clearly that the tertiary structure is utterly absent, giving more support to the fact that their aromatase gene is non-functional. 

      As noted above, we have further validated the loss of cyp19a1b function by measuring cyp19a1b transcript levels in the brain and predicting the three-dimensional structure of the mutant protein. These analyses confirmed that cyp19a1b function is indeed lost, thereby increasing the reliability of our conclusions. For further details, please refer to Response to reviewer #3’s comment 1 on weaknesses.

      With all of this said, the work is important, and it is possible that with a reframing of the impact of their work in the context of their findings, I could consider the work complete. I think with a proper reframing, the work is still impactful. 

      In accordance with this feedback, and as described above, we have reframed the manuscript by removing the female data and focusing exclusively on males. This revision clarifies the scope of our study and reinforces the support for our conclusions. For further details, please refer to Response to reviewer #1’s comment 6 on weaknesses.

      (1) Clearly state in the Figure 1 legend that each data point for male aggressive behaviors represents the total # of behaviors calculated over the 4 males in each experimental tank.

      In response to this comment, we have revised the legend of Figure 1K (line 797). The original legend, “(K) Total number of each aggressive act observed among cyp19a1b<sup>+/+</sup>, cyp19a1b<sup>+/−</sup>, or cyp19a1<sup>−/−</sup> males in the tank (n = 6, 7, and 5, respectively),” has been updated to “(K) Total number of each aggressive act performed by cyp19a1b<sup>+/+</sup>, cyp19a1b<sup>+/−</sup>, and cyp19a1b<sup>−/−</sup> males. Each data point represents the sum of acts recorded for the 4 males of the same genotype in a single tank (n = 6, 7, and 5 tanks, respectively).” This clarifies that each data point reflects the total behaviors of the 4 males within each tank.

      (2) The authors wrote under "Response to reviewer #1's major comment "...the development of male behaviors may require moderate neuroestrogen levels that are sufficient to induce the expression of ara and arb, but not esr2b, in the underlying neural circuitry": "This may account for the lack of aggression recovery in E2-treated cyp19a1b-deficient males in this study.".

      What is meant by the latter statement? What accounts for the lack of aggression? The lack of increase in esr2b? Please clarify. 

      Line 365: In response to this comment, “This may account for the lack of aggression recovery in E2treated cyp19a1b-deficient males in this study.” has been revised to “Considering this, the lack of aggression recovery in E2-treated cyp19a1b-deficient males in this study may be explained by the possibility that the E2 dose used was sufficient to induce not only ara and arb but also esr2b expression in aggression-relevant circuits, which potentially suppressed aggression.”

      This revision clarifies that, while moderate brain estrogen levels are sufficient to promote male behaviors via induction of ara and arb, the E2 dose used in this study may have additionally induced esr2b in circuits relevant to aggression, potentially underlying the lack of aggression recovery.

      (3) This is a continuation of my comment/concern directly above. If the induction of ara and arb aren't enough, then how can, as the authors state, androgen signaling be the primary driver of these behaviors? 

      In response to this follow-up comment, we would like to clarify that, as described above, the lack of aggression recovery in E2-treated cyp19a1b-deficient males is not due to insufficient induction of ara and arb, but instead is likely because esr2b was also induced in aggression-relevant circuits, which may have suppressed aggression. Therefore, the concern that androgen signaling cannot be the primary driver of these behaviors is not applicable.

      (4) The authors' point about sticking with the terminology for the ar genes as "ara" and "arb" is not convincing. The whole point of needing a change to match the field of neuroendocrinology as a whole (that is, across all vertebrates) is researchers, especially those with high standing like the Okubo group, adopt the new terminology. Indeed, the Okubo group is THE leader in medaka neuroendocrinology. It would go a long way if they began adopting the new terminology of "ar1" and "ar2". I understand this may be laborious to a degree, and each group can choose to use their terminology, but I'd be remiss if I didn't express my opinion that changing the terminology could help our field as a whole. 

      We sincerely appreciate the reviewer’s thoughtful comments regarding nomenclature consistency in vertebrate neuroendocrinology. We understand the motivation behind the suggestion to adopt ar1 and ar2. However, we consider the established nomenclature of ara and arb to be more appropriate for the following reasons.

      First, adopting the ar1/ar2 nomenclature would introduce a discrepancy between gene and protein symbols. According to the NCBI International Protein Nomenclature Guidelines (Section 2B.Abbreviations and symbols;

      https://www.ncbi.nlm.nih.gov/genbank/internatprot_nomenguide/), the ZFIN Zebrafish Nomenclature Conventions (Section 2. PROTEINS:https://zfin.atlassian.net/wiki/spaces/general/pages/1818394635/ZFIN+Zebrafish+Nomenclature+Con ventions), and the author guidelines of many journal

      (e.g.,https://academic.oup.com/molehr/pages/Gene_And_Protein_Nomenclature), gene and protein symbols should be identical (with proteins designated in non-italic font and with the first letter capitalized). Maintaining consistency between gene and protein symbols helps avoid unnecessary confusion. The ara/arb nomenclature allows this, whereas ar1/ar2 does not.

      Second, the two androgen receptor genes in teleosts are paralogs derived from the third round of wholegenome duplication that occurred early in teleost evolution. For such duplicated genes, the ZFIN Zebrafish Nomenclature Conventions (Section 1.2. Duplicated genes) recommend appending the suffixes “a” and “b” to the approved symbol of the human or mouse ortholog. This convention clearly indicates that these genes are whole-genome duplication paralogs and provides an intuitive way to represent orthologous and paralogous relationships between teleost genes and those of other vertebrates. As a result, it has been widely adopted, and we consider it logical and beneficial to apply the same principle to androgen receptors.

      In light of these considerations, we respectfully maintain that the ara/arb nomenclature is more suitable for the present manuscript than the alternative ar1/ar2 system.

      (5) In the discussion please discuss these potentially unexpected findings.

      (a) gal was unaffected in female cyp19a1 mutants, but they exhibit mating behaviors towards females. Given gal is higher in males and these females act like females, what does this mean about the function of gal/its utility in being a male-specific marker (is it one??)? 

      (b) esr2b expression is higher in female cyp19a1 mutants. this is unexpected as well given esr2b is required for female-typical mating and is higher in females compared to males and E2 increases esr2b expression. please explain...well, what this means for our idea of what esr2b expression tell us. 

      We thank the reviewer for the insightful comments. As the female data have been removed from the manuscript, discussion of these findings in female cyp19a1b mutants is no longer necessary.

      Reviewer #3 (Recommendations For The Authors):

      The authors have addressed a number of answers to the reviewer's comments, notably they provided missing methodological information and rephrased the text. However, the authors have not addressed the main issues raised by the reviewers. Notably, it is regrettable that the reduced amount of brain aromatase cannot be confirmed, this seems to be the primary step when validating a new mutant. Even if protein products of the two genes may not be discriminated (which I can understand), it should be possible to evaluate the expression of a common messenger and/or peptide and confirm that aromatase expression is reduced in the brain. Since Cyp19a1b is relatively more abundant in the brain Cyp19a1a, this would strengthen the conclusion and provide confidence that the mutant indeed does silence aromatase expression in the brain. Although these short comings are acknowledged in the rebuttal letter, this is not mentioned in the discussion. Doing so would make the manuscript more transparent and clearer. 

      As noted in Response to reviewer #3’s comment 1 on weaknesses, we have validated the loss of Cyp19a1b function by measuring its transcript levels in the brain and predicting the three-dimensional structure of the mutant protein. These analyses confirmed that Cyp19a1b function is indeed lost, thereby increasing the reliability of our conclusions.

      FigS1 - panels C&D please indicate in which tissue were hormones measured. Blood?

      We thank the reviewer for pointing this out. In our study, “peripheral” refers to the caudal half of the body excluding the head and visceral organs, not blood. Accordingly, we have revised the figure legend and the description in the Materials and Methods section as follows:

      Legend for Figure 1B (line 787) now reads: “Levels of E2, testosterone, and 11KT in the brain (A) and peripheral tissues (caudal half of the body) (B) of adult cyp19a1b<sup>+/+</sup>, cyp19a1b<sup>+/−</sup>, and cyp19a1b<sup>−/−</sup> males (n = 3 per genotype).”

      Materials and methods (line 431): The sentence “Total lipids were extracted from the brain and peripheral tissues (from the caudal half) of” has been revised to “Total lipids were extracted from the brain and from peripheral tissues, specifically the caudal half of the body excluding the head and visceral organs, of.”

      Additional Alterations:

      We have reformatted the text and supporting materials to comply with the journal’s Author Guidelines. The following changes have been made:

      (1) Figures and supplementary files are now provided separately from the main text.

      (2) The title page has been reformatted without any changes to its content.

      (3) In-text citations have been changed from numerical references to the author–year format.

      (4) Figure labels have been revised from “Fig. 1,” “Fig. S1,” etc., to “Figure 1,” “Figure 1—figure supplement 1,” etc.

      (5) Table labels have been revised from “Table S1,” etc., to “Supplementary file 1,” etc.

      (6) Line 324: The typo “is” has been corrected to “are”.

      (7) Line 382: The section heading “Materials and Methods” has been changed to “Materials and methods” (lowercase “m”).

      (8) Line 383: The Key Resources Table has been placed at the beginning of the Materials and methods section.

      (9) Line 389: The sentence “Sexually mature adults (2–6 months) were used for experiments, and tissues were consistently sampled 1–5 hours after lights on.” has been revised to “Sexually mature adults (2–6 months) were used for experiments and assigned randomly to experimental groups. Tissues were consistently sampled 1–5 hours after lights on.”

      (10)  Line 393: The sentence “All fish were handled in accordance with the guidelines of the Institutional Animal Care and Use Committee of the University of Tokyo.” has been removed.

      (11)  Line 589: The following sentence has been added: “No power analysis was conducted due to the lack of relevant data; sample size was estimated based on previous studies reporting inter-individual variation in behavior and neural gene expression in medaka.”

      (12)  Line 598: The reference list has been reordered from numerical sequence to alphabetical order by author.

      (13)  In the figure legends, notations such as “A and B” have been revised to “A, B.”

    1. Author response:

      We would like to thank both reviewers for taking the time to review the manuscript in detail. Your comments have been extremely useful and constructive. A revised version of the manuscript will seek to address the weaknesses raised, clarifying the reasons for the assumptions made, the impact they have and how they influence the policy implication of the work. We will clarify the language to differentiate the work from the standard sub-national tailoring which is typically conducted to support National Malaria Programmes and emphasise why our mechanistic model can provide greater information than simple summary statistics.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Reviews):

      Summary:

      Argunşah et al. describe and investigate the mechanisms underlying the differential response dynamics of barrel vs septa domains of the whisker-related primary somatosensory cortex (S1). Upon repeated stimulation, the authors report that the response ratio between multi- and single-whisker stimulation increases in layer (L) 4 neurons of the septal domain, while remaining constant in barrel L4 neurons. This difference is attributed to the short-term plasticity properties of interneurons, particularly somatostatin-expressing (SST+) neurons. This claim is supported by the increased density of SST+ neurons found in L4 of the septa compared to barrels, along with a stronger response of (L2/3) SST+ neurons to repeated multi- vs single-whisker stimulation. The role of the synaptic protein Elfn1 is then examined. Elfn1 KO mice exhibited little to no functional domain separation between barrel and septa, with no significant difference in single- versus multi-whisker response ratios across barrel and septal domains. Consistently, a decoder trained on WT data fails to generalize to Elfn1 KO responses. Finally, the authors report a relative enrichment of S2- and M1-projecting cell densities in L4 of the septal domain compared to the barrel domain.

      Strengths:

      This paper describes and aims to study a circuit underlying differential response between barrel columns and septal domains of the primary somatosensory cortex. This work supports the view that barrel and septal domains contribute differently to processing single versus multi-whisker inputs, suggesting that the barrel cortex multiplexes sensory information coming from the whiskers in different domains.

      We thank the reviewer for the very neat summary of our findings that barrel cortex multiplexes converging information in separate domains.

      Weaknesses:

      While the observed divergence in responses to repeated SWS vs MWS between the barrel and septal domains is intriguing, the presented evidence falls short of demonstrating that short-term plasticity in SST+ neurons critically underpins this difference. The absence of a mechanistic explanation for this observation limits the work’s significance. The measurement of SST neurons’ response is not specific to a particular domain, and the Elfn1 manipulation does not seem to be specific to either stimulus type or a particular domain.

      We appreciate the reviewer’s perspective. Although further research is needed to understand the circuit mechanisms underlying the observed phenomenon, we believe our data suggest that altering the short-term dynamics of excitatory inputs onto SST neurons reduces the divergent spiking dynamics in barrels versus septa during repetitive single- and multi-whisker stimulation. Future work could examine how SST neurons, whose somata reside in barrels and septa, respond to different whisker stimuli and the circuits in which they are embedded. At this time, however, the authors believe there is no alternative way to test how the short-term dynamics of excitatory inputs onto SST neurons, as a whole, contribute to the temporal aspects of barrel versus septa spiking.

      The study's reach is further constrained by the fact that results were obtained in anesthetized animals, which may not generalize to awake states.

      We appreciate the reviewer’s concern regarding the generalizability of our findings from anesthetized animals to awake states. Anesthesia was employed to ensure precise individual whisker stimulation (and multi-whisker in the same animal), which is challenging in awake rodents due to active whisking. While anesthesia may alter higher-order processing, core mechanisms, such as short and long term plasticity in the barrel cortex, are preserved under anesthesia (Martin-Cortecero et al., 2014; Mégevand et al., 2009).

      The statistical analysis appears inappropriate, with the use of repeated independent tests, dramatically boosting the false positive error rate.

      Thank you for your feedback on our analysis using independent rank-based tests for each time point in wild-type (WT) animals. To address concerns regarding multiple comparisons and temporal dependencies (for Figure 1F and 4D for now but we will add more in our revision), we performed a repeated measures ANOVA for WT animals (13 Barrel, 8 Septa, 20 time points), which revealed a significant main effect of Condition (F(1,19) = 16.33, p < 0.001) and a significant Condition-Time interaction (F(19,361) = 2.37, p = 0.001). Post-hoc tests confirmed significant differences between Barrel and Septa at multiple time points (e.g., p < 0.0025 at times 3, 4, 6, 7, 8, 10, 11, 12, 16, 19 after Bonferroni posthoc correction), supporting a differential multi-whisker vs. single-whisker ratio response in WT animals. In contrast, a repeated measures ANOVA for knock-out (KO) animals (11 Barrel, 7 Septa, 20 time points) showed no significant main effect of Condition (F(1,14) = 0.17, p = 0.684) or Condition-Time interaction (F(19,266) = 0.73, p = 0.791), indicating that the BarrelSepta difference observed in WT animals is absent in KO animals.

      Furthermore, the manuscript suffers from imprecision; its conclusions are occasionally vague or overstated. The authors suggest a role for SST+ neurons in the observed divergence in SWS/MWS responses between barrel and septal domains. However, this remains speculative, and some findings appear inconsistent. For instance, the increased response of SST+ neurons to MWS versus SWS is not confined to a specific domain. Why, then, would preferential recruitment of SST+ neurons lead to divergent dynamics between barrel and septal regions? The higher density of SST+ neurons in septal versus barrel L4 is not a sufficient explanation, particularly since the SWS/MWS response divergence is also observed in layers 2/3, where no difference in SST+ neuron density is found.

      Moreover, SST+ neuron-mediated inhibition is not necessarily restricted to the layer in which the cell body resides. It remains unclear through which differential microcircuits (barrel vs septum) the enhanced recruitment of SST+ neurons could account for the divergent responses to repeated SWS versus MWS stimulation.

      We fully appreciate the reviewer’s comment. We currently do not provide any evidence on the contribution of SST neurons in the barrels versus septa in layer 4 on the response divergence of spiking observed in SWS versus MWS. We only show that these neurons differentially distribute in the two domains in this layer. It is certainly known that there is molecular and circuit-based diversity of SST-positive neurons in different layers of the cortex, so it is plausible that this includes cells located in the two domains of vS1, something which has not been examined so far. Our data on their distribution are one piece of information that SST neurons may have a differential role in inhibiting barrel stellate cells versus septa ones. Morphological reconstructions of SST neurons in L4 of the somatosensory barrel cortex has shown that their dendrites and axons project locally and may confine to individual domains, even though not specifically examined (Fig. 3 of Scala F et al., 2019). The same study also showed that L4 SST cells receive excitatory input from local stellate cells) and is known that they are also directly excited by thalamocortical fibers (Beierlein et al., 2003; Tan et al., 2008), both of which facilitate.

      As shown in our supplementary figure, the divergence is also observed in L2/3 where, as the reviewer also points out, where we do not have a differential distribution of SST cells, at least based on a columnar analysis extending from L4. There are multiple scenarios that could explain this “discrepancy” that one would need to examine further in future studies. One straightforward one is that the divergence in spiking in L2/3 domains may be inherited from L4 domains, where L4 SST act on. Another is that even though L2/3 SST neurons are not biased in their distribution their input-output function is, something which one would need to examine by detailed in vitro electrophysiological and perhaps optogenetic approaches in S1. Despite the distinctive differences that have been found between the L4 circuitry in S1 and V1 (Scala F et al., 2019), recent observations indicate that small but regular patches of V1 marked by the absence of muscarinic receptor 2 (M2) have high temporal acuity (Ji et al., 2015), and selectively receive input from SST interneurons (Meier et al., 2025). Regions lacking M2 have distinct input and output connectivity patterns from those that express M2 (Meier et al., 2021; Burkhalter et al., 2023). These findings, together with ours, suggest that SST cells preferentially innervate and regulate specific domains columns- in sensory cortices.

      Regardless of the mechanism, the Elfn1 knock-out mouse line almost exclusively affects the incoming excitability onto SST neurons (see also reply to comment below), hence what can be supported by our data is that changing the incoming short-term synaptic plasticity onto these neurons brings the spiking dynamics between barrels and septa closer together.

      The Elfn1 KO mouse model seems too unspecific to suggest the role of the short-term plasticity in SST+ neurons in the differential response to repeated SWS vs MWS stimulation across domains. Why would Elfn1-dependent short-term plasticity in SST+ neurons be specific to a pathway, or a stimulation type (SWS vs MWS)? Moreover, the authors report that Elfn1 knockout alters synapses onto VIP+ as well as SST+ neurons (Stachniak et al., 2021; previous version of this paper)-so why attribute the phenotype solely to SST+ circuitry? In fact, the functional distinctions between barrel and septal domains appear largely abolished in the Elfn1 KO.

      Previous work by others and us has shown that globally removing Elfn1 selectively removes a synaptic process from the brain without altering brain anatomy or structure. This allows us to study how the temporal dynamics of inhibition shape activity, as opposed to inhibition from particular cell types. We will nevertheless update the text to discuss more global implications for SST interneuron dynamics and include a reference to VIP interneurons that contain Elfn1.

      When comparing SWS to MWS, we find that MWS replaces the neighboring excitation which would normally be preferentially removed by short-term plasticity in SST interneurons, thus providing a stable control comparison across animals and genotypes. On average, VIP interneurons failed to show modulation by MWS. We were unable to measure a substantial contribution of VIP cells to this process and also note that the Elfn1 expressing multipolar neurons comprise only ~5% of VIP neurons (Connor and Peters, 1984; Stachniak et al., 2021), a fraction that may be lost when averaging from 138 VIP cells. Moreover, the effect of Elfn1 loss on VIP neurons is quite different and marginal compared to that of SST cells, suggesting that the primary impact of Elfn1 knockout is mediated through SST+ interneuron circuitry. Therefore, even if we cannot rule out that these 5% of VIP neurons contribute to barrel domain segregation, we are of the opinion that their influence would be very limited if any.

      Reviewer #2 (Public Reviews):

      Summary:

      Argunsah and colleagues demonstrate that SST-expressing interneurons are concentrated in the mouse septa and differentially respond to repetitive multi-whisker inputs. Identifying how a specific neuronal phenotype impacts responses is an advance.

      Strengths:

      (1)  Careful physiological and imaging studies.

      (2)  Novel result showing the role of SST+ neurons in shaping responses.

      (3)  Good use of a knockout animal to further the main hypothesis.

      (4)  Clear analytical techniques.

      We thank the reviewer for their appreciation of the study.

      Weaknesses:

      No major weaknesses were identified by this reviewer. Overall, I appreciated the paper but feel it overlooked a few issues and had some recommendations on how additional clarifications could strengthen the paper. These include:

      (1) Significant work from Jerry Chen on how S1 neurons that project to M1 versus S2 respond in a variety of behavioral tasks should be included (e.g. PMID: 26098757). Similarly, work from Barry Connor’s lab on intracortical versus thalamocortical inputs to SST neurons, as well as excitatory inputs onto these neurons (e.g. PMID: 12815025) should be included.

      We thank the reviewer for these valuable resources that we overlooked. We will include Chen et al. (2015), Cruikshank et al. (2007) and Gibson et al. (1999) to contextualize S1 projections and SST+ inputs, strengthening the study’s foundation as well as Beierlein et al. (2003) which nicely show both local and thalamocortical facilitation of excitatory inputs onto L4 SST neurons, in contrast to PV cells. The paper also shows the gradual recruitment of SST neurons by thalamocortical inputs to provide feed-forward inhibition onto stellate cells (regular spiking) of the barrel cortex L4 in rat.

      (2) Using Layer 2/3 as a proxy to what is happening in layer 4 (~line 234). Given that layer 2/3 cells integrate information from multiple barrels, as well as receiving direct VPm thalamocortical input, and given the time window that is being looked at can receive input from other cortical locations, it is not clear that layer 2/3 is a proxy for what is happening in layer 4.

      We agree with the reviewer that what we observe in L2/3 is not necessarily what is taking place in L4 SST-positive cells. The data on L2/3 was included to show that these cells, as a population, can show divergent responses when it comes to SWS vs MWS, which is not seen in L2/3 VIP neurons. Regardless of the mechanisms underlying it, our overall data support that SST-positive neurons can change their activation based on the type of whisker stimulus and when the excitatory input dynamics onto these neurons change due to the removal of Elfn1 the recruitment of barrels vs septa spiking changes at the temporal domain. Having said that, the data shown in Supplementary Figure 3 on the response properties of L2/3 neurons above the septa vs above the barrels (one would say in the respective columns) do show the same divergence as in L4. This suggests that a circuit motif may exist that is common to both layers, involving SST neurons that sit in L4, L5 or even L2/3. This implies that despite the differences in the distribution of SST neurons in septa vs barrels of L4 there is an unidentified input-output spatial connectivity motif that engages in both L2/3 and L4. Please also see our response to a similar point raised by reviewer 1.

      (3) Line 267, when discussing distinct temporal response, it is not well defined what this is referring to. Are the neurons no longer showing peaks to whisker stimulation, or are the responses lasting a longer time? It is unclear why PV+ interneurons which may not be impacted by the Elfn1 KO and receive strong thalamocortical inputs, are not constraining activity.

      We thank the reviewer for their comment and will clarify the statement.

      This convergence of response profiles was further clear in stimulus-aligned stacked images, where the emergent differences between barrels and septa under SWS were largely abolished in the KO (Figure 4B). A distinction between directly stimulated barrels and neighboring barrels persisted in the KO. In addition, the initial response continued to differ between barrel and septa and also septa and neighbor (Figure 4B). This initial stimulus selectivity potentially represents distinct feedforward thalamocortical activity, which includes PV+ interneuron recruitment that is not directly impacted by the Elfn1 KO (Sun et al., 2006; Tan et al., 2008). PV+ cells are strongly excited by thalamocortical inputs, but these exhibit short-term depression, as does their output, contrasting with the sustained facilitation observed in SST+ neurons. These findings suggest that in WT animals, activity spillover from principal barrels is normally constrained by the progressive engagement of SST+ interneurons in septal regions, driven by Elfn1-dependent facilitation at their excitatory synapses. In the absence of Elfn1, this local inhibitory mechanism is disrupted, leading to longer responses in barrels, delayed but stronger responses in septa, and persistently stronger responses in unstimulated neighbors, resulting in a loss of distinction between the responses of barrel and septa domains that normally diverge over time (see Author response image 1 below).

      Author response image 1.

      (A) Barrel responses are longer following whisker stimulation in KO. (B) Septal responses are slightly delayed but stronger in KO. (C) Unstimulated neighbors show longer persistent responses in KO.

       

      (4) Line 585 “the earliest CSD sink was identified as layer 4…” were post-hoc measurements made to determine where the different shank leads were based on the post-hoc histology?

      Post hoc histology was performed on plane-aligned brain sections which would allow us to detect barrels and septa, so as to confirm the insertion domains of each recorded shank. Layer specificity of each electrode therefore could therefore not be confirmed by histology as we did not have coronal sections in which to measure electrode depth.

      (5) For the retrograde tracing studies, how were the M1 and S2 injections targeted (stereotaxically or physiologically)? How was it determined that the injections were in the whisker region (or not)?

      During the retrograde virus injection, the location of M1 and S2 injections was determined by stereotaxic coordinates (Yamashita et al., 2018). After acquiring the light-sheet images, we were able to post hoc examine the injection site in 3D and confirm that the injections were successful in targeting the regions intended. Although it would have been informative to do so, we did not functionally determine the whisker-related M1 and whisker-related S2 region in this experiment.

      (6) Were there any baseline differences in spontaneous activity in the septa versus barrel regions, and did this change in the KO animals?

      Thank you for this interesting question. Our previous study found that there was a reduction in baseline activity in L4 barrel cortex of KO animals at postnatal day (P)12, but no differences were found at P21 (Stachniak et al., 2023).

      Reviewer #3 (Public Reviews):

      Summary:

      This study investigates the functional differences between barrel and septal columns in the mouse somatosensory cortex, focusing on how local inhibitory dynamics, particularly involving Elfn1-expressing SST⁺ interneurons, may mediate temporal integration of multiwhisker (MW) stimuli in septa. Using a combination of in vivo multi-unit recordings, calcium imaging, and anatomical tracing, the authors propose that septa integrate MW input in an Elfn1-dependent manner, enabling functional segregation from barrel columns.

      Strengths:

      The core hypothesis is interesting and potentially impactful. While barrels have been extensively characterized, septa remain less understood, especially in mice, and this study's focus on septal integration of MW stimuli offers valuable insights into this underexplored area. If septa indeed act as selective integrators of distributed sensory input, this would add a novel computational role to cortical microcircuits beyond what is currently attributed to barrels alone. The narrative of this paper is intellectually stimulating.

      We thank the reviewer for finding the study intellectually stimulating.

      Weaknesses:

      The methods used in the current study lack the spatial and cellular resolution needed to conclusively support the central claims. The main physiological findings are based on unsorted multi-unit activity (MUA) recorded via low-channel-count silicon probes. MUA inherently pools signals from multiple neurons across different distances and cell types, making it difficult to assign activity to specific columns (barrel vs. septa) or neuron classes (e.g., SST⁺ vs. excitatory).

      The recording radius (~50-100 µm or more) and the narrow width of septa (~50-100 µm or less) make it likely that MUA from "septal" electrodes includes spikes from adjacent barrel neurons.

      The authors do not provide spike sorting, unit isolation, or anatomical validation that would strengthen spatial attribution. Calcium imaging is restricted to SST⁺ and VIP⁺ interneurons in superficial layers (L2/3), while the main MUA recordings are from layer 4, creating a mismatch in laminar relevance.

      We thank the reviewer for pointing out the possibility of contamination in septal electrodes. Importantly, it may not have been highlighted, although reported in the methods, but we used an extremely high threshold (7.5 std, in methods, line 583) for spike detection in order to overcome the issue raised here, which restricts such spatial contaminations. Since the spike amplitude decays rapidly with distance, at high thresholds, only nearby neurons contribute to our analysis, potentially one or two. We believe that this approach provides a very close approximation of single unit activity (SUA) in our reported data. We will include a sentence earlier in the manuscript to make this explicit and prevent further confusion.

      Regarding the point on calcium imaging being performed on L2/3 SST and VIP cells instead of L4. Both reviewer 1 and 2 brought up the same issue and we responded as follows. As shown in our supplementary figure, the divergence is also observed in L2/3 where we do not have a differential distribution of SST cells, at least based on a columnar analysis extending from L4. There are multiple scenarios that could explain this “discrepancy” that one would need to examine further in future studies. One straightforward one is that the divergence in spiking in L2/3 domains may be inherited from L4 domains, where L4 SST act on. Another is that even though L2/3 SST neurons are not biased in their distribution their input-output function is, something which one would need to examine by detailed in vitro electrophysiological and perhaps optogenetic approaches in S1. Despite the distinctive differences that have been found between the L4 circuitry in S1 and V1 (Scala F et al., 2019), recent observations indicate that small but regular patches of V1 marked by the absence of muscarinic receptor 2 (M2) have high temporal acuity (Ji et al., 2015), and selectively receive input from SST interneurons (Meier et al., 2025). Regions lacking M2 have distinct input and output connectivity patterns from those that express M2 (Meier et al., 2021; Burkhalter et al., 2023). These findings, together with ours, suggest that SST cells preferentially innervate and regulate specific domains -columns- in sensory cortices.

      Furthermore, while the role of Elfn1 in mediating short-term facilitation is supported by prior studies, no new evidence is presented in this paper to confirm that this synaptic mechanism is indeed disrupted in the knockout mice used here.

      We thank Reviewer #3 for noting the absence of new evidence confirming Elfn1’s disruption of short-term facilitation in our knockout mice. We acknowledge that our study relies on previously strong published data demonstrating that Elfn1 mediates short-term synaptic facilitation of excitatory inputs onto SST+ interneurons (Sylwestrak and Ghosh, 2012; Tomioka et al., 2014; Stachniak et al., 2019, 2023). These studies consistently show that Elfn1 knockout abolishes facilitation in SST+ synapses, leading to altered temporal dynamics, which we hypothesize underlies the observed loss of barrel-septa response divergence in our Elfn1 KO mice (Figure 4). Nevertheless, to address the point raised, we will clarify in the revised manuscript (around lines 245-247 and 271-272) that our conclusions are based on these established findings, stating: “Building on prior evidence that Elfn1 knockout disrupts short-term facilitation in SST+ interneurons (Sylwestrak and Ghosh, 2012; Tomioka et al., 2014; Stachniak et al., 2019, 2023), we attribute the abolished barrel-septa divergence in Elfn1 KO mice to altered SST+ synaptic dynamics, though direct synaptic measurements were not performed here.”

      Additionally, since Elfn1 is constitutively knocked out from development, the possibility of altered circuit formation-including changes in barrel structure and interneuron distribution, cannot be excluded and is not addressed.

      We thank Reviewer #3 for raising the valid concern that constitutive Elfn1 knockout could potentially alter circuit formation, including barrel structure and interneuron distribution. To address this, we will clarify in the revised manuscript (around line ~271 and in the Discussion) that in our previous studies that included both whole-cell patch-clamp in acute brain slices ranging from postnatal day 11 to 22 (P11 - P21) and in vivo recordings from barrel cortex at P12 and P21, we saw no gross abnormalities in barrel structure, with Layer 4 barrels maintaining their characteristic size and organization, consistent with wildtype (WT) mice (Stachniak et al., 2019, 2023). While we cannot fully exclude subtle developmental changes, prior studies indicate that Elfn1 primarily modulates synaptic function rather than cortical cytoarchitecture (Tomioka et al., 2014). Elfn1 KO mice show no gross morphological or connectivity differences and the pattern and abundance of Elfn1 expressing cells (assessed by LacZ knock in) appears normal (Dolan and Mitchell, 2013).

      We will add the following to the Discussion: “Although Elfn1 is constitutively knocked out, we find here and in previous studies that barrel structure is preserved (Stachniak et al., 2019, 2023). Further, the distribution of Elfn1 expressing interneurons is not different in KO mice, suggesting minimal developmental disruption (Dolan and Mitchell, 2013).

      Nonetheless, we acknowledge that subtle circuit changes cannot be ruled out without the usage of time-depended conditional knockout of the gene.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors): 

      (1) My biggest concern is regarding statistics. Did the authors repeatedly apply independent tests (Mann-Whitney) without any correction for multiple comparisons (Figures 1 and 4)? In that case, the chances of a spurious "significant" result rise dramatically. 

      In response to the reviewer’s comment, we now present new statistical results by utilizing ANOVA and blended these results in the manuscript between lines 172 and 192 for WT data and 282 and 298 for Elfn1 KO data. This new statistical approach shows the same differences as we had previously reported, hence consolidating the statements made. 

      (2) The findings only hint at a mechanism involving SST+ neurons for how SWS and MWS are processed differently in the barrel vs septal domains. As a direct test of SST+ neuron involvement in the divergence of barrel and septal responses, the authors might consider SST-specific manipulations - for example, inhibitory chemo- or optogenetics during SWS and MWS stimulation.

      We thank the reviewer for this comment and agree that a direct manipulation of SST+ neurons via inhibitory chemo- or opto-genetics could provide further supporting evidence for the main claims in our study. We have opted out from performing these experiments for this manuscript as we feel they can be part of a future study.  At the same time, it is conceivable that such manipulations and depending on how they are performed may lead to larger and non-specific effects on cortical activity, since SST neurons will likely be completely shut down. So even though we certainly appreciate and value the strengths of such approaches, our experiments have addressed a more nuanced hypothesis, namely that the synaptic dynamics onto SST+ neurons matter for response divergence of septa versus barrels, which could not have been easily and concretely addressed by manipulating SST+ cell firing activity.  

      (3) In general, it is hard to comprehend what microcircuit could lead to the observed divergence in the MWS/SWS ratio in the barrel vs septal domain. There preferential recruitment of SST+ neurons during MWS is not specific to a particular domain, and the higher density of SST+ neurons specifically in L4 septa cannot per se explain the diverging MWS/SWS ratio in L4 septal neurons since similar ratio divergence is observed across domains in L2/3 neurons without increase SST+ neuron density in L2/3. This view would also assume that SST+ inhibition remains contained to its own layer and domain. Is this the case? Is it that different microcircuits between barrels and septa differently shape the response to repeated MWS? This is partially discussed in the paper; can the authors develop on that? What would the proposed mechanism be? Can the short-term plasticity of the thalamic inputs (VPM vs POm) be part of the picture?

      We thank the reviewer for raising this important point. We propose that the divergence in MWS/SWS ratios across barrel and septal domains arises from dynamic microcircuit interactions rather than static anatomical features such as SST+ density, which we describe and can provide a hint. In L2/3, where SST+ density is uniform, divergence persists, suggesting that trans-laminar and trans-domain interactions are key. Barrel domains, primarily receiving VPM inputs, exhibit short-term depression onto excitatory cells and engage PV+ and SST+ neurons to stabilize the MWS/SWS ratio, with Elfn1-dependent facilitation of SST+ neurons gradually increasing inhibition during repetitive SWS. Septal domains, in contrast, are targeted by facilitating POm inputs, combined with higher L4 SST+ density and Elfn1-mediated facilitation, producing progressive inhibitory buildup that amplifies the MWS/SWS ratio. SST+ projections in septa may extend trans-laminarly and laterally, influencing L2/3 and neighboring barrels, thereby explaining L2/3 divergence despite uniform SST+ density in L2/3. In this regards, direct laminar-dependent manipulations will be required to confirm whether L2/3 divergence is inherited from L4 dynamics. In Elfn1 KO mice, the loss of facilitation in SST+ neurons likely flattens these dynamics, disrupting functional segregation. Future experiments using VPM/POm-specific optogenetic activation and SST+ silencing will be critical to directly test this model.

      We expanded the discussion accordingly.

      (4) Can the decoder generalize between SWS and MWS? In this condition, if the decoder accuracy is higher for barrels than septa, it would support the idea that septa are processing the two stimuli differently. 

      Our results show that septal decoding accuracy is generally higher than barrel accuracy when generalizing from multi-whisker stimulation (MWS) to single-whisker stimulation (SWS), indicating distinct information processing in septa compared to barrels.

      In wild-type (WT) mice, septal accuracy exceeds barrel accuracy across all time windows (150ms, 51-95ms, 1-95ms), with the largest difference in the 51-95ms window (0.9944 vs. 0.9214 at pulse 20, 10Hz stimulation). This septal advantage grows with successive pulses, reflecting robust, separable neural responses, likely driven by the posterior medial nucleus (POm)’s strong MWS integration contrasting with minimal SWS activation. Barrel responses, driven by consistent ventral posteromedial nucleus (VPM) input for both stimuli, are less distinguishable, leading to lower accuracy.

      In Elfn1 knockout (KO) mice, which disrupt excitatory drive to somatostatin-positive (SST+) interneurons, barrel accuracy is higher initially in the 1-50ms window (0.8045 vs. 0.7500 at pulse 1), suggesting reduced early septal distinctiveness. However, septal accuracy surpasses barrels in later pulses and time windows (e.g., 0.9714 vs. 0.9227 in 51-95ms at pulse 20), indicating restored septal processing. This supports the role of SST+ interneurons in shaping distinct MWS responses in septa, particularly in late-phase responses (51-95ms), where inhibitory modulation is prominent, as confirmed by calcium imaging showing stronger SST+ activation during MWS.

      These findings demonstrate that septa process SWS and MWS differently, with higher decoding accuracy reflecting structured, POm- and SST+-driven response patterns. In Elfn1 KO mice, early deficits in septal processing highlight the importance of SST+ interneurons, with later recovery suggesting compensatory mechanisms. 

      We have added Supplementary Figure 4 and included this interpretation between lines 338353. 

      We thank the reviewer for suggesting this analysis.

      (5) It is not clear to me how the authors achieve SWS. How is it that the pipette tip "placed in contact with the principal whisker" does not detach from the principal whisker or stimulate other whiskers? Please clarify the methods. 

      Targeting the specific principal whisker is performed under the stereoscope.  

      Specifically, we have added this statement in line 628:

      “We trimmed the whiskers where necessary, to avoid them touching each other and to avoid stimulating other whiskers. By putting the pipette tip very close (almost touching) to the principal whisker, the movement of the tip (limited to 1mm) would reliably move the targeted whisker. The specificity of the stimulation of the selected principal whisker was observed under the stereoscope.”

      (6) The method for calculating decoder accuracy is not clearly described-how can accuracy exceed 1? The authors should clarify this metric and provide measures of variability (e.g., confidence intervals or standard deviations across runs) to assess the significance of their comparisons. Additionally, using a consistent scale across all plots would improve interoperability. 

      We thank the reviewer for raising this point. We have now changed the way accuracies are calculated and adopted a common scale among different plots (see updated Figure 5). We have also changed the methods section accordingly.

      (7) Figure 1: The sample size is not specified. It looks like the numbers match the description in the methods, but the sample size should be clearly stated here. 

      These are the numbers the reviewer is inquiring about. 

      WT: (WT) animals: a 280 × 95 × 20 matrix for the stimulated barrel (14 Barrels, 95ms, 20 pulses), a 180 × 95 × 20 matrix for the septa (9 Septa, 95ms, 20 pulses), and a 360 × 95 × 20 matrix for the neighboring barrel (18 Neighboring barrels, 95ms, 20 pulses). N=4 mice.

      KO: 11-barrel columns, 7 septal columns, 11 unstimulated neighbors from N=4 mice.

      Panels D-F are missing axes and axis labels (firing rate, p-value). Panel D is mislabeled (left, middle, and right). I can't seem to find the yellow line. 

      Thank you for this observation. We made changes in the figures to make them easier to navigate based on the collective feedback from the reviewers.

      Why is changing the way to compare the differences in the responses to repeated stimulation between SWS and MWS? 

      To assess temporal accumulation of information, we compared responses to repeated single-whisker stimulation (SWS) and multi-whisker stimulation (MWS) using an accumulative decoding approach rather than simple per-pulse firing rates. This method captures domain-specific integration dynamics over successive pulses.

      The use of the term "principal whisker" is confusing, as it could refer to the whisker that corresponds to the recorded barrel. 

      When we use the term principal whisker, the intention is indeed to refer to the whisker corresponding to the recorded barrel during single whisker stimulation. The term principal whisker is removed from Figure legend 1 and legend S1C where it may have led to  ambiguity.    

      Why the statement "after the start of active whisking"? Mice are under anesthesia here; it does not appear to be relevant for the figure. 

      “After the start of active whisking” refers to the state of the barrel cortex circuitry at the time of recordings. The particular reference we use comes from the habit of assessing sensory processing also from a developmental point of view. The reviewer is correct that it has nothing to do the with the status of the experiment. Nevertheless, since the reviewer found that it may create confusion, we have now taken it out. 

      (8) Figure 3: The y-axis label is missing for panel C. 

      This is now fixed. (dF/F).

      (9) Figure 4: Axis labels are missing.

      Added.

      Minor: 

      (10) Line 36: "progressive increase in septal spiking activity upon multi-whisker stimulation". There is no increase in septal spiking activity upon MWS; the ratio MWS/SWS increases.

      We have changed the sentence as follows: Genetic removal of Elfn1, which regulates the incoming excitatory synaptic dynamics onto SST+ interneurons, leads to the loss of the progressive increase in septal spiking ratio (MWS/SWS) upon stimulation.

      (11) Line 105: domain-specific, rather than column-specific, for consistency.

      We have changed it.

      (12) Lines 173-174: "a divergence between barrel and septa domain activity also occurred in Layer 4 from the 2nd pulse onward (Figure 1E)". The authors only show a restricted number of comparisons. Why not show the p-values as for SWS?

      The statistics is now presented in current Figure 1E.

      (13) Lines 151-153: "Correspondingly, when a single whisker is stimulated repeatedly, the response to the first pulse is principally bottom-up thalamic-driven responses, while the later pulses in the train are expected to also gradually engage cortico-thalamo-cortical and cortico-cortical loops." Can the authors please provide a reference?

      We have now added the following references : (Kyriazi and Simons, 1993; Middleton et al., 2010; Russo et al., 2025).

      (14) Lines 184-186: "Our electrophysiological experiments show a significant divergence of responses over time upon both SWS and MWS in L4 between barrels (principal and neighboring) and adjacent septa, with minimal initial difference". The only difference between the neighboring barrel and septa is the responses to the initial pulse. Can the author clarify? 

      We have now changed the sentence as follows: Our electrophysiological experiments show a significant divergence of responses between domains upon both SWS and MWS in L4. (Line 198 now)

      (15) Line 214: "suggest these interneurons may play a role in diverging responses between barrels and septa upon SWS". Why SWS specifically?

      We have changed the sentence as follows: These results confirmed that SST+ and VIP+ interneurons have higher densities in septa compared to barrels in L4 and suggest these interneurons may play a role in diverging responses between barrels and septa. (Line 231 now).

      (16) Line 235: "This result suggests that differential activation of SST+ interneurons is more likely to be involved in the domain-specific temporal ratio differences between barrels and septa". Why? The results here are not domain-specific.

      We have now revised this statement to: This result suggested that temporal ratio differences specific to barrels and septa might involve differential activation of SST+ interneurons rather than VIP+ interneurons.

      (17) Lines 241-243: "SST+ interneurons in the cortex are known to show distinct short-term synaptic plasticity, particularly strong facilitation of excitatory inputs, which enables them to regulate the temporal dynamics of cortical circuits." Please provide a reference.

      We have now added the following references: (Grier et al., 2023; Liguz-Lecznar et al., 2016).

      (18) Lines 245-247: "A key regulator of this plasticity is the synaptic protein Elfn1, which mediates short-term synaptic facilitation of excitation on SST+ interneurons (Stachniak et al., 2021, 2019; Tomioka et al., 2014)". Is Stachniak et al., 2021 not about the role of Elf1n in excitatory-to-VIP+ neuron synapses?

      The reviewer correctly spotted this discrepancy . This reference has now been removed from this statement.

      (19) Lines 271-272: "Building on our findings that Elfn1-dependent facilitation in SST+ interneurons is critical for maintaining barrel-septa response divergence". The authors did not show that.

      We have now changed the statement to: Building on our findings that Elfn1 is critical for maintaining barrel-septa response divergence  

      (20) Line 280: second firing peak, not "peal".

      Thank you, it is now fixed.

      (21) Lines 304-305: "These results highlight the critical role of Elfn1 in facilitating the temporal integration of 305 sensory inputs through its effects on SST+ interneurons". This claim is also overstated. 

      We have now changed the statement to: These results highlight the contribution of Elfn1 to the temporal integration of sensory inputs. (Line 362)

      (22) Line 329: Any reason why not cite Chen et al., Nature 2013?

      We have now added this reference, as also pointed out by reviewer 1.

      (23) Line 341-342: "wS1" and "wS2" instead of S1 and S2 for consistency.

      Thanks, we have now updated the terms.

      Reviewer #2 (Recommendations for the authors): 

      (1) Figure 3D - the SW conditions are labeled but not the MW conditions (two right graphs) - they should be labeled similarly (SSTMW, VIPMW). 

      The two right graphs in Figure 3D represent paired SW vs MW comparisons of the evoked responses for SST and VIP populations, respectively.

      (2) Figure 6 D and E I think it would be better if the Depth measurements were to be on the yaxis, which is more typical of these types of plots. 

      We thank the reviewer for this comment. Although we appreciate this may be the case, we feel that the current presentation may be easier for the reader to navigate, and we have hence kept it. 

      (3) Having an operational definition of septa versus barrel would be useful. As the authors point out, this is a tough distinction in a mouse, and often you read papers that use Barrel Wall versus Barrel Hollow/Center - operationally defining how these areas were distinguished would be helpful. 

      We thank the reviewer for this comment and understand the point made.

      We have now updated the methods section in line 611: 

      DiI marks contained within the vGlut2 staining were defined as barrel recordings, while DiI marks outside vGlut2 staining were septal recordings.

      Reviewer #3 (Recommendations for the authors): 

      To support the manuscript's major claims, the authors should consider the following:

      (1) Validate the septal identity of the neurons studied, either anatomically or functionally at the single-cell level (e.g., via Ca²⁺ imaging with confirmed barrel/septa mapping). 

      We thank the reviewer for this suggestion, but we feel that these extensive experiments are beyond the scope of this study. 

      (2) Provide both anatomical and physiological evidence to assess the possibility of altered cortical development in Elfn1 KO mice, including potential changes in barrel structure or SST⁺ cell distribution. 

      To address the reviewer’s point, we have now added the following to the Discussion: “Although Elfn1 is constitutively knocked out, we find here and in previous studies that barrel structure is preserved (Stachniak et al., 2019, 2023). Further, the distribution of Elfn1 expressing interneurons is not different in KO mice, suggesting minimal developmental disruption (Dolan and Mitchell, 2013). Nonetheless, we acknowledge that subtle circuit changes cannot be ruled out without conditional knockouts.”,

      (3) Examine the sensory responses of SST⁺ and VIP⁺ interneurons in deeper cortical layers, particularly layer 4, which is central to the study's main conclusions.

      We thank the reviewer for this suggestion and appreciate the value it would bring to the study. We nevertheless feel that these extensive experiments are beyond the scope of this study and hence opted out from performing them. 

      Minor Comments:

      (1)  The authors used a CLARITY-based passive clearing protocol, which is known to sometimes induce tissue swelling or distortion. This may affect anatomical precision, especially when assigning neurons to narrow domains such as septa versus barrels. Please clarify whether tissue expansion was measured, corrected, or otherwise accounted for during analysis.

      Yes, the tissue expansion was accounted during analysis for the laminar specification. We excluded the brains with severe distortion. 

      (2) While the anatomical data are plotted as a function of "depth from the top of layer 4," the manuscript does not specify the precise depth ranges used to define individual cortical layers in the cleared tissue. Given the importance of laminar specificity in projection and cell type analyses, the criteria and boundaries used to delineate each layer should be explicitly stated.

      Thank you for pointing this out. We now include the criteria for delineating each layer in the manuscript. “Given that the depth of Layer 4 (L4) can be reliably measured due to its welldefined barrel boundaries, and that the relative widths of other layers have been previously characterized (El-Boustani et al., 2018), we estimated laminar boundaries proportionally. Specifically, Layer 2/3 was set to approximately 1.3–1.5 times the width of L4, Layer 5a to ~0.5 times, and Layer 5b to a similar width as L4. Assuming uniform tissue expansion across the cortical column, we extrapolated the remaining laminar thicknesses proportionally.”

      (3)  In several key comparisons (e.g., SST⁺ vs. VIP⁺ interneurons, or S2-projecting vs. M1projecting neurons), it is unclear whether the same barrel columns were analyzed across conditions. Given the anatomical and functional heterogeneity across wS1 columns, failing to control for this may introduce significant confounds. We recommend analyzing matched columns across groups or, if not feasible, clearly acknowledging this limitation in the manuscript.

      We thank the reviewer for raising this important point. For the comparison of SST⁺ versus VIP⁺ interneurons, it would in principle have been possible to analyze the same barrel columns across groups. However, because some of the cleared brains did not reach the optimal level of clarity, our choice of columns was limited, and we were not always able to obtain sufficiently clear data from the same columns in both groups. Similarly, for the analysis of S2- versus M1-projecting neurons, variability in the position and spread of retrograde virus injections made it difficult to ensure measurements from identical barrel columns. We have now added a statement in the Discussion to acknowledge this limitation.

      (4) Figure 1C: Clarify what each point in the t-SNE plot represents-e.g., a single trial, a recording channel, or an averaged response. Also, describe the input features used for dimensionality reduction, including time windows and preprocessing steps.

      In response to the reviewer’s comment, we have now added the following in the methods: In summary, each point in the t-SNE plots represents an averaged response across 20 trials for a specific domain (barrel, septa, or neighbor) and genotype (WT or KO), with approximately 14 points per domain derived from the 280 trials in each dataset. The input features are preprocessed by averaging blocks of 20 trials into 1900-dimensional vectors (95ms × 20), which are then reduced to 2D using t-SNE with the specified parameters. This approach effectively highlights the segregation and clustering patterns of neural responses across cortical domains in both WT and KO conditions.

      (5) Figures 1D, E (left panels): The y-axes lack unit labeling and scale bars. Please indicate whether values are in spikes/sec, spikes/bin, or normalized units.

      We have now clarified this. 

      (6) Figures 1D, E (right panels): The color bars lack units. Specify whether the values represent raw firing rates, z-scores, or other normalized measures. Replace the vague term "Matrix representation" with a clearer label such as "Pulse-aligned firing heatmap."

      Thank you, we have now done it.

      (7) Figure 1E (bottom panel): There appears to be no legend referring to these panels. Please define labels such as "B" and "S." 

      Thank you, we have now done it.

      (8) Figure 1E legend: If it duplicates the legend from Figure 1D, this should be made explicit or integrated accordingly. 

      We have changed the structure of this figure.

      (9) Figure 1F: Define "AUC" and explain how it was computed (e.g., area under the firing rate curve over 0-50 ms). Indicate whether the plotted values represent percentages and, if so, label the y-axis accordingly. If normalization was applied, describe the procedure. Include sample sizes (n) and specify what each data point represents (e.g., animal, recording site). 

      The following paragraph has been added in the methods section:

      The Area Under the Curve (AUC) was computed as the integral of the smoothed firing rate (spikes per millisecond) over a 50ms window following each whisker stimulation pulse, using trapezoidal integration. Firing rate data for layer 4 barrel and septal regions in wild-type (WT) and knockout (KO) mice were smoothed with a 3-point moving average and averaged across blocks of 20 trials. Plotted values represent the percentage ratio of multi-whisker (MW) to single whisker (SW) AUC with error bars showing the standard error of the mean. Each data point reflects the mean AUC ratio for a stimulation pulse across approximately 11 blocks (220 trials total). The y-axis indicates percentages.

      (10) Figure 3C: Add units to the vertical axis.

      We have added them.

      (11) Figure 3D: Specify what each line represents (e.g., average of n cells, individual responses?). 

      Each line represents an average response of a neuron.  

      (12) Figure 4C legend: Same with what?". No legend refers to the bottom panels - please revise to clarify. 

      Thank you. We have now changed the figure structure and legends and fixed the missing information issue.

      (13) Supplementary Figure 1B: Indicate the physical length of the scale bar in micrometers. 

      This has been fixed. The scale bar is 250um.

      (14) Indicate the catalog number or product name of the 8×8 silicon probe used for recordings.

      We have added this information. It is the A8x8-Edge-5mm-100-200-177-A64

      References

      (1) Beierlein, M., Gibson, J. R. & Connors, B. W. (2003). Two dynamically distinct inhibitory networks in layer 4 of the neocortex. J. Neurophysiol. 90, 2987–3000.

      (2) Burkhalter, A., D’Souza, R. D. & Ji, W. (2023). Integration of feedforward and feedback information streams in the modular architecture of mouse visual cortex. Annu. Rev. Neurosci. 46, 259–280.

      (3) Chen, J. L., Margolis, D. J., Stankov, A., Sumanovski, L. T., Schneider, B. L. & Helmchen, F. (2015). Pathway-specific reorganization of projection neurons in somatosensory cortex during learning. Nat. Neurosci. 18, 1101–1108.

      (4) Connor, J. R. & Peters, A. (1984). Vasoactive intestinal polypeptide-immunoreactive neurons in rat visual cortex. Neuroscience 12, 1027–1044.

      (5) Cruikshank, S. J., Lewis, T. J. & Connors, B. W. (2007). Synaptic basis for intense thalamocortical activation of feedforward inhibitory cells in neocortex. Nat. Neurosci. 10, 462–468.

      (6) Dolan, J. & Mitchell, K. J. (2013). Mutation of Elfn1 in mice causes seizures and hyperactivity. PLoS One 8, e80491.

      (7) Gibson, J. R., Beierlein, M. & Connors, B. W. (1999). Two networks of electrically coupled inhibitory neurons in neocortex. Nature 402, 75–79.

      (8) Ji, W., Gămănuţ, R., Bista, P., D’Souza, R. D., Wang, Q. & Burkhalter, A. (2015). Modularity in the organization of mouse primary visual cortex. Neuron 87, 632–643.

      (9) Martin-Cortecero, J. & Nuñez, A. (2014). Tactile response adaptation to whisker stimulation in the lemniscal somatosensory pathway of rats. Brain Res. 1591, 27–37.

      (10) Mégevand, P., Troncoso, E., Quairiaux, C., Muller, D., Michel, C. M. & Kiss, J. Z. (2009). Long-term plasticity in mouse sensorimotor circuits after rhythmic whisker stimulation. J. Neurosci. 29, 5326–5335.

      (11) Meier, A. M., Wang, Q., Ji, W., Ganachaud, J. & Burkhalter, A. (2021). Modular network between postrhinal visual cortex, amygdala, and entorhinal cortex. J. Neurosci. 41, 4809– 4825.

      (12) Meier, A. M., D’Souza, R. D., Ji, W., Han, E. B. & Burkhalter, A. (2025). Interdigitating modules for visual processing during locomotion and rest in mouse V1. bioRxiv 2025.02.21.639505.

      (13) Scala, F., Kobak, D., Shan, S., Bernaerts, Y., Laturnus, S., Cadwell, C. R., Hartmanis, L., Froudarakis, E., Castro, J. R., Tan, Z. H., et al. (2019). Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas. Nat. Commun. 10, 4174.

      (14) Stachniak, T. J., Sylwestrak, E. L., Scheiffele, P., Hall, B. J. & Ghosh, A. (2019). Elfn1induced constitutive activation of mGluR7 determines frequency-dependent recruitment of somatostatin interneurons. J. Neurosci. 39, 4461–4475.

      (15) Stachniak, T. J., Kastli, R., Hanley, O., Argunsah, A. Ö., van der Valk, E. G. T., Kanatouris, G. & Karayannis, T. (2021). Postmitotic Prox1 expression controls the final specification of cortical VIP interneuron subtypes. J. Neurosci. 41, 8150–8166.

      (16) Stachniak, T. J., Argunsah, A. Ö., Yang, J. W., Cai, L. & Karayannis, T. (2023). Presynaptic kainate receptors onto somatostatin interneurons are recruited by activity throughout development and contribute to cortical sensory adaptation. J. Neurosci. 43, 7101–7118.

      (17) Sun, Q.-Q., Huguenard, J. R. & Prince, D. A. (2006). Barrel cortex microcircuits: Thalamocortical feedforward inhibition in spiny stellate cells is mediated by a small number of fast-spiking interneurons. J. Neurosci. 26, 1219–1230.

      (18) Sylwestrak, E. L. & Ghosh, A. (2012). Elfn1 regulates target-specific release probability at CA1-interneuron synapses. Science 338, 536–540.

      (19) Tan, Z., Hu, H., Huang, Z. J. & Agmon, A. (2008). Robust but delayed thalamocortical activation of dendritic-targeting inhibitory interneurons. Proc. Natl. Acad. Sci. USA 105, 2187–2192.

      (20) Tomioka, N. H., Yasuda, H., Miyamoto, H., Hatayama, M., Morimura, N., Matsumoto, Y., Suzuki, T., Odagawa, M., Odaka, Y. S., Iwayama, Y., et al. (2014). Elfn1 recruits presynaptic mGluR7 in trans and its loss results in seizures. Nat. Commun. 5, 4501.

      (21) Yamashita, T., Vavladeli, A., Pala, A., Galan, K., Crochet, S., Petersen, S. S. & Petersen, C. C. (2018). Diverse long-range axonal projections of excitatory layer 2/3 neurons in mouse barrel cortex. Front. Neuroanat. 12, 33.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This important manuscript provides insights into the competition between Splicing Factor 1 (SF1) and Quaking (QKI) for binding at the ACUAA branch point sequence in a model intron, regulating exon inclusion. The study employs rigorous transcriptomic, proteomic, and reporter assays, with both mammalian cell culture and yeast models. Nevertheless, while the data are convincing, broadening the analysis to additional exons and narrowing the manuscript's title to better align with the experimental scope would strengthen the work.

      Public Reviews:

      Reviewer #1 (Public review):

      In this manuscript, the authors aimed to show that SF1 and QKI compete for the intron branch point sequence ACUAA and provide evidence that QKI represses inclusion when bound to it.

      Major strengths of this manuscript include:

      (1) Identification of the ACUAA-like motif in exons regulated by QKI and SF1.

      (2) The use of the splicing reporter and mutant analysis to show that upstream and downstream ACUAAC elements in intron 10 of RAI are required for repressing splicing.

      (3) The use of proteomic to identify proteins in C2C12 nuclear extract that binds to the wild type and mutant sequence.

      (4) The yeast studies showing that ectopic lethality when Qki5 expression was induced, due to increased mis-splicing of transcripts that contain the ACUAA element.

      The authors conclusively show that the ACUAA sequence is bound by QKI and provide strong evidence that this leads to differences in exons inclusion and exclusion. In animal cells, and especially in human, branchpoint sequences are degenerate but seem to be recognized by specific splicing factors. Although a subset of splicing factors shows tissue-specific expression patterns most don't, suggesting that yet-to-be-identified mechanisms regulate splicing. This work suggests that an alternate mechanism could be related to the binding affinity of specific RNA binding factors for branchpoint sequences coupled with the level of these different splicing factors in a given cell.

      We thank the reviewer for the positive comments.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Pereira de Castro and coworkers are studying potential competition between a more standard splicing factor SF1, and an alternative splicing factor called QK1. This is interesting because they bind to overlapping sequence motifs and could potentially have opposing effects on promoting the splicing reaction. To test this idea, the authors KD either SF1 or QK1 in mammalian cells and uncover several exons whose splicing regulation follows the predicted pattern of being promoted for splicing by SF1 and repressed by QK1. Importantly, these have introns enriched in SF1 and QK1 motifs. The authors then focus on one exon in particular with two tandem motifs to study the mechanism of this in greater detail and their results confirm the competition model. Mass spec analysis largely agrees with their proposal; however, it is complicated by the apparently quick transition of SF1-bound complexes to later splicing intermediates. An inspired experiment in yeast shows how QK1 competition could potentially have a detrimental impact on splicing in an orthogonal system. Overall, these results show how splicing regulation can be achieved by competition between a "core" and alternative splicing factor and provide additional insight into the complex process of branch site recognition. The manuscript is exceptionally clear and the figures and data are very logically presented. The work will be valuable to those in the splicing field who are interested in both mechanism and bioinformatics approaches to deconvolve any apparent "splicing code" being used by cells to regulate gene expression. Criticisms are minor and the most important of them stem from overemphasis on parts of the manuscript on the evolutionary angle when evolution itself wasn't analyzed per se.

      We thank the reviewer for the positive comments and very clear and fair critical points.

      Strengths:

      (1) The main discovery of the manuscript involving evidence for SF1/QK1 competition is quite interesting and important for this field. This evidence has been missing and may change how people think about branch site recognition.

      (2) The experiments and the rationale behind them are exceptionally clearly and logically presented. This was wonderful!

      Thank you so much. We felt the overall flow of the paper and data make for a nice “story” that conveys a relatively easy-to-understand explanation for a complex subject.

      (3) The experiments are carried out to a high standard and well-designed controls are included.

      (4) The extrapolation of the result to yeast in order to show the potentially devastating consequences of the QK1 competition was very exciting and creative.

      We agree this is a very exciting result and finding! Thanks.

      Weaknesses:

      Overall the weaknesses are relatively minor and involve cases where clarification is necessary, some additional analysis could bolster the arguments, and suggestions for focusing the manuscript on its strengths.

      (1) The title (Ancient...evolutionary outcomes), abstract, and some parts of the discussion focus heavily on the evolutionary implications of this work. However, evolutionary analysis was not performed in these studies (e.g., when did QK1 and SF1 proteins arise and/or diverge? How does this line up with branch site motifs and evolution of U2? Any insight from recent work from Scott Roy et al?). I think this aspect either needs to be bolstered with experimental work/data or this should be tamped down in the manuscript. I suggest highlighting the idea expressed in the sentence "A nuanced implication of this model is that loss-of-function...". To me, this is better supported by the data and potentially by some analysis of mutations associated with human disease.

      We have revised the title and dampened the evolutionary aspects of the previous version of the manuscript.

      (2) One paper that I didn't see cited was that by Tanackovic and Kramer (Mol Biol Cell 2005). This paper is relevant because they KD SF1 and found it nonessential for splicing in vivo. Do their results have implications for those here? How do the results of the KD compare? Could QK1 competition have influenced their findings (or does their work influence the "nuanced implication" model referenced above?)?

      This is an interesting point, and thank you for the suggestion. We have now included a brief description of this study in the Introduction of the revised manuscript and do note that the authors measured intron retention of a beta globin reporter and SF3A1, SF3A2, and SF3A3 during SF1 knockdown, but did not detect elevated unspliced RNA in these targets.

      (3) Can the authors please provide a citation for the statement "degeneracy is observed to a higher degree in organisms with more alternative splicing"? Does recent evolutionary analysis support this?

      We have removed the statement, as it did not add much to the content and I am not sure I can state the concept I was attempting to convey in a simple manner with few citations.

      (4) For the data in Figure 3, I was left wondering if NMD was confounding this analysis. Can the authors respond to this and address this concern directly?

      We have not measured if the reporters used in Figure 3 produce protein(s). Presumably, though, all spliced reporter RNA would be degraded equally (the included/skipped isoforms’ “reading frames” are not altered from one another). This would not be case for unspliced nuclear reporter RNA, however. Given this difference, and that our analysis can not resolve the subcellular localization of the different reporter species, we have removed the measurement of and subsequent results describing unspliced reporter RNA from Figure 3.

      (5) To me, the idea that an engaged U2 snRNP was pulled down in Figure 4F would be stronger if the snRNA was detected. Was that able to be observed by northern or primer extension? Would SF1 be enriched if the U2 snRNA was degraded by RNaseH in the NE?

      We did not measure any co-associating RNAs in this experimental approach, but agree that this approach would strengthen the evidence for it.

      (6) I'm wondering how additive the effects of QK1 and SF1 are... In Figure 2, if QK1 and SF1 are both knocked down, is the splicing of exon 11 restored to "wt" levels?

      This is an interesting question that we were unfortunately unable to address experimentally here.

      (7) The first discussion section has two paragraphs that begin "How does competition between SF1..." and "Relatively little is known about how...". I found the discussion and speculation about localization, paraspekles, and lncRNAs interesting but a bit detracting from the strengths of the manuscript. I would suggest shortening these two paragraphs into a single one.

      We have revised the Discussion.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, the authors were trying to establish whether competition between the RNA-binding proteins SF1 and QKI controlled splicing outcomes. These two proteins have similar binding sites and protein sequences, but SF1 lacks a dimerization motif and seems to bind a single version of the binding sequence. Importantly, these binding sequences correspond to branchpoint consensus sequences, with SF1 binding leading to productive splicing, but QKI binding leading instead to association with paraspeckle proteins. They show that in human cells SF1 generally activates exons and QKI represses, and a large group of the jointly regulated exons (43% of joint targets) are reciprocally controlled by SF1 and QKI. They focus on one of these exons RAI14 that shows this reciprocal pattern of regulation, and has 2 repeats of the binding site that make it a candidate for joint regulation, and confirm regulation within a minigene context. The authors used the assembly of proteins within nuclear extracts to explain the effect of QKI versus SF1 binding. Finally, the authors show that the expression of QKI is lethal in yeast, and causes splicing defects.

      How this fits in the field. This study is interesting and provides a conceptual advance by providing a general rule on how SF1 and QKI interact in relation to binding sites, and the relative molecular fates followed, so is very useful. Most of the analysis seems to focus on one example, although the molecular analysis and global work significantly add to the picture from the previously published paper about NUMB joint regulation by QKI and SF (Zong et al, cited in text as reference 50, that looked at SF1 and QKI binding in relation to a duplicated binding site/branchpoint sequence in NUMB).

      Thank you for the encouraging remarks.

      Strengths:

      The data presented are strong and clear. The ideas discussed in this paper are of wide interest, and present a simple model where two binding sites generate a potentially repressive QKI response, whereas exons that have a single upstream sequence are just regulated by SF1. The assembly of splicing complexes on RNAs derived from RAI14 in nuclear extracts, followed by mass spec gave interesting mechanistic insight into what was occurring as a result of QKI versus SF1 binding.

      Weaknesses:

      I did not think the title best summarises the take-home message and could be perhaps a bit more modest. Although the authors investigated splicing patterns in yeast and human cells, yeast do not have QKI so there is no ancient competition in that case, and the study did not really investigate physiological or evolutionary outcomes in splicing, although it provides interesting speculation on them. Also as I understood it, the important issue was less conserved branchpoints in higher eukaryotes enabling alternative splicing, rather than competition for the conserved branchpoint sequence. So despite the the data being strong and properly analysed and discussed in the paper, could the authors think whether they fit best with the take-home message provided in the title? Just as a suggestion (I am sure the authors can do a better job), maybe "molecular competition between variant branchpoint sequences predict physiological and evolutionary outcomes in splicing"?

      Thank you for this point (Reviewer 2 had a similar comment) and the suggestion. We have revised the title.

      Although the authors do provide some global data, most of the detailed analysis is of RAI14. It would have been useful to examine members of the other quadrants in Figure 1C as well for potential binding sites to give a reason why these are not co-regulated in the same way as RAI14. How many of the RAI14 quadrants had single/double sites (the motif analysis seemed to pull out just one), and could one of the non-reciprocally regulated exons be moved into a different quadrant by addition or subtraction of a binding site or changing the branchpoint (using a minigene approach for example).

      This is an interesting point that we have considered. Our intent with the focus on RAI14 was to use a naturally occurring intron bps with evidence of strong QKI binding that did not require a high degree of sequence manipulation or engineering.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Most of my recommendations are really centered on the figures. In their current state, they detract from the data shown and could be improved: I recommend the authors use a uniform font. For example, Figure 1E and F have at least three different fonts of varying sizes making it very messy. In Figure 1C, the authors could bold the Ral14 ex11 or simply indicate that the blue is this exon in the legend, thus removing the text from this very busy graph. In Figure 4F, I would recommend, having all the labels the same size and putting those genes of interest like Sf3a1 in bold. This could also be done in Figure 4E.

      Thank you for the suggestion and we have edited these (FYI the font in Fig’s 1E and 1F were from the rMAPS default output, but I agree, it gives a sloppy appearance).

      (2) In Figures 4D and 4G, is there QKI binding to the downstream deletion mutant after 30 minutes? Also, in Figure 4G, are these all from the same blot? The band sizes seem to be very different between lanes. If these were not on the same blot, the original gels should be submitted.

      A small amount of Qki appears to be binding after 30 min. All lanes/blots are from the same gels/membranes; see new Supplemental Figure 4 for the original (uncropped) images of the blots.

      (3) The authors should indicate, the source and concentration of the antibodies used for their WB. They should also indicate the primers used for RT-PCRs.

      We have revised the methods to include the antibody information and have uploaded a supplemental table 8 with all oligonucleotide sequences used (which I (Sam Fagg) neglected to do initially, so that’s my bad).

      Reviewer #2 (Recommendations for the authors):

      (1) This may come down to the author's preference but branch point and branch site are frequently two words, not a single compound word (branch point vs. branchpoint). In addition, the authors may want to use branchsite with the abbreviation BS more frequently since they often don't describe the specific point of branching, and bp and bps could be confused for the more frequent abbreviations for base pair(s).

      Good suggestion; we have edited the text accordingly.

      (2) In general the addition of page numbers and line numbers to the manuscript would greatly aid reviewers!

      Point taken…

      (3) Introduction; "...under normal growth conditions they are efficiently spliced". I would say MOST introns in yeast are efficiently spliced. This is definitely not universal.

      Text edited to indicate that most are efficiently spliced.

      (4) Introduction; " recognition of the bps by SF1 (mammals) (20)". The choice of reference 20 is an odd one here. I think the Robin Reed and Michael Rosbash paper was the first to show SF1 was the human homolog of BBP.

      Got it, thanks (added #14 here and kept #20 also since it shows the structure of SF1 in complex with a UACUAAC bps.)

      (5) Results; "QK1 and SF1 co-regulate.."; it may be useful for the reader if you could explain in more detail why exon inclusion and intron retention are expected outcomes for QK1 knockdown and vice versa for SF1. The exon inclusion here is more obvious than the intron retention phenotype. (In other words, if more exons are included shouldn't it follow that more introns are removed?)

      We explain the expected results for exon inclusion in the Introduction and this paragraph of the Results. Although we have observed more intron retention under QKI loss-of-function approaches before, I am uncertain where the reviewer sees that we indicate any expected result for intron retention from either QKI or SF1 knockdown. I believe the statement you refer to might be on line 162 and starts with: “Consistent with potentially opposing functions in splicing…” ?

      Also, I agree that if SF1 is a “splicing activator,” one might expect more IR in its absence (but this is not the case; there is, in fact, less), but nonetheless, the opposite outcome is observed with QKI knockdown (more IR). It is unclear why this is the case, and we did not investigate it.

      (6) Results; "QK1 and SF1 co-regulate.."; "Thus the most highly represented set.." To me, the most highly represented set is those which are not both QK1-repressed and SF1-activated. Does this indicate that other factors are involved at most sites than simple competition between these two?

      We have revised the sentence in question to include the text “by quadrant” in order to convey our meaning more precisely.

      (7) Throughout the manuscript, 5 apostrophes and 3 apostrophes are used instead of 5 prime symbols and 3 prime symbols.

      Thank you for pointing that out. We have fixed each instance of this.

      (8) Sometimes SF1 is written as Sf1. (also Tatsf1)

      This was a mouse/human gene/protein nomenclature error that we have fixed; thank you for pointing this out.

      (9) You may want to make sure that figures are labeled consistently with the manuscript text. In Figure 1B, it is RI rather than IR. In Figure 4 it is myoblast NE rather than C2C12 nuclear extract.

      We have fixed these, checked for other examples, and where relevant, edited those too.

      (10) I think Figure 1A could be improved by also including a depiction of the domain arrangements of SF1 and QK1.

      Done.

      (11) I was a bit confused with all the lines in Figure 1E and 1F. What is the difference between the log (pVal) and upregulated plots? Can these figures be simplified or explained more thoroughly?

      Based on this comment and one from Reviewer 1, we have slightly revised the wording (and font) on the output, which hopefully clarifies. These are motif enrichment plots generated by rMAPS (Refs 61 and 62) analysis of rMATS (Ref 60) data for exons more included (depicted by the red lines) or more skipped (depicted by the blue lines) compared to control versus a “background” set of exons that are detectable but unchanged. The -log<sub>10</sub> is P-value (dotted line) indicates the significance of exons more included in shRNA treatment vs control shRNA (previously read “upregulated”) compared to background exons that are detectable but unchanged; the solid lines indicate the motif score; these are described in the references indicated.

      (12) Figure 1B, it is a bit hard to conclude that there is more AltEx or "RI/IR" in one sample vs. the other from these plots since the points overlay one another. Can you include numbers here?

      Added (and deleted Suppl Fig S1, which was simply a chart showing the numbers).

      (13) How was PSI calculated in Figure 2A?

      VAST-tools (we state this in the legend in the revised version).

      You may want to include rel protein (or the lower limit of detection) for Figure 2B to be consistent with 2C. Why is KD of SF1 so poor and variable between 2C and 2D?

      We have not investigated this, but these blots show an optimized result that we were able to obtain for the knockdown in each cell type. It may be that HEK293 cells (Fig 2B) have a stronger requirement for SF1 than C2C12 cells…? I would argue that it is not necessarily “poor” in Fig 2C, as we observe ~70% depletion of the protein.

      Why are two bands present in the gel?

      Two to three isoforms of SF1 are present in most cell types.

      A good (or bad, really) example of an SF1 western blot (and knockdown of ~35% in K562 or ~45% in HepG2 can also be seen on the ENCODE project website, for reference:

      https://www.encodeproject.org/documents/6001a414-b096-4073-94ff-3af165617eb5/@@download/attachment/SF1_BGKLV28-49.pdf

      By comparison, I think ours are much more cosmetically pleasing, and our knockdown (especially in C2C12) is much more efficient.

      (14) Figure 3, The asterisk refers to a cryptic product. Can the uaAcuuuCAG be used as a branch point? Presumably the natural 3' SS is now too close so this would result in activation of a downstream 3'SS?

      We did not pursue determining the identity of this minor and likely artefactual product, but we (and others) have observed a similar phenomenon when using splicing reporter-based mutational approaches.

      (15) For the methods. The "RNA extraction, RT -PCR,..." subheading needs to be on its own line. Please add (w/v) or (v/v) to percentages where appropriate. Please convert ug to the symbol for "micro".

      Thank you, we have made these changes.

      (16) In Figure 4B, the text here and legend are microscopic. Even with reading glasses, I couldn't make anything out!

      We have increased the font sizes for the text and scale bar…when referring to “legend” does the reviewer mean the scale bar?

      (17) As a potential discussion item, it is worth noting that SF1 could also repress splicing if it could either not engage with U2AF or be properly displaced by U2 snRNP so the snRNA could pair. I was wondering if QK1 could similarly be activating if it could engage with U2AF. I'm unsure if this could be tested by domain swaps (and is beyond the scope of this paper). It just may be worth speculating about.

      Good point and suggestion…we are looking into this.

      Reviewer #3 (Recommendations for the authors):

      (1) Is the reference in the text to Figure 5F correct for actin splicing (this is just before the discussion)?

      I see references several lines up from this, but I do not see a reference just before the discussion…?

      (2) I was not sure why the minigene experiments showed such high levels of intron retention that seemed to be impacted also by deletion of the branchpoint sequences, and suggest that the two branchpoints are not equal in strength.

      Neither were we, but Reviewer 2 has suggested that degradation of the spliced products could be rapid (NMD substrates) which could complicate the interpretation of what appears to be higher levels of intron retention. Given the possibility that this could be a non-physiological artefact, we have removed the measurement of unspliced reporter and now only show the spliced products (equally subject to degradation) and report their percent inclusion.

    1. Author response:

      The following is the authors’ response to the current reviews.

      We thank the editors of eLife and the reviewers for their thorough evaluation of our study. As regards the final comments of reviewer 1 please note that all experimental replicates were first analyzed separately, and were then pooled, since the observed changes were comparable between experiments. This mean that statistical analyses were done on pooled biological replicates.


      The following is the authors’ response to the original reviews.

      General Statements

      We thank the reviewers for their thorough and constructive evaluation of our work. We have revised the manuscript carefully and addressed all the criticisms raised, in particular the issues mentioned by several of the reviewers (see point-by-point response below). We have also added a number of explanations in the text for the sake of clarity, while trying to keep the manuscript as concise as possible.

      In our view, the novelty of our research is two-fold. From a neurobiological point of view, we provide conclusive evidence for the existence of glycine receptors (GlyRs) at inhibitory synapses in various brain regions including the hippocampus, dentate gyrus and sub-regions of the striatum. This solves several open questions and has fundamental implications for our understanding of the organisation and function of inhibitory synapses in the telencephalon. Secondly, our study makes use of the unique sensitivity of single molecule localisation microscopy (SMLM) to identify low protein copy numbers. This is a new way to think about SMLM as it goes beyond a mere structural characterisation and towards a quantitative assessment of synaptic protein assemblies.

      Point-by-point description of the revisions

      Reviewer #1 (Evidence, reproducibility and clarity): 

      In this manuscript, the authors investigate the nanoscopic distribution of glycine receptor subunits in the hippocampus, dorsal striatum, and ventral striatum of the mouse brain using single-molecule localization microscopy (SMLM). They demonstrate that only a small number of glycine receptors are localized at hippocampal inhibitory synapses. Using dual-color SMLM, they further show that clusters of glycine receptors are predominantly localized within gephyrinpositive synapses. A comparison between the dorsal and ventral striatum reveals that the ventral striatum contains approximately eight times more glycine receptors and this finding is consistent with electrophysiological data on postsynaptic inhibitory currents. Finally, using cultured hippocampal neurons, they examine the differential synaptic localization of glycine receptor subunits (α1, α2, and β). This study is significant as it provides insights into the nanoscopic localization patterns of glycine receptors in brain regions where this protein is expressed at low levels. Additionally, the study demonstrates the different localization patterns of GlyR in distinct striatal regions and its physiological relevance using SMLM and electrophysiological experiments. However, several concerns should be addressed. 

      The following are specific comments: 

      (1) Colocalization analysis in Figure 1A. The colocalization between Sylite and mEos-GlyRβ appears to be quite low. It is essential to assess whether the observed colocalization is not due to random overlap. The authors should consider quantifying colocalization using statistical methods, such as a pixel shift analysis, to determine whether colocalization frequencies remain similar after artificially displacing one of the channels. 

      Following the suggestion of reviewer 1, we re-analysed CA3 images of Glrb<sup>eos/eos</sup> hippocampal slices by applying a pixel-shift type of control, in which the Sylite channel (in far red) was horizontally flipped relative to the mEos4b-GlyRβ channel (in green, see Methods). As expected, the number of mEos4b-GlyRβ detections per gephyrin cluster was markedly reduced compared to the original analysis (revised Fig. 1B), confirming that the synaptic mEos4b detections exceed chance levels (see page 5). 

      (2) Inconsistency between Figure 3A and 3B. While Figure 3B indicates an ~8-fold difference in the number of mEos4b-GlyRβ detections per synapse between the dorsal and ventral striatum, Figure 3A does not appear to show a pronounced difference in the localization of mEos4bGlyRβ on Sylite puncta between these two regions. If the images presented in Figure 3A are not representative, the authors should consider replacing them with more representative examples or providing an expanded images with multiple representative examples. Alternatively, if this inconsistency can be explained by differences in spot density within clusters, the authors should explain that. 

      The pointillist images in Fig. 3A are essentially binary (red-black). Therefore, the density of detections at synapses cannot be easily judged by eye. For clarity, the original images in Fig. 3A have been replaced with two other examples that better reflect the different detection numbers in the dorsal and ventral striatum. 

      (3) Quantification in Figure 5. It is recommended that the authors provide quantitative data on cluster formation and colocalization with Sylite puncta in Figure 5 to support their qualitative observations. 

      This is an important point that was also raised by the other reviewers. We have performed additional experiments to increase the data volume for analysis. For quantification, we used two approaches. First, we counted the percentage of infected cells in which synaptic localisation of the recombinant receptor subunit was observed (Fig. 5C). We found that mEos4b-GlyRa1 consistently localises at synapses, indicating that all cells express endogenous GlyRb. When neurons were infected with mEos4b-GlyRb, fewer cells had synaptic clusters, meaning that indeed, GlyR alpha subunits are the limiting factor for synaptic targeting. In cultures infected with mEos4b-GlyRa2, only very few neurons displayed synaptic localisation (as judged by epifluorescence imaging). We think this shows that GlyRa2 is less capable of forming heteromeric complexes than GlyRa1, in line with our previous interpretation (see pp. 9-10, 13). 

      Secondly, we quantified the total intensity of each subunit at gephyrin-positive domains, both in infected neurons as well as non-infected control cultures (Fig. 5D). We observed that mEos4bGlyRa1 intensity at gephyrin puncta was higher than that of the other subunits, again pointing to efficient synaptic targeting of GlyRa1. Gephyrin cluster intensities (Sylite labelling) were not significantly different in GlyRb and GlyRa2 expressing neurons compared to the uninfected control, indicating that the lentiviral expression of recombinant subunits does not fundamentally alter the size of mixed inhibitory synapses in hippocampal neurons. Interestingly, gephyrin levels were slightly higher in hippocampal neurons expressing mEos4b-GlyRa1. In our view, this comes from an enhanced expression and synaptic targeting of mEos4b-GlyRa1 heteromers with endogenous GlyRb, pointing to a structural role of GlyRa1/b in hippocampal synapses (pp. 10, 13).

      The new data and analyses have been described and illustrated in the relevant sections of the manuscript.

      (4) Potential for pseudo replication. It's not clear whether they're performing stats tests across biological replica, images, or even synapses. They often quote mean +/- SEM with n = 1000s, and so does that mean they're doing tests on those 1000s? Need to clarify. 

      All experiments were repeated at least twice to ensure reproducibility (N independent experiments). Statistical tests were performed on pooled data across the biological replicates; n denotes the number of data points used for testing (e.g., number of synaptic clusters, detections, cells, as specified in each case). We have systematically given these numbers in the revised manuscript (n, N, and other experimental parameters such as the number of animals used, coverslips, images or cells). Data are generally given as mean +/- SEM or as mean +/- SD as indicated.

      (5) Does mEoS effect expression levels or function of the protein? Can't see any experiments done to confirm this. Could suggest WB on homogenate, or mass spec? 

      The Glrb<sup>eos/eos</sup> knock-in mouse line has been characterised previously and does not to display any ultrastructural or functional deficits at inhibitory synapses (Maynard et al. 2021 eLife). GlyRβ expression and glycine-evoked responses were not significantly different to those of the wildtype. The synaptic localisation of mEos4b-GlyRb in KI animals demonstrates correct assembly of heteromeric GlyRs and synaptic targeting. Accordingly, the animals do not display any obvious phenotype. We have clarified this in the manuscript (p. 4). In the case of cultured neurons, long-term expression of fluorescent receptor subunits with lentivirus   has proven ideal to achieve efficient synaptic targeting. The low and continuous supply of recombinant receptors ensures assembly with endogenous subunits to form heteropentameric receptor complexes (e.g. [Patrizio et al. 2017 Sci Rep]). In the present study, lentivirus infection did not induce any obvious differences in the number or size of inhibitory synapses compared to control neurons, as judged by Sylite labelling of synaptic gephyrin puncta (new Fig. 5D).

      (6) Quantification of protein numbers is challenging with SMLM. Issues include i) some of FP not correctly folded/mature, and ii) dependence of localisation rate on instrument, excitation/illumination intensities, and also the thresholds used in analysis. Can the authors compare with another protein that has known expression levels- e.g. PSD95? This is quite an ask, but if they could show copy number of something known to compare with, it would be useful. 

      We agree that absolute quantification with SMLM is challenging, since the number of detections depends on fluorophore maturation, photophysics, imaging conditions, and analysis thresholds (discussed in Patrizio & Specht 2016, Neurophotonics). For this reason, only very few datasets provide reliable copy numbers, even for well-studied proteins such as PSD-95. One notable exception is the study by Maynard et al. (eLife 2021) that quantified endogenous GlyRβcontaining receptors in spinal cord synapses using SMLM combined with correlative electron microscopy. The strength of this work was the use of a KI mouse strain, which ensures that mEos4b-GlyRβ expression follows intrinsic regional and temporal profiles. The authors reported a stereotypic density of ~2,000 GlyRs/µm² at synapses, corresponding to ~120 receptors per synapse in the dorsal horn and ~240 in the ventral horn, taking into account various parameters including receptor stoichiometry and the functionality of the fluorophore. These values are very close to our own calculations of GlyR numbers at spinal cord synapses that were obtained slightly differently in terms of sample preparation, microscope setup, imaging conditions, and data analysis, lending support to our experimental approach. Nevertheless, the obtained GlyR copy numbers at hippocampal synapses clearly have to be taken as estimates rather than precise figures, because the number of detections from a single mEos4b fluorophore can vary substantially, meaning that the fluorophores are not represented equally in pointillist images. This can affect the copy number calculation for a specific synapse, in particular when the numbers are low (e.g. in hippocampus), however, it should not alter the average number of detections (Fig. 1B) or the (median) molecule numbers of the entire population of synapses (Fig. 1C). We have discussed the limitations of our approach (p. 11).

      (7) Rationale for doing nanobody dSTORM not clear at all. They don't explain the reason for doing the dSTORM experiments. Why not just rely on PALM for coincidence measurements, rather than tagging mEoS with a nanobody, and then doing dSTORM with that? Can they explain? Is it to get extra localisations- i.e. multiple per nanobody? If so, localising same FP multiple times wouldn't improve resolution. Also, no controls for nanobody dSTORM experiments- what about non-spec nb, or use on WT sections? 

      As discussed above (point 6), the detection of fluorophores with SMLM is influenced by many parameters, not least the noise produced by emitting molecules other than the fluorophore used for labelling. Our study is exceptional in that it attempts to identify extremely low molecule numbers (down to 1). To verify that the detections obtained with PALM correspond to mEos4b, we conducted robust control experiments (including pixel-shift as suggested by the reviewer, see point 1, revised Fig. 1B). The rationale for the nanobody-based dSTORM experiments was twofold: (1) to have an independent readout of the presence of low-copy GlyRs at inhibitory synapses and (2) to analyse the nanoscale organisation of GlyRs relative to the synaptic gephyrin scaffold using dual-colour dSTORM with spectral demixing (see p. 6). The organic fluorophores used in dSTORM (AF647, CF680) ensure high photon counts, essential for reliable co-localisation and distance analysis. PALM and dSTORM cannot be combined in dual-colour mode, as they require different buffers and imaging conditions. 

      The specificity of the anti-Eos nanobody was demonstrated by immunohistochemistry in spinal cord cultures expressing mEos4b-GlyRb and wildtype control tissue (Fig. S3). In response to the reviewer's remarks, we also performed a negative control experiment in Glrb<sup>eos/eos</sup> slices (dSTORM), in which the nanobody was omitted (new Fig. S4F,G). Under these conditions, spectral demixing produced a single peak corresponding to CF680 (gephyrin) without any AF647 contribution (Fig. S4F). The background detection of "false" AF647 detections at synapses was significantly lower than in the slices labelled with the nanobody. We conclude that the fluorescence signal observed in our dual-colour dSTORM experiments arises from the specific detection of mEos4b-GlyRb by the nanobody, rather than from background, crossreactivity or wrong attribution of colour during spectral demixing. We have added these data and explanations in the results (p. 7) and in the figure legend of Fig. S4F,G.

      (8) What resolutions/precisions were obtained in SMLM experiments? Should perform Fourier Ring Correlation (FRC) on SR images to state resolutions obtained (particularly useful for when they're presenting distance histograms, as this will be dependent on resolution). Likewise for precision, what was mean precision? Can they show histograms of localisation precision. 

      This is an interesting question in the context of our experiments with low-copy GlyRs, since the spatial resolution of SMLM is limited also by the density of molecules, i.e. the sampling of the structure in question (Nyquist-Shannon criterion). Accordingly, the priority of the PALM experiments was to improve the sensibility of SMLM for the identification of mEos4b-GlyRb subunits, rather than to maximize the spatial resolution. The mean localisation precision in PALM was 33 +/- 12 nm, as calculated from the fitting parameters of each detection (Zeiss, ZEN software), which ultimately result from their signal-to-noise ratio. This is a relatively low precision for SMLM, which can be explained by the low brightness of mEos4b compared to organic fluorophores together with the elevated fluorescence background in tissue slices.

      In the case of dSTORM, the aim was to study the relative distribution of GlyRs within the synaptic scaffold, for which a higher localisation precision was required (p. 6). Therefore, detections with a precision ≥ 25 nm were filtered during analysis with NEO software (Abbelight). The retained detections had a mean localisation precision of 12 +/- 5 for CF680 (Sylite) and 11 +/- 4 for AF647 (nanobody). These values are given in the revised manuscript (pp. 18, 22).

      (9) Why were DBSCAN parameters selected? How can they rule out multiple localisations per fluor? If low copy numbers (<10), then why bother with DBSCAN? Could just measure distance to each one. 

      Multiple detections of the same fluorophore are intrinsic to dSTORM imaging and have not been eliminated from the analysis. Small clusters of detections likely represent individual molecules (e.g. single receptors in the extrasynaptic regions, Fig. 2A). DBSCAN is a robust clustering method that is quite insensitive to minor changes in the choice of parameters. For dSTORM of synaptic gephyrin clusters (CF680), a relatively low length (80 nm radius) together with a high number of detections (≥ 50 neighbours) were chosen to reconstruct the postsynaptic domain with high spatial resolution (see point 8). In the case of the GlyR (nanobody-AF647), the clustering was done mostly for practical reasons, as it provided the coordinates of the centre of mass of the detections. The low stringency of this clustering (200 nm radius, ≥ 5 neighbours) effectively filters single detections that can result from background noise or incorrect demixing. An additional reference explaining the use of DBSCAN including the choice of parameters is given on p. 22 (see also R2 point 4).

      (10) For microscopy experiment methods, state power densities, not % or "nominal power". 

      Done. We now report the irradiance (laser power density) instead of nominal power (pp. 18, 21). 

      (11) In general, not much data presented. Any SI file with extra images etc.? 

      The original submission included four supplementary figures with additional data and representative images that should have been available to the reviewer (Figs. S1-S4). The SI file has been updated during revision (new Fig. S4E-G). 

      (12) Clarification of the discussion on GlyR expression and synaptic localization: The discussion on GlyR expression, complex formation, and synaptic localization is sometimes unclear, and needs terminological distinctions between "expression level", "complex formation" and "synaptic localization". For example, the authors state:"What then is the reason for the low protein expression of GlyRβ? One possibility is that the assembly of mature heteropentameric GlyR complexes depends critically on the expression of endogenous GlyR α subunits." Does this mean that GlyRβ proteins that fail to form complexes with GlyRα subunits are unstable and subject to rapid degradation? If so, the authors should clarify this point. The statement "This raises the interesting possibility that synaptic GlyRs may depend specifically on the concomitant expression of both α1 and β transcripts." suggests a dependency on α1 and β transcripts. However, is the authors' focus on synaptic localization or overall protein expression levels? If this means synaptic localization, it would be beneficial to state this explicitly to avoid confusion. To improve clarity, the authors should carefully distinguish between these different aspects of GlyR biology throughout the discussion. Additionally, a schematic diagram illustrating these processes would be highly beneficial for readers. 

      We thank the reviewer to point this out. We are dealing with several processes; protein expression that determines subunit availability and the assembly of pentameric GlyRs complexes, surface expression, membrane diffusion and accumulation of GlyRb-containing receptor complexes at inhibitory synapses. We have edited the manuscript, particularly the discussion and tried to be as clear as possible in our wording.

      We chose not to add a schematic illustration for the time being, because any graphical representation is necessarily a simplification. Instead, we preferred to summarise the main numbers in tabular form (Table 1). We are of course open to any other suggestions.

      (13) Interpretation of GlyR localization in the context of nanodomains. The distribution of GlyR molecules on inhibitory synapses appears to be non-homogeneous, instead forming nanoclusters or nanodomains, similar to many other synaptic proteins. It is important to interpret GlyR localization in the context of nanodomain organization. 

      The dSTORM images in Fig. 2 are pointillist representations that show individual detections rather than molecules. Small clusters of detections are likely to originate from a single AF647 fluorophore (in the case of nanobody labelling) and therefore represent single GlyRb subunits. Since GlyR copy numbers are so low at hippocampal synapses (≤ 5), the notion of nanodomain is not directly applicable. Our analysis therefore focused on the integration of GlyRs within the postsynaptic scaffold, rather than attempting to define nanodomain structures (see also response to point 8 of R1). A clarification has been added in the revised manuscript (p. 6).

      Reviewer #1 (Significance): 

      The paper presents biological and technical advances. The biological insights revolve mostly on the documentation of Glycine receptors in particular synapses in forebrain, where they are typically expressed at very low levels. The authors provide compelling data indicating that the expression is of physiological significance. The authors have done a nice job of combining genetically-tagged mice with advanced microscopy methods to tackle the question of distributions of synaptic proteins. Overall these advances are more incremental than groundbreaking. 

      We thank the reviewer for acknowledging both the technical and biological advances of our study. While we recognize that our work builds upon established models, we consider that it also addresses important unresolved questions, namely that GlyRs are present and specifically anchored at inhibitory synapses in telencephalic regions, such as the hippocampus and striatum. From a methodological point of view, our study demonstrates that SMLM can be applied not only for structural analysis of highly abundant proteins, but also to reliably detect proteins present at very low copy numbers. This ability to identify and quantify sparse molecule populations adds a new dimension to SMLM applications, which we believe increases the overall impact of our study beyond the field of synaptic neuroscience.

      Reviewer #2 (Evidence, reproducibility and clarity): 

      In their manuscript "Single molecule counting detects low-copy glycine receptors in hippocampal and striatal synapses" Camuso and colleagues apply single molecule localization microscopy (SMLM) methods to visualize low copy numbers of GlyRs at inhibitory synapses in the hippocampal formation and the striatum. SMLM analysis revealed higher copy numbers in striatum compared to hippocampal inhibitory synapses. They further provide evidence that these low copy numbers are tightly linked to post-synaptic scaffolding protein gephyrin at inhibitory synapses. Their approach profits from the high sensitivity and resolution of SMLM and challenges the controversial view on the presence of GlyRs in these formations although there are reports (electrophysiology) on the presence of GlyRs in these particular brain regions. These new datasets in the current manuscript may certainly assist in understanding the complexity of fundamental building blocks of inhibitory synapses. 

      However I have some minor points that the authors may address for clarification: 

      (1) In Figure 1 the authors apply PALM imaging of mEos4b-GlyRß (knockin) and here the corresponding Sylite label seems to be recorded in widefield, it is not clearly stated in the figure legend if it is widefield or super-resolved. In Fig 1 A - is the scale bar 5 µm? Some Sylite spots appear to be sized around 1 µm, especially the brighter spots, but maybe this is due to the lower resolution of widefield imaging? Regarding the statistical comparison: what method was chosen to test for normality distribution, I think this point is missing in the methods section. 

      This is correct; the apparent size of the Sylite spots does not reflect the real size of the synaptic gephyrin domain due to the limited resolution of widefield imaging including the detection of outof-focus light. We have clarified in the legend of Fig. 1A that Sylite labelling was with classic epifluorescence microscopy. The scale bar in Fig. 1A corresponds to 5 µm. Since the data were not normally distributed, nonparametric tests (Kruskal- Wallis one-way ANOVA with Dunn’s multiple comparison test or Mann-Whitney U-test for pairwise comparisons) were used (p. 23). 

      Moreover I would appreciate a clarification and/or citation that the knockin model results in no structural and physiological changes at inhibitory synapses, I believe this model has been applied in previous studies and corresponding clarification can be provided. 

      The Glrbeos/eos mouse model has been described previously and does not exhibit any structural or physiological phenotypes (Maynard et al. 2021 eLife). The issue was also raised by reviewer R1 (point 5) and has been clarified in the revised manuscript (p. 4).

      (2) In the next set of experiments the authors switch to demixing dSTORM experiments - an explanation why this is performed is missing in the text - I guess better resolution to perform more detailed distance measurements? For these experiments: which region of the hippocampus did the authors select, I cannot find this information in legend or main text. 

      Yes, the dSTORM experiments enable dual-colour structural analysis at high spatial resolution (see response to R1 point 7). An explanation has been added (p. 6).

      (3) Regarding parameters of demixing experiments: the number of frames (10.000) seems quite low and the exposure time higher than expected for Alexa 647. Can the authors explain the reason for chosing these particular parameters (low expression profile of the target - so better separation?, less fluorophores on label and shorter collection time?) or is there a reference that can be cited? The laser power is given in the methods in percentage of maximal output power, but for better comparison and reproducibility I recommend to provide the values of a power meter (kW/cm2) as lasers may change their maximum output power during their lifetime. 

      Acquisition parameters (laser power, exposure time) for dSTORM were chosen to obtain a good localisation precision (~12 nm; see R1 point 8). The number of frames is adequate to obtain well sampled gephyrin scaffolds in the CF680 channel. In the case of the GlyR (nanobody-AF647), the concept of spatial resolution does not really apply due to the low number of targets (see R1, point 13). Power density (irradiance) values have now been given (pp. 18, 21).

      (4) For analysis of subsynaptic distribution: how did the authors decide to choose the parameters in the NEO software for DBSCAN clustering - was a series of parameters tested to find optimal conditions and did the analysis start with an initial test if data is indeed clustered (K-ripley) or is there a reference in literature that can be provided? 

      DBSCAN parameters were optimised manually, by testing different values. Identification of dense and well-delimited gephyrin clusters (CF680) was achieved with a small radius and a high number of detections (80 nm, ≥ 50 neighbours), whereas filtering of low-density background in the AF647 channel (GlyRs) required less stringent parameters (200 nm, ≥ 5) due to the low number of target molecules. Similar parameters were used in a previous publication (Khayenko et al. 2022, Angewandte Chemie). The reference has been provided on p. 22 (see also R1 point 9).

      (5) A conclusion/discussion of the results presented in Figure 5 is missing in the text/discussion. 

      This part of the manuscript has been completely overhauled. It includes new experimental data, quantification of the data (new Fig.5), as well as the discussion and interpretation of our findings (see also R1, point 3). In agreement with our earlier interpretation, the data confirm that low availability of GlyRa1 subunits limits the expression and synaptic targeting of GlyRa1/b heteropentamers. The observation that GlyRa1 overexpression with lentivirus increases the size of the postsynaptic gephyrin domain further points to a structural role, whereby GlyRs can enhance the stability (and size) of inhibitory synapses in hippocampal neurons, even at low copy numbers (pp. 13-14). 

      (6) In line 552 "suspension" is misleading, better use "solution" 

      Done.

      Reviewer #2 (Significance): 

      Significance: The manuscript provides new insights to presence of low-copy numbers by visualizing them via SMLM. This is the first report that visualizes GlyR optically in the brain applying the knock-in model of mEOS4b tagged GlyRß and quantifies their copy number comparing distribution and amount of GlyRs from hippocampus and striatum. Imaging data correspond well to electrophysiological measurements in the manuscript. 

      Field of expertise: Super-Resolution Imaging and corresponding analysis 

      Reviewer #4 (Evidence, reproducibility and clarity): 

      In this study, Camuso et al., make use of a knock-in mouse model expressing endogenously mEos4b-tagged GlyRβ to detect endogenous glycine receptors using single-molecule localization microscopy. The main conclusion from this study is that in the hippocampus GlyRβ molecules are barely detected, while inhibitory synapses in the ventral striatum seem to express functionally relevant GlyR numbers. 

      I have a few points that I hope help to improve the strength of this study. 

      - In the hippocampus, this study finds that the numbers of detections are very low. The authors perform adequate controls to indicate that these localizations are above noise level. Nevertheless, it remains questionable that these reflect proper GlyRs. The suggestion that in hippocampal synapses the low numbers of GlyRβ molecules "are important in assembly or maintenance of inhibitory synaptic structures in the brain" is on itself interesting, but is not at all supported. It is also difficult to envision how such low numbers could support the structure of a synapse. A functional experiment showing that knockdown of GlyRs affects inhibitory synapse structure in hippocampal neurons would be a minimal test of this. 

      It is not clear what the reviewer means by “it remains questionable that these reflect proper GlyRs”. The PALM experiments include a series of stringent controls (see R1, point 1) demonstrating the existence of low-copy GlyRs at inhibitory synapses in the hippocampus (Fig. 1) and in the striatum (Fig. 3), and are backed up by dSTORM experiments (Fig. 2). We have no reason to doubt that these receptors are fully functional (as demonstrated for the ventral striatum (Fig. 4). However, due to their low number, a role in inhibitory synaptic transmission is clearly limited, at least in the hippocampus and dorsal striatum. 

      We therefore propose a structural role, where the GlyRs could be required to stabilise the postsynaptic gephyrin domain in hippocampal neurons. This is based on the idea that the GlyRgephyrin affinity is much higher than that of the GABAAR-gephyrin interaction (reviewed in Kasaragod & Schindelin 2018 Front Mol Neurosci). Accordingly, there is a close relationship between GlyRs and gephyrin numbers, sub-synaptic distribution, and dynamics in spinal cord synapses that are mostly glycinergic (Specht et al. 2013 Neuron; Maynard et al. 2021 eLife; Chapdelaine et al. 2021 Biophys J). It is reasonable to assume that low-copy GlyRs could play a similar structural role at hippocampal synapses. A knockdown experiment targeting these few receptors is technically very challenging and beyond the scope of this study. However, in response to the reviewer's question we have conducted new experiments in cultured hippocampal neurons (new Fig. 5). They demonstrate that overexpression of GlyRa1/b heteropentamers increases the size of the postsynaptic domain in these neurons, supporting our interpretation of a structural role of low-copy GlyRs (p. 14).

      - The endogenous tagging strategy is a very strong aspect of this study and provides confidence in the labeling of GlyRβ molecules. One caveat however, is that this labeling strategy does not discriminate whether GlyRβ molecules are on the cell membrane or in internal compartments. Can the authors provide an estimate of the ratio of surface to internal GlyRβ molecules? 

      Gephyrin is known to form a two-dimensional scaffold below the synaptic membrane to which inhibitory GlyRs and GABAARs attach (reviewed in Alvarez 2017 Brain Res). The majority of the synaptic receptors are therefore thought to be located in the synaptic membrane, which is supported by the close relationship between the sub-synaptic distribution of GlyRs and gephyrin in spinal cord neurons (e.g. Maynard et al. 2021 eLife). To demonstrate the surface expression of GlyRs at hippocampal synapses we labelled cultured hippocampal neurons expressing mEos4b-GlyRa1 with anti-Eos nanobody in non-permeabilised neurons (see Author response image 1). The close correspondence between the nanobody (AF647) and the mEos4b signal confirms that the majority of the GlyRs are indeed located in the synaptic membrane.

      Author response image 1.

      Left: Lentivirus expression of mEos4b-GlyRa1 in fixed and non-permeabilised hippocampal neurons (mEos4b signal). Right: Surface labelling of the recombinant subunit with anti-Eos nanoboby (AF647). 

      - “We also estimated the absolute number of GlyRs per synapse in the hippocampus. The number of mEos4b detections was converted into copy numbers by dividing the detections at synapses by the average number of detections of individual mEos4b-GlyRβ containing receptor complexes”. In essence this is a correct method to estimate copy numbers, and the authors discuss some of the pitfalls associated with this approach (i.e., maturation of fluorophore and detection limit). Nevertheless, the authors did not subtract the number of background localizations determined in the two negative control groups. This is critical, particularly at these low-number estimations. 

      We fully agree that background subtraction can be useful with low detection numbers. In the revised manuscript, copy numbers are now reported as background-corrected values. Specifically, the mean number of detections measured in wildtype slices was used to calculate an equivalent receptor number, which was then subtracted from the copy number estimates across hippocampus, spinal cord and striatum. This procedure is described in the methods (p. 20) and results (p. 5, 8), and mentioned in the figure legends of Fig. 1C, 3C. The background corrected values are given in the text and Table 1.

      - Furthermore, the authors state that "The advantage of this estimation is that it is independent of the stoichiometry of heteropentameric GlyRs". However, if the stoichometry is unknown, the number of counted GlyRβ subunits cannot simply be reported as the number of GlyRs. This should be discussed in more detail, and more carefully reported throughout the manuscript. 

      The reviewer is right to point this out. There is still some debate about the stoichiometry of heteropentameric GlyRs. Configurations with 2a:3b, 3a:2b and 4a:1b subunits have been advanced (e.g. Grudzinska et al. 2005 Neuron; Durisic et al. 2012 J Neurosci; Patrizio et al. 2017 Sci Rep; Zhu & Gouaux 2021 Nature). We have therefore chosen a quantification that is independent of the underlying stoichiometry. Since our quantification is based on very sparse clusters of mEos4b detections that likely originate from a single receptor complex (irrespective of its stoichiometry), the reported values actually reflect the number of GlyRs (and not GlyRb subunits). We have clarified this in the results (p. 5) and throughout the manuscript (Table 1). 

      - The dual-color imaging provides insights in the subsynaptic distribution of GlyRβ molecules in hippocampal synapses. Why are similar studies not performed on synapses in the ventral striatum where functionally relevant numbers of GlyRβ molecules are found? Here insights in the subsynaptic receptor distribution would be of much more interest as it can be tight to the function. 

      This is an interesting suggestion. However, the primary aim of our study was to identify the existence of GlyRs in hippocampal regions. At low copy numbers, the concept of sub-synaptic domains (SSDs, e.g. Yang et al. 2021 EMBO Rep) becomes irrelevant (see R1 point 13). It should be pointed out that the dSTORM pointillist images (Fig. 2A) represent individual GlyR detections rather than clusters of molecules. In the striatum, our specific purpose was to solve an open question about the presence of GlyRs in different subregions (putamen, nucleus accumbens).

      - It is unclear how the experiments in Figure 5 add to this study. These results are valid, but do not seem to directly test the hypothesis that "the expression of α subunits may be limiting factor controlling the number of synaptic GlyRs". These experiments simply test if overexpressed α subunits can be detected. If the α subunits are limiting, measuring the effect of α subunit overexpression on GlyRβ surface expression would be a more direct test. 

      Both R1 and R2 have also commented on the data in Fig. 5 and their interpretation. We have substantially revised this section as described before (see R1 point 3) including additional experiments and quantification of the data (new Fig. 5). The findings lend support to our earlier hypothesis that GlyR alpha subunits (in particular GlyRa1) are the limiting factor for the expression of heteropentameric GlyRa/b in hippocampal neurons (pp. 13-14). Since the GlyRa1 subunit itself does not bind to gephyrin (Patrizio et al. 2017 Sci Rep), the synaptic localisation of the recombinant mEos4b-GlyRa1 subunits is proof that they have formed heteropentamers with endogenous GlyRb subunits and driven their membrane trafficking, which the GlyRb subunits are incapable of doing on their own.

      Reviewer #4 (Significance): 

      These results are based on carefully performed single-molecule localization experiments, and are well-presented and described. The knockin mouse with endogenously tagged GlyRβ molecules is a very strong aspect of this study and provides confidence in the labeling, the combination with single-molecule localization microscopy is very strong as it provides high sensitivity and spatial resolution. 

      The conceptual innovation however seems relatively modest, these results confirm previous studies but do not seem to add novel insights. This study is entirely descriptive and does not bring new mechanistic insights. 

      This study could be of interest to a specialized audience interested in glycine receptor biology, inhibitory synapse biology and super-resolution microscopy. 

      My expertise is in super-resolution microscopy, synaptic transmission and plasticity 

      As we have stated before, the novelty of our study lies in the use of SMLM for the identification of very small numbers of molecules, which requires careful control experiments. This is something that has not been done before and that can be of interest to a wider readership, as it opens up SMLM for ultrasensitive detection of rare molecular events. Using this approach, we solve two open scientific questions: (1) the demonstration that low-copy GlyRs are present at inhibitory synapses in the hippocampus, (2) the sub-region specific expression and functional role of GlyRs in the ventral versus dorsal striatum.

      The following review was provided later under the name “Reviewer #4”. To avoid confusion with the last reviewer from above we will refer to this review as R4-2.

      Reviewer #4-2 (Evidence, reproducibility and clarity):  

      Summary:

      Provide a short summary of the findings and key conclusions (including methodology and model system(s) where appropriate).

      The authors investigate the presence of synaptic glycine receptors in the telencephalon, whose presence and function is poorly understood. 

      Using a transgenically labeled glycine receptor beta subunit (Glrb-mEos4b) mouse model together with super-resolution microscopy (SLMM, dSTORM), they demonstrate the presence of a low but detectable amount of synaptically localized GLRB in the hippocampus. While they do not perform a functional analysis of these receptors, they do demonstrate that these subunits are integrated into the inhibitory postsynaptic density (iPSD) as labeled by the scaffold protein gephyrin. These findings demonstrate that a low level of synaptically localized glycerine receptor subunits exist in the hippocampal formation, although whether or not they have a functional relevance remains unknown.

      They then proceed to quantify synaptic glycine receptors in the striatum, demonstrating that the ventral striatum has a significantly higher amount of GLRB co-localized with gephyrin than the dorsal striatum or the hippocampus. They then recorded pharmacologically isolated glycinergic miniature inhibitory postsynaptic currents (mIPSCs) from striatal neurons. In line with their structural observations, these recordings confirmed the presence of synaptic glycinergic signaling in the ventral striatum, and an almost complete absence in the dorsal striatum. Together, these findings demonstrate that synaptic glycine receptors in the ventral striatum are present and functional, while an important contribution to dorsal striatal activity is less likely.

      Lastly, the authors use existing mRNA and protein datasets to show that the expression level of GLRA1 across the brain positively correlates with the presence of synaptic GLRB.

      The authors use lentiviral expression of mEos4b-tagged glycine receptor alpha1, alpha2, and beta subunits (GLRA1, GLRA1, GLRB) in cultured hippocampal neurons to investigate the ability of these subunits to cause the synaptic localization of glycine receptors. They suggest that the alpha1 subunit has a higher propensity to localize at the inhibitory postsynapse (labeled via gephyrin) than the alpha2 or beta subunits, and may therefore contribute to the distribution of functional synaptic glycine receptors across the brain.

      Major comments:

      - Are the key conclusions convincing?

      The authors are generally precise in the formulation of their conclusions.

      (1) They demonstrate a very low, but detectable, amount of a synaptically localized glycine receptor subunit in a transgenic (GlrB-mEos4b) mouse model. They demonstrate that the GLRB-mEos4b fusion protein is integrated into the iPSD as determined by gephyrin labelling. The authors do not perform functional tests of these receptors and do not state any such conclusions.

      (2) The authors show that GLRB-mEos4b is clearly detectable in the striatum and integrated into gephyrin clusters at a significantly higher rate in the ventral striatum compared to the dorsal striatum, which is in line with previous studies.

      (3) Adding to their quantification of GLRB-mEos4b in the striatum, the authors demonstrate the presence of glycinergic miniature IPSCs in the ventral striatum, and an almost complete absence of mIPSCs in the dorsal striatum. These currents support the observation that GLRB-mEos4b is more synaptically integrated in the ventral striatum compared to the dorsal striatum.

      (4) The authors show that lentiviral expression of GLRA1-mEos4b leads to a visually higher number of GLR clusters in cultured hippocampal neurons, and a co-localization of some clusters with gephyrin. The authors claim that this supports the idea that GLRA1 may be an important driver of synaptic glycine receptor localization. However, no quantification or statistical analysis of the number of puncta or their colocalization with gephyrin is provided for any of the expressed subunits. Such a claim should be supported by quantification and statistics 

      A thorough analysis and quantification of the data in Fig.5 has been carried out as requested by all the other reviewers (e.g. R1, point 3). The new data and results have been described in the revised manuscript (pp. 9-10, 13-14).

      - Should the authors qualify some of their claims as preliminary or speculative, or remove them altogether?

      One unaddressed caveat is the fact that a GLRB-mEos4b fusion protein may behave differently in terms of localization and synaptic integration than wild-type GLRB. While unlikely, it is possible that mEos4b interacts either with itself or synaptic proteins in a way that changes the fused GLRB subunit’s localization. Such an effect would be unlikely to affect synaptic function in a measurable way, but might be detected at a structural level by highly sensitive methods such as SMLM and STORM in regions with very low molecule numbers (such as the hippocampus). Since reliable antibodies against GLRB in brain tissue sections are not available, this would be difficult to test. Considering that no functional measures of the hippocampal detections exist, we would suggest that this possible caveat be mentioned for this particular experiment.

      This question has also been raised before (R1, point 5). According to an earlier study the mEos4b-GlyRb knock-in does not cause any obvious phenotypes, with the possible exception of minor loss of glycine potency (Maynard et al. 2021 eLife). The fact that the synaptic levels in the spinal cord in heterozygous animals are precisely half of those of homozygous animals argues against differences in receptor expression, heteropentameric assembly, forward trafficking to the plasma membrane and integration into the synaptic membrane as confirmed using quantitative super-resolution CLEM (Maynard et al. 2021 eLife). Accordingly, we did not observe any behavioural deficits in these animals, making it a powerful experimental model. We have added this information in the revised manuscript (p. 4). 

      In addition, without any quantification or statistical analysis, the author’s claims regarding the necessity of GLRA1 expression for the synaptic localization of glycine receptors in cultured hippocampal neurons should probably be described as preliminary (Fig. 5).

      As mentioned before, we have substantially revised this part (R1, point 3). The quantification and analysis in the new Fig. 5 support our earlier interpretation.

      - Would additional experiments be essential to support the claims of the paper? Request additional experiments only where necessary for the paper as it is, and do not ask authors to open new lines of experimentation.

      The authors show that there is colocalization of gephyrin with the mEos4b-GlyRβ subunit using the Dual-colour SMLM. This is a powerful approach that allows for a claim to be made on the synaptic location of the glycine receptors. The images presented in Figure 1, together with the distance analysis in Figure 2, display the co-localization of the fluorophores. The co-localization images in all the selected regions, hippocampus and striatum, also show detections outside of the gephyrin clusters, which the authors refer to as extrasynaptic. These punctated small clusters seem to have the same size as the ones detected and assigned as part of the synapse. It would be informative if the authors analysed the distribution, density and size of these nonsynaptic clusters and presented the data in the manuscript and also compared it against the synaptic ones. Validating this extrasynaptic signal by staining for a dendritic marker, such as MAP-2 or maybe a somatic marker and assessing the co-localization with the non-synaptic clusters would also add even more credibility to them being extrasynaptic. 

      The existence of extrasynaptic GlyRs is well attested in spinal cord neurons (e.g. Specht et al. 2013 Neuron; this study see Fig. S2). The fact that these appear as small clusters of detections in SMLM recordings results from the fact that a single fluorophore can be detected several times in consecutive image frames and because of blinking. Therefore, small clusters of detections likely represent single GlyRs (that can be counted), and not assemblies of several receptor complexes. Due to their diffusion in the neuronal membrane, they are seen as diffuse signals throughout the somatodendritic compartment in epifluorescence images (e.g. Fig. 5A). SMLM recordings of the same cells resolves this diffuse signal into discrete nanoclusters representing individual receptors (Fig. 5B). It is not clear what information co-localisation experiments with specific markers could provide, especially in hippocampal neurons, in which the copy numbers (and density) of GlyRs is next to zero.

      In addition we would encourage the authors to quantify the clustering and co-localization of virally expressed GLRA1, GLRA2, and GLRB with gephyrin in order to support the associated claims (Fig. 5). Preferably, the density of GLR and gephyrin clusters (at least on the somatic surface, the proximal dendrites, or both) as well as their co-localization probability should be quantified if a causal claim about subunit-specific requirements for synaptic localization is to be made.

      Quantification of the data have been carried out (new Fig.5C,D). The results have been described before (R1, point 3) and support our earlier interpretation of the data (pp. 13-14).

      Lastly, even though it may be outside of the scope of such a study analysing other parts of the hippocampal area could provide additional important information. If one looks at the Allen Institute’s ISH of the beta subunit the strongest signal comes from the stratum oriens in the CA1 for example, suggesting that interneurons residing there would more likely have a higher expression of the glycine receptors. This could also be assessed by looking more carefully at the single cell transcriptomics, to see which cell types in the hippocampus show the highest mRNA levels. If the authors think that this is too much additional work, then perhaps a mention of this in the discussion would be good. 

      We have added the requested information from the ISH database of the Allen Institute in the discussion as suggested by the reviewer (p. 12). However, in combination with the transcriptomic data (Fig. S1) our finding strongly suggest that the expression of synaptic GlyRs depends on the availability of alpha subunits rather than on the presence of the GlyRb transcript. This is obvious when one compares the mRNA levels in the hippocampus with those in the basal ganglia (striatum) and medulla. While the transcript concentrations of GlyRb are elevated in all three regions and essentially the same, our data show that the GlyRb copy numbers at synapses differ over more than 2 orders of magnitude (Fig. 1B, Table 1). 

      - Are the suggested experiments realistic in terms of time and resources? It would help if you could add an estimated cost and time investment for substantial experiments.

      Since the labeling and some imaging has been performed already, the requested experiment would be a matter of deploying a method of quantification. In principle, it should not require any additional wet-lab experiments, although it may require additional imaging of existing samples.

      - Are the data and the methods presented in such a way that they can be reproduced?

      Yes, for the most part.

      - Are the experiments adequately replicated and statistical analysis adequate?

      Yes

      Minor comments:

      - Specific experimental issues that are easily addressable.

      N/A

      - Are prior studies referenced appropriately?

      Yes

      - Are the text and figures clear and accurate?

      Yes, although quantification in figure 5 is currently not present.

      A quantification has been added (see R1, point 3).

      - Do you have suggestions that would help the authors improve the presentation of their data and conclusions?

      This paper presents a method that could be used to localize receptors and perhaps other proteins that are in low abundance or for which a detailed quantification is necessary. I would therefore suggest that Figure S4 is included into Figure 2 as the first panel, showcasing the demixing, followed by the results. 

      We agree in principle with this suggestion. However, the revised Fig. S4 is more complex and we think that it would distract from the data shown in Fig. 2. Given that Fig. S4 is mostly methodological and not essential to understand the text, we have kept it in the supplement for the time being. We leave the final decision on this point to the editor.

      Reviewer #4-2 (Significance): 

      [This review was supplied later]

      - Describe the nature and significance of the advance (e.g. conceptual, technical, clinical) for the field.

      Using a novel and high resolution method, the authors have provided strong evidence for the presence of glycine receptors in the murine hippocampus and in the dorsal striatum. The number of receptors calculated is small compared to the numbers found in the ventral striatum. This is the first study to quantify receptor numbers in these region. In addition it also lays a roadmap for future studies addressing similar questions. 

      - Place the work in the context of the existing literature (provide references, where appropriate).

      This is done well by the authors in the curation of the literature. As stated above, the authors have filled a gap in the presence of glycine receptors in different brain regions, a subject of importance in understanding the role they play in brain activity and function. 

      - State what audience might be interested in and influenced by the reported findings.

      Neuroscientists working at the synaptic level, on inhibitory neurotransmission and on fundamental mechanisms of expression of genes at low levels and their relationship to the presence of the protein would be interested. Furthermore, researchers in neuroscience and cell biology may benefit from and be inspired by the approach used in this manuscript, to potentially apply it to address their own aims. 

      We thank the reviewer for the positive assessment of the technical and biological implications of our work, as well as the interest of our findings to a wide readership of neuroscientists and cell biologists. 

      - Define your field of expertise with a few keywords to help the authors contextualize your point of view. Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate.

      Synaptic transmission, inhibitory cells and GABAergic synapses functionally and structurally, cortex and cortical circuits. No strong expertise in super-resolution imaging methods.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review): 

      Summary: 

      This very thorough anatomical study addresses the innervation of the Drosophila male reproductive tract. Two distinct glutamatergic neuron types were classified: serotonergic (SGNs) and octopaminergic (OGNs). By expansion microscopy, it was established that glutamate and serotonin /octopamine are co-released. The expression of different receptors for 5-HT and OA in muscles and epithelial cells of the innervation target organs was characterized. The pattern of neurotransmitter receptor expression in the target organs suggests that seminal fluid and sperm transport and emission are subjected to complex regulation. While silencing of abdominal SGNs leads to male infertility and prevents sperm from entering the ejaculatory duct, silencing of OGNs does not render males infertile. 

      Strengths: 

      The studied neurons were analysed with different transgenes and methods, as well as antibodies against neurotransmitter synthesis enzymes, building a consistent picture of their neurotransmitter identity. The careful anatomical description of innervation patterns together with receptor expression patterns of the target organs provides a solid basis for advancing the understanding of how seminal fluid and sperm transport and emission are subjected to complex regulation. The functional data showing that SGNs are required for male fertility and for the release of sperm from the seminal vesicle into the ejaculatory duct is convincing. 

      Weaknesses: 

      The functional analysis of the characterized neurons is not as comprehensive as the anatomical description, and phenotypic characterization was limited to simple fertility assays. It is understandable that a full functional dissection is beyond the scope of the present work. The paper contains experiments showing neuron-independent peristaltic waves in the reproductive tract muscles, which are thematically not very well integrated into the paper. Although very interesting, one wonders if these experiments would not fit better into a future work that also explores these peristaltic waves and their interrelation with neuromodulation mechanistically. 

      Reviewer #2 (Public review): 

      Summary: 

      Cheverra et al. present a comprehensive anatomical and functional analysis of the motor neurons innervating the male reproductive tract in Drosophila melanogaster, addressing a gap in our understanding of the peripheral circuits underlying ejaculation and male fertility. They identify two classes of multi-transmitter motor neurons-OGNs (octopamine/glutamate) and SGNs (serotonin/glutamate)-with distinct innervation patterns across reproductive organs. The authors further characterize the differential expression of glutamate, octopamine, and serotonin receptors in both epithelial and muscular tissues of these organs. Behavioral assays reveal that SGNs are essential for male fertility, whereas OGNs and glutamatergic transmission are dispensable. This work provides a high-resolution map linking neuromodulatory identity to organ-specific motor control, offering a valuable framework to explore the neural basis of male reproductive function. 

      Strengths: 

      Through the use of an extensive set of GAL4 drivers and antibodies, this work successfully and precisely defines the neurons that innervate the male reproductive tract, identifying the specific organs they target and the nature of the neurotransmitters they release. It also characterizes the expression patterns and localization of the corresponding neurotransmitter receptors across different tissues. The authors describe two distinct groups of dual-identity neurons innervating the male reproductive tract: OGNs, which co-express octopamine and glutamate, and SGNs, which co-express serotonin and glutamate. They further demonstrate that the various organs within the male reproductive system differentially express receptors for these neurotransmitters. Based on these findings, the authors propose that a single neuron capable of co-releasing a fast-acting neurotransmitter alongside a slower-acting one may more effectively synchronize and stagger events that require precise timing. This, together with the differential expression of ionotropic glutamate receptors and metabotropic aminergic receptors in postsynaptic muscle tissue, adds an additional layer of complexity to the coordinated regulation of fluid secretion, organ contractility, and directional sperm movement-all contributing to the optimization of male fertility. 

      Weaknesses: 

      The main weakness of the manuscript is the lack of detail in the presentation of the results. Specifically, all microscopy image figures are missing information about the number of samples (N), and in the case of colocalization experiments, quantitative analyses are not provided. Additionally, in the first behavioral section, it would be beneficial to complement the data table with figures similar to those presented later in the manuscript for consistency and clarity. 

      Wider context: 

      This study delivers the first detailed anatomical map connecting multi-transmitter motor neurons with specific male reproductive structures. It highlights a previously unrecognized functional specialization between serotonergic and octopaminergic pathways and lays the groundwork for exploring fundamental neural mechanisms that regulate ejaculation and fertility in males. The principles uncovered here may help explain how males of Drosophila and other organisms adjust reproductive behaviors in response to environmental changes. Furthermore, by shedding light on how multi-transmitter systems operate in reproductive control, this model could provide insights into therapeutic targets for conditions such as male infertility and prostate cancer, where similar neuronal populations are involved in humans. Ultimately, this genetically accessible system serves as a powerful tool for uncovering how multi-transmitter neurons orchestrate coordinated physiological actions necessary for the functioning of complex organs. 

      Reviewer #3 (Public review): 

      Summary: 

      This work provides an overview of the motor neuron landscape in the male reproductive system. Some work had been done to elucidate the circuits of ejaculation in the spine, as well as the cord, but this work fills a gap in knowledge at the level of the reproductive organs. Using complementary approaches, the authors show that there are two types of motor neurons that are mutually exclusive: neurons that co-express octopamine and glutamate and neurons that co-express serotonin and glutamate. They also show evidence that both types of neurons express large dense core vesicles, indicating that neuropeptides play a role in male fertility. This paper provides a thorough characterization of the expression of the different glutamate, octopamine, and serotonin receptors in the different organs and tissues of the male reproductive system. The differential expression in different tissues and organs allows building initial theories on the control of emission and expulsion. Additionally, the authors characterize the expression of synaptic proteins and the neuromuscular junction sites. On a mechanistic level, the authors show that neither octopamine/glutamate neuron transmission nor glutamate transmission in serotonin/glutamate neurons is required for male fertility. This final result is quite surprising and opens up many questions on how ejaculation is coordinated. 

      Strengths: 

      This work fills an important gap in the characterization of innervation of the male reproductive system by providing an extensive characterization of the motor neurons and the potential receptors of motor neuron release. The authors show convincing evidence of glutamate/monoamine co-release and of mutual exclusivity of serotonin/glutamate and octopamine/glutamate neurons. 

      Weaknesses: 

      (1) Often, it is mentioned that the expression is higher or lower or regional without quantification or an indication of the number of samples analysed. 

      (2) The experiment aimed at tracking sperm in the male reproductive system is difficult to interpret when it is not assessed whether ejaculation has occurred. 

      (3) The experiment looking at peristaltic waves in the male organs is missing labeling of the different regions and quantification of the observed waves. 

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors): 

      (1) While the peripheral innervations are very carefully described, it is not clear to which SGNs and OGNs (i.e., cell bodies in the central nervous system) these innervations belong. Are SV, AG, and ED innervated by branches of one neuron or by separate neurons? Multi-color flip-out experiments could provide an answer to this. 

      We agree this is important and are planning these experiments for follow-up study.

      (2) In contrast, for the analysis of the VT19028 split line (Figure 9), only vnc and cell body images are shown. How do the arborisations of these split combinations look in the periphery? Are the same reproductive organs innervated as shown in Figure 2?

      Figure 9S3 was inadvertently omitted from the initial submission.  That figure is now included and shows that the VT019028 split broadly innervates the SV, AG, and ED.

      (3) In the discussion, I think it would be helpful to offer some potential explanations for the role of octopaminergic and glutamatergic signaling. If not required for basic fertility, they probably have some other role.

      Thank you, we have included speculation in the Discussion section "Potential for adaptation to environment".

      (4) Line 543: Figure 8S4 E, (not 8E). 

      Correction made.

      Reviewer #2 (Recommendations for the authors): 

      (1) Line 213-217 

      Comment:

      The use of "significantly less expression" may be misleading, as no quantification or statistical analysis is provided to support this comparison. 

      Suggestion:

      Consider using a more neutral term, such as "markedly less" or "noticeably less," unless quantitative data and statistical analysis are included to substantiate the claim.

      Good recommendation.This suggestion has been incorporated.

      (2) Line 264-267 

      Comment:

      The observation regarding the distinct morphology of SGNs and OGNs is interesting and could strengthen the argument regarding functional differences. 

      Suggestion: 

      Consider including a quantification of morphological complexity (e.g., branching) to support the claim. A method such as Sholl analysis (Sholl, 1953), as adapted in Fernández et al., 2008, could be applied. 

      This is a good suggestion, and we will consider it as part of a follow-up study.

      (3) Line 269-271 

      Comment:

      The anatomical context of the observation is not explicitly stated. 

      Suggestion:

      Add "in the ED" for clarity: "With the TRH-GAL4 experiment in the ED, vGlut-40XMYC (Figure 5S1, A and E) and 6XV5-vMAT (Figure 5S1, B and F) were both present with a highly overlapping distribution (Figure 5S1, I)." 

      Suggestion has been incorporated.

      (4) Line 275-276 

      Comment:

      The claim about the reduced ability to distinguish SGNs and OGNs in the ED would benefit from quantitative support. 

      Suggestion:

      Include a morphological comparison or quantification between SGNs and OGNs in the ED and SV to reinforce this point.

      Certain information on morphological comparison can be inferred within the images themselves, and we will include quantitation in a follow-up study.

      (5) Line 277-279 

      Comment:

      As with line 269, the anatomical site could be specified more clearly. 

      Suggestion: 

      Rephrase as: "With the Tdc2-GAL4 experiment in the ED, vGlut-40XMYC (Figure 5S1, M and Q) and 6XV5-vMAT (Figure 5S1, N and R) were both observed in a highly overlapping distribution (Figure 5S1, U)." 

      Suggestion has been incorporated.

      (6) Line 348-350 

      Comment:

      The phrase "significantly higher density" implies a statistical comparison that is not shown. 

      Suggestion:

      If no quantification is provided, replace with a qualitative term such as "visibly higher" or "notably more dense." Alternatively, add a quantitative analysis with statistical testing to justify the use of "significantly." 

      Suggestion has been incorporated.

      (7) Lines 415-458 (Section comment) 

      Comment:

      There appears to be differential localization of neurotransmitter receptor expression (glutamate in muscle vs. 5-HT in epithelium or neurons), which could have functional implications. 

      Suggestion:

      Expand this section to briefly discuss the differential localization patterns of these receptors and potential implications for signal transduction in male reproductive tissues. 

      (8) Lines 638-682 (Section comment) 

      Comment:

      The table summarizing fertility phenotypes would be more informative with additional detail on experimental outcomes. 

      Suggestion:

      Add a column showing the number of fertile males over the total tested (e.g., "n fertile / n total"). Also, clarify whether the fertility assays are identical to those reported in Figure 10S2, and whether similar analyses were conducted for females. Consider including a figure summarizing fertility results for all genotypes listed in the table, similar to Figure 10S2. 

      The fertility tests reported in Table 1 were separate from those reported in Figure 10S2.  For these tests, the results were clear-cut with 100% of males and females reported as infertile exhibiting the infertile phenotype.  For the males and females reported as fertile, it was also clear-cut with nearly 100% showing fertility at a high level.  In subsequent figures we attempted to assess degrees of fertility.

      (9) Line 724-727 

      Comment:

      There seems to be a mistake in the identification of the driver lines used to silence OA neurons. Also, figure references might be incorrect. 

      Suggestion:

      The OA neuron driver line should be corrected to "Tdc2-GAL4-DBD ∩ AbdB-AD" instead of TRH-GAL4. Additionally, the figure references should be verified; specifically, the letter "B" (in "Figure 10B, D" and "10B, E") appears to be unnecessary or misplaced.

      Thanks for catching this, the corrections have been made.

      (10) Line 872-877 

      Comment:

      The discussion on the co-release of fast-acting glutamate and slower aminergic neurotransmitters is interesting and well-articulated. However, it remains somewhat disconnected from the behavioral findings. 

      Suggestion:

      Consider linking this proposed mechanism to the results observed in the mating duration assays. For instance, the sequential action of neurotransmitters described here could potentially underlie the prolonged mating observed when specific neuromodulators are active, helping to functionally integrate molecular and behavioral data. 

      (11) Line 926-928 

      Comment:

      The interpretation of 5-HT7 receptor expression in the sphincter is compelling, suggesting a role in regulating its function. However, this anatomical observation could be further contextualized with the functional data. 

      Suggestion:

      It may strengthen the interpretation to explicitly connect this finding with the fertility assays, where SGNs - presumably acting via serotonergic signaling - are shown to be necessary for male fertility. This would support a functional role for 5-HT7 in reproductive success via sphincter regulation.

      This has been added. 

      (12) Figure 1 

      Comment:

      The figure legend is generally clear, but could benefit from more consistency and precision in the color-coded labeling. Additionally, the naming of some structures could be more explicit. 

      Suggestion: 

      Revise the figure and the legend as follows:

      Figure 1. The Drosophila male reproductive system. A) Schematic diagram showing paired testes (colour), SVs (green), AGs (purple), Sph (red), ED (gray), and EB (colour). B) Actual male reproductive system. Te - testes, SV - seminal vesicle, AG - accessory gland, Sph - singular sphincter, ED - ejaculatory duct, EB - ejaculatory bulb. Scale bar: 200 µm.

      This suggestion has been incorporated.

      (13) Figure 3S2 

      Comment:

      There appears to be a typographical error in the description of the genotypes, which may lead to confusion. 

      Suggestion:

      Correct the legend to reflect the appropriate genotypes:

      Figure 3S2. Expression of vGlut-LexA and Tdc2-GAL4 in the Drosophila male reproductive system. A, D, G, J, M, P) vGlut-LexA, LexAop-6XmCherry; B, E, H, K, N, Q) Tdc2-GAL4, UAS-6XGFP; C, F, I, L, O, R) Overlay. Scale bars: O - 50 µm; R - 10 µm.

      The corrections have been made.

      (14) Figure 3S3

      Comment:

      The genotypes for panels D and E appear to be incomplete; the DBD component of the split-GAL4 drivers is missing. 

      Suggestion:

      Update the figure legend to: 

      Figure 3S3. Fruitless and Doublesex expression in the Drosophila male reproductive system. A) fru-GAL4, UAS-6XGFP; B) vGlut-LexA, LexAop-6XmCherry; C) Overlay; D) Tdc2-AD ∩ dsx-GAL4-DBD; E) TRH-AD ∩ dsx-GAL4-DBD. Scale bar: 200 µm.

      The corrections have been made.

      (15) Figure 4S4 

      Comment: 

      There is a repeated segment in the figure legend, which makes it unclear and redundant. 

      Suggestion:

      Edit the legend to remove the duplicated lines: 

      Figure 4S4. Expression of vGlut, TβH-GFP, and 5-HT at the junction of the SV and AGs with the ED of the Drosophila male reproductive system. A) vGlut-40XV5; B) TβH-GFP; C) 5-HT; D) vGlut-40XV5, TβH-GFP overlay; E) vGlut-40XV5, 5-HT overlay; F) TβH-GFP, 5-HT overlay. Scale bar: 50 µm.

      The correction has been made.

      (16) Figure 6S5 

      Comment:

      Within this figure, the orientation and/or scale of the tissue varies noticeably between individual panels, making it difficult to directly compare the different experimental conditions. 

      Suggestion:

      For improved clarity and interpretability, consider standardizing the orientation and size of the tissue shown across all panels within the figure. Consistent presentation will facilitate direct comparisons between treatments or genotypes. 

      There is often variation in the size of the male reproductive organs. They were all acquired at the same magnification. The only point of this figure is there is no vGAT or vAChT at these NMJs and the result is unambiguously negative. 

      (17) Figure 10 

      Comment:

      Panel A appears redundant, as it shows the same information as the other panels but without indicating statistical significance. 

      Suggestion:

      Consider removing panel A and keeping only the remaining four graphs, which include relevant statistical comparisons and clearly show significant differences.

      We realize there is some redundancy of panel A with the other panels, but we feel there is value in having all the genotypes in a single panel for comparison.

      Reviewer #3 (Recommendations for the authors): 

      Here are some suggestions to improve the manuscript: 

      (1) Prot B GFP experiment: the authors should explain better the time chosen to look at the sperm content of the male reproductive system. At 10 minutes, it is expected that the male has already ejaculated, and therefore, a failure to ejaculate would result in more sperm in the reproductive system, not less. Since we are not certain when the male ejaculates, it would be important to do the analysis at different time points.

      In the Prot-GFP experiments, the 10-minute time point was chosen because we nearly always observe sperm in the ejaculatory duct of control males.  In the experimental males, we never observed sperm in the ejaculatory duct at this time point.  Also, no Prot-GFP sperm were observed in the reproductive tract of females mated to experimental males even when mating was allowed to go to completion, while abundant sperm were found in females mated to Prot-GFP controls.  Figure 10S1 has been updated to include Images of these female reproductive systems.  The results showing the absence of Prot-GFP sperm in the female reproductive tract mated to experimental males indicates sperm transfer in these males isn't occurring earlier during the copulation process than in control males and that we didn't miss it by only examining at the ejaculatory duct.

      (2) Discuss what may be the role of the octopamine/glutamate neurons and glutamate transmission in serotonin/glutamate neurons in the male reproductive system, given that they are not required for fertility (at least under the context in which it was tested). It is quite a striking result that deserves some attention. 

      We agree it is a surprising result and have included speculation on the role of glutamate and octopamine in male reproduction in the Discussion section "Potential for adaptation to environment".

      (3) Very important: 

      (a) Figure 3 is present in the Word document but not the PDF. 

      (b) Figure 9S3 is not present 

      (c) In Figure 5 X), the legend does not correspond to the panel.

      All of these corrections have been made. 

      (4) Other suggestions:

      (a) A summary schematic (or several) of the findings would make it an easier read.

      (b) Explain why the ejaculatory bulb was left out of the analysis.

      (c) Explain in the main text some of the tools, such as, BONT-C and the conditional vGlut mutation.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review): 

      Summary: 

      In this paper, the authors developed a chemical labeling reagent for P2X7 receptors, called X7-uP. This labeling reagent selectively labels endogenous P2X7 receptors with biotin based on ligand-directed NASA chemistry (Ref. 41). After labeling the endogenous P2X7 receptor with biotin, the receptor can be fluorescently labeled with streptavidin-AlexaFluor647. The authors carefully examined the binding properties and labeling selectivity of X7-uP to P2X7, characterized the labeling site of P2X7 receptors, and demonstrated fluorescence imaging of P2X7 receptors. The data obtained by SDS-PAGE, Western blot, and fluorescence microscopy clearly show that X7-uP labels the P2X7 receptor. Finally, the authors fluorescently labeled the endogenous P2X7 in BV2 cells, which are a murine microglia model, and used dSTORM to reveal a nanoscale P2X7 redistribution mechanism under inflammatory conditions at high resolution. 

      Strengths: 

      X7-uP selectively labels endogenous P2X7 receptors with biotin. Streptavidin-AlexaFluor647 binds to the biotin labeled to the P2X7 receptor, allowing visualization of endogenous P2X7 receptors. 

      We thank the reviewer for their positive comment.

      Weaknesses: 

      Weaknesses & Comments 

      (1) The P2X7 receptor exists in a trimeric form. If it is not a monomer under the conditions of the pull-down assay in Figure 2C, the quantitative values may not be accurate. 

      We thank the reviewer for this comment. As shown in Figure 2C, the band observed on the denaturing SDS-PAGE corresponds to the monomeric form of the P2X7 receptor. While we cannot exclude the presence of non-monomeric species under native conditions, no such higher-order forms are visible in the gel. This observation supports the conclusion that the quantitative values presented are based on the monomeric form and are therefore reliable.

      (2) In Figure 3, GFP fluorescence was observed in the cell. Are all types of P2X receptors really expressed on the cell surface ? 

      We thank the reviewer for this excellent comment, which was also raised by reviewer 2. To address this concern, we performed a commercial cell-surface protein biotinylation assay to assess whether GFP-tagged P2X receptors reach the plasma membrane. As expected, all P2X subtypes except P2X6 were detected at the cell surface in HEK293T cells, thereby validating our confocal fluorescence microscopy assay. These new data are now included in Figure 3 — figure supplement 1.

      (3) The reviewer was not convinced of the advantages of the approach taken in this paper, because the endogenous receptor labeling in this study could also be done using conventional antibody-based labeling methods. 

      We thank the reviewer for raising this important point and would like to highlight several advantages of our approach compared to conventional antibody-based labeling.

      First, commercially available P2X7 antibodies often suffer from poor specificity and are generally not suitable for reliably detecting endogenous P2X7 receptors, as documented in previous studies (e.g., PMID: 16564580 and PMID: 15254086). While recent advances have been made using nanobodies with improved specificity for P2X7 (e.g., PMID: 30074479 and PMID: 38953020), our strategy is distinct and complementary to nanobody-based approaches.

      Second, antibodies rely on non-covalent interactions with the receptor, which can result in dissociation over time. In contrast, our X7-uP probe covalently biotinylates lysine residues on the P2X7 receptor through stable amide bond formation. This covalent labeling ensures that the biotin moiety remains permanently attached, an advantage not afforded by reversible binding strategies.

      Third, by selectively biotinylating P2X7 receptors, our method provides a versatile platform for the chemical attachment of a wide range of probes or functional moieties. Although we did not demonstrate this application in the current study, we believe this modularity represents an additional advantage of our approach.

      We have now revised the discussion to highlight these key advantages, allowing the reader to form their own opinion. We hope this addresses the reviewer’s concerns and clarifies the benefits of our approach.

      (4) Although P2X7 was successfully labeled in this paper, it is not new as a chemistry. There is a need for more attractive functional evaluation such as live trafficking analysis of endogenous P2X7. 

      We agree with the reviewer that the underlying chemistry is not novel per se. However, to our knowledge, it has not previously been applied to the P2X7 receptor, and thus constitutes a novel application with specific relevance for studying native P2X7 biology.

      We also appreciate the reviewer’s suggestion regarding live trafficking analysis of endogenous P2X7. While this is indeed a valuable and interesting direction, we believe it lies beyond the scope of the present study, as it would first require demonstrating that the labeling itself does not affect P2X7 function (see below). This important step would necessitate additional experiments, which we consider more appropriate for a follow-up investigation.

      (5) The reviewer has concerns that the use of the large-size streptavidin to label the P2X7 receptor may perturbate the dynamics of the receptor. 

      We thank the reviewer for raising this important point. Although we did not directly measure receptor dynamics, it is indeed possible that tetrameric streptavidin (tStrept-A 647) could promote P2X7 clustering by cross-linking nearby receptors due to its tetravalency (see also point 7 raised by the reviewer). To address this concern, we performed additional dSTORM experiments using a monomeric form of streptavidin-Alexa 647 (mSA) (see PMID: 26979420). Owing to its reduced size and lack of tetravalency, mSA has been shown to minimize artificial crosslinking of synaptic receptors (PMID: 26979420). A drawback of using mSA, however, is that the monomeric form carries only two fluorophores (estimated degree of labeling, DOL ≈ 2, PMID: 26979420), whereas the tetrameric form, according to the manufacturer’s certificate of analysis (Invitrogen S21374), has an average DOL of three fluorophores per monomer, resulting in a total of ~12 fluorophores per streptavidin.

      We tested three conditions with mSA incubation: (i) control BV2 cells (without X7-uP), (ii) untreated X7-uP-labeled BV2 cells, and (iii) X7-uP-labeled BV2 cells treated with LPS and ATP (using the same concentrations and incubation times described in the manuscript). As shown in Author response image 1, only LPS+ATP treatment induced a clear increase in the mean cluster density compared to quiescent (untreated) BV2 cells. This effect closely matches the results obtained with tStrept-A 647, supporting the conclusion the tetrameric streptavidin does not artificially promote P2X7 clustering. It is also possible that the cellular environment of BV2 microglia differs from the confined architecture of synapses, which may further explain why cross-linking effects are less pronounced in our system.

      As expected, the overall fluorescence signal with mSA was about tenfold lower than with tStrept-A 647, consistent with the expected fluorophore stoichiometry. This lower signal may explain why the values for the untreated condition appeared slightly higher than for the control, although the difference was not statistically significant (P = 0.1455).

      We hope these additional experiments adequately address the reviewer’s concerns.

      Author response image 1.

      BV2 labeling with monomeric streptavidin–Alexa 647 (mSA).(A) Bright-field and dSTORM images of BV2 cells labeled with mSA in the presence (untreated and LPS+ATP) or absence (control) of 1 µM X7-uP. Treatment: LPS (1 µg/mL for 24 hours) and ATP (1 mM for 30 minutes). Scale bars, 10 µm. Insets: Magnified dSTORM images. Scale bars, 1 µm.(B) Quantification of the number of localizations (n = 2 independent experiments). Bars represent mean ± s.e.m. One-way ANOVA with Tukey’s multiple comparisons (P values are indicated above the graph).

      (6) It is better to directly label Alexa647 to the P2X7 receptor to avoid functional perturbation of P2X7. 

      Directly labeling of Alexa647 to the P2X7 receptor would require the design and synthesis of a novel probe, which is currently not available. Implementing such a strategy would involve substantial new experimental work that lies beyond the scope of the present study.

      (7) In all imaging experiments, the addition of streptavidin, which acts as a cross-linking agent, may induce P2X7 receptor clustering. This concern would be dispelled if the receptors were labeled with a fluorescent dye instead of biotin and observed. 

      We refer the reviewer to our response in point 5, where we addressed this concern by comparing tetrameric and monomeric streptavidin conjugates. As noted above (see also point 6), directly labeling the receptor with a fluorescent dye would require the development of a new probe, which is outside the scope of the present study.

      (8) There are several mentions of microglia in this paper, even though they are not used. This can lead to misunderstanding for the reader. The author conducted functional analysis of the P2X7 receptor in BV-2 cells, which are a model cell line but not microglia themselves. The text should be reviewed again and corrected to remove the misleading parts that could lead to misunderstanding. e.g. P8. lines 361-364

      First, it combines N-cyanomethyl NASA chemistry with the high-affinity AZ10606120 ligand, enabling rapid labeling in microglia (within 10 min)

      P8. lines 372-373 

      Our results not only confirm P2X7 expression in microglia, as previously reported (6, 26-33), but also reveal its nanoscale localization at the cell surface using dSTORM. 

      We agree with the reviewer’s comment. We have now modified the text, including the title.

      Reviewer #2 (Public review): 

      Summary: 

      In this manuscript, Arnould et. al. develop an unbiased, affinity-guided reagent to label P2X7 receptor and use super-resolution imaging to monitor P2X7 redistribution in response to inflammatory signaling. 

      Strengths: 

      I think the X7-uP probe that they developed is very useful for visualizing localization of P2X7 receptor. They convincingly show that under inflammatory conditions, there is a reorganization of P2X7 localization into receptor clusters. Moreover, I think they have shown a very clever way to specifically label any receptor of interest. This has broad appeal 

      We thank the reviewer for their positive comment.

      Weaknesses: 

      Overall, the manuscript is novel and interesting. However, I do have some suggestions for improvement. 

      (1) While the authors state that chemical modification of AZ10606120 to produce the X7-UP reagent has "minimal impact" on the inhibition of P2X7, we can see from Figure 2A and 2B that it does not antagonize P2X7 as effectively as the original antagonist. For the sake of completeness and quantitation, I think it would be great if the authors could determine the IC50 for X7-uP and compare it to the IC50 of AZ10606120. 

      We thank the reviewer for this insightful comment. Unfortunately, due to the limited availability of X7-uP, we were not able to establish a complete concentration–response curve to determine its IC<sub>50</sub>, which would require testing at concentrations >1 µM. Nevertheless, to estimate the effect of the modification, we assessed current inhibition at 300 µM X7-uP and compared it with the reported IC<sub>50</sub> of AZ10606120 (10 nM). Under these conditions, both compounds produced a similar level of inhibition, indicating that while the chemical modification reduces potency relative to AZ10606120, X7-uP still functions as an effective probe for P2X7. We have now included these data in Figure 2 and revised the text accordingly.

      (2) Do the authors know whether modification of the lysines with biotin affects the receptor's affinity for ATP (or ability to be activated by ATP)? What about P2X7 that has been modified with biotin and then labeled with Alexa 647? For the sake of completeness and quantitation, I think it would be great if the authors could determine the EC50 of biotinylated P2X7 for ATP as well as biotinylated and then Alexa 647 labeled P2X7 for ATP and compare these values to the affinity of unmodified WT P2X7 for ATP.

      We thank the reviewer for raising this important point. At present, we have not determined whether modification of lysine residues with biotin, or subsequent labeling with Alexa647, affects the ATP sensitivity or functional properties of P2X7. However, we believe this does not impact the conclusions of the current study, as all functional assays were conducted prior to X7-uP labeling. The labeling is used here as a terminal "snapshot" to visualize the endogenous receptor without interfering with the functional characterization.

      We fully agree that assessing the functional integrity of P2X7 following biotinylation and fluorophore labeling—such as by determining the EC<sub>50</sub> for ATP—would be essential for studies involving dynamic or post-labeling functional analyses, such as live trafficking. However, as noted earlier in our response to Reviewer 1 (point 4), these experiments lie beyond the scope of the current study.

      (3) It is a little misleading to color the fluorescence signal from mScarlet green (for example, in Figure 3 and Figure 4). The fluorescence is not at the same wavelength as GFP. In fact, the wavelength (570 nm - 610 nm) for emission is closer to orange/red than to green. I think this color should be changed to differentiate the signal of mScarlet from the GFP signal used for each of the other P2X receptor subtypes. 

      As suggested, we changed the mScarlet color to orange for all relevant figures.

      (4) It is my understanding that P2X6 does not form homotrimers. Thus, I was a little surprised to see that the density and distribution of P2X6-GFP in Figure 3 looks very similar to the density and distribution of the other P2X subtypes. Do the authors have an explanation for this? Are they looking at P2X6 protomers inserted into the plasma membrane? Does the cell line have endogenous P2X receptor subtypes? Is Figure 3 showing heterotrimers with P2X6 receptor? A little explanation might be helpful.

      We thank the reviewer for raising this important point. Indeed, it is well established that P2X6 does not form functional channels, which supports the conclusion that it does not form homotrimeric complexes. Although previous studies have shown that P2X6–GFP expression is generally lower, more diffuse, and not efficiently targeted to the cell surface compared with other P2X subtypes (see PMID: 12077178), the similar fluorescence distribution and density observed in our Figure 3 do not imply that P2X6 forms homotrimers.

      We did not directly assess the presence of endogenous P2X6 in our HEK293T cells; however, according to the Human Protein Atlas, there is no detectable P2X6 RNA expression in HEK293 cells (nTPM = 0), indicating that endogenous P2X6 is not expressed in this cell line. To further investigate surface expression (see also point 2 of reviewer 1), we performed a commercial cell-surface protein biotinylation assay to assess whether GFP-tagged P2X6 reaches the plasma membrane. As expected, P2X6 was not detected at the cell surface in HEK293T cells, whereas GFP-tagged P2X1 to P2X5 were readily detected. These results further support the conclusion that P2X6 does not insert into the plasma membrane as a homotrimer, thereby validating our confocal fluorescence microscopy assay. These new data are now included in Figure 3 — figure supplement 1.

      (5) It is easy to overlook the fact that the antagonist leaves the binding pocket once the biotin has been attached to the lysines. It might be helpful if the authors made this a little more apparent in Figure 1 or in the text describing the NASA chemistry reaction.

      We thank the reviewer for this insightful suggestion. To address this, we have modified Figure 1A and updated the legend.

      Reviewer #3 (Public review): 

      Summary: 

      This manuscript describes the development of a covalent labeling probe (X7-uP) that selectively targets and tags native P2X7 receptors at the plasma membrane of BV2 microglial cells. Using super-resolution imaging (dSTORM), the authors demonstrate that P2X7 receptors form nanoscale clusters upon microglial activation by lipopolysaccharide (LPS) and ATP, correlating with synergistic IL-1β release. These findings advance understanding of P2X7 reorganization during inflammation and provide a generalizable labeling strategy for monitoring endogenous P2X7 in immune cells. 

      Strengths: 

      (1) The authors designed X7-uP by coupling a high-affinity, P2X7-specific antagonist (AZ10606120) with N-cyanomethyl NASA chemistry to achieve site-directed biotinylation. This approach offers high specificity, minimal off-target reactivity, and a straightforward pull-down/imaging readout. 

      (2) The results connect P2X7's nanoscale clustering directly with IL-1β secretion in microglia, reinforcing the role of P2X7 in inflammation. By localizing endogenous P2X7 at single-molecule resolution, the authors reveal how LPS priming and ATP stimulation synergistically reorganize the receptor. 

      (3) The authors systematically validate their method in recombinant systems (HEK293 cells) and in BV2 cells, showing selective inhibition, mutational confirmation of the binding site, and Western blot pulldown experiments.

      We thank the reviewer for their positive comment.

      Weaknesses: 

      (1) While the data strongly indicate that P2X7 clustering contributes to IL-1β release, the manuscript would benefit from additional experiments (if feasible) or discussion on how receptor clustering interfaces with downstream inflammasome assembly. Clarification of whether the P2X7 clusters physically colocalize with known inflammasome proteins would solidify the mechanism. 

      We thank the reviewer for this valuable suggestion. Determining the physical colocalization of P2X7 clusters with known inflammasome components would provide important insight into the molecular partners involved in inflammasome activation. However, we believe that such an investigation would constitute a substantial study on its own and therefore lies beyond the scope of the present work.

      Nevertheless, in response to the reviewer’s suggestion, we have added a short paragraph at the end of the Discussion section addressing potential mechanisms by which P2X7 clustering may contribute to downstream inflammasome activation. We also revised the text to tone down the hypothesis of physical colocalization.

      (2) The authors might expand on the scope of X7-uP in other native cells that endogenously express P2X7 (e.g., macrophages, dendritic cells). Although they mention the possibility, demonstrating the probe's applicability in at least one other primary immune cell type would strengthen its general utility. 

      We thank the reviewer for this valuable suggestion. Again, we believe that such an investigation would constitute a substantial study on its own and therefore lies beyond the scope of the present work.

      (3) The authors do include appropriate negative controls, yet providing additional details (e.g., average single-molecule on-time or blinking characteristics) in supplementary materials could help readers assess cluster calculations. 

      As suggested, we have included additional data showing single-molecule blinking events in untreated and LPS+ATP-treated BV2 cells, along with the corresponding movies. The data are now presented in Figure 5—supplement figure 3A and B and Figure 5—Videos 1 and 2.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors): 

      (1) On line 96, the authors refer to the "ballast" domain of P2X7 receptor but do not cite the original article from which this nomenclature originated (McCarthy et al., 2019, Cell). This article should be cited to give appropriate credit. 

      Done.

      (2) On line 602, the authors state that they use models from PDB 1MK5 and 6U9W to generate the cartoons in Figure 6. The manuscripts from which these PDB files were generated need to be appropriately cited. 

      Done.

      (3) On line 319, the authors say "300 mM BzATP" but I think they mean 300 uM.

      Done. Thank you for catching the typo.

      Reviewer #3 (Recommendations for the authors): 

      Overall, excellent data quality. The paper would benefit from a discussion of the physiological implications of clustering. It would also be helpful to elaborate about the potential mechanisms for clustering: diffusion and/or insertion. Finally, the authors should comment on work by Mackinnon's (PMID: 39739811) and Santana lab (PMID: 31371391) on two distinct models for clustering of proteins. 

      As suggested by the reviewer, we have revised the discussion to incorporate their comments. First, we have added the following text:

      “Upon BV2 activation, we observed significant nanoscale reorganization of P2X7. Both LPS and ATP (or BzATP) trigger P2X7 upregulation and clustering, increasing the overall number of surface receptors and the number of receptors per cluster, from one to three (Figure 6). By labeling BV2 cells with X7-uP shortly after IL-1b release, we were able to correlate the nanoscale distribution of P2X7 with the functional state of BV2 cells, consistent with the two-signal, synergistic model for IL-1b secretion observed in microglia and other cell types (Ferrari et al, 1996; Perregaux et al, 2000; Ferrari et al, 2006; Di Virgilio et al, 2017; He et al, 2017; Swanson et al, 2019). In this model, LPS priming leads to intracellular accumulation of pro-IL-1b, while ATP stimulation activates P2X7, triggering NLRP3 inflammasome activation and the subsequent release of mature IL-1b.

      What is the mechanism underlying P2X7 upregulation that leads to an overall increase in surface receptors—does it result from the lateral diffusion of previously masked receptors already present at the plasma membrane, or from the insertion of newly synthesized receptors from intracellular pools in response to LPS and ATP? Although our current data do not distinguish between these possibilities, a recent study suggests that the a1 subunit of the Na<sup>+</sup>/K</sup>+</sup>-ATPase (NKAa1) forms a complex with P2X7 in microglia, including BV2 cells, and that LPS+ATP induces NKAa1 internalization (Huang et al, 2024). This internalization appears to release P2X7 from NKAa1, allowing P2X7 to exist in its free form. We speculate that the internalization of NKAa1 induced by both LPS and ATP exposes previously masked P2X7 sites, including the allosteric AZ10606120 sites, thus making them accessible for X7-uP labeling.”

      Second, we have added a short paragraph at the end of the Discussion section addressing potential mechanisms by which P2X7 clustering may contribute to downstream inflammasome activation:

      “What mechanisms underlie P2X7 clustering in response to inflammatory signals? Several models have been proposed to explain membrane protein clustering, including recruitment to structural scaffolds (Feng & Zhang, 2009), partitioning into membrane domains enriched in specific chemical components such as lipid rafts (Simons & Ikonen, 1997), and self-assembly mechanisms (Sieber et al, 2007). These self-assembly mechanisms include an irreversible stochastic model (Sato et al, 2019) and a more recent reversible self-oligomerization model which gives rise to higher-order transient structures (HOTS) (Zhang et al, 2025). Supported by cryogenic optical localization microscopy with very high resolution (~5 nm), the HOTS model has been observed in various membrane proteins, including ion channels and receptors (Zhang et al, 2025). Furthermore, HOTS are suggested to be dynamically modulated and to play a functional role in cell signaling, potentially influencing both physiological and pathological processes (Zhang & MacKinnon, 2025). While this hypothesis is compelling, our current dSTORM data lack sufficient spatial resolution to confirm whether P2X7 trimers form HOTS via self-oligomerization. Further biophysical and ultra-high-resolution imaging studies are required to test this model in the context of P2X7 clustering.”

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #1 (Public review):

      Summary:

      This manuscript by Pournejati et al investigates how BK (big potassium) channels and CaV1.3 (a subtype of voltage-gated calcium channels) become functionally coupled by exploring whether their ensembles form early-during synthesis and intracellular trafficking-rather than only after insertion into the plasma membrane. To this end, the authors use the PLA technique to assess the formation of ion channel associations in the different compartments (ER, Golgi or PM), single-molecule RNA in situ hybridization (RNAscope), and super-resolution microscopy.

      Strengths:

      The manuscript is well written and addresses an interesting question, combining a range of imaging techniques. The findings are generally well-presented and offer important insights into the spatial organization of ion channel complexes, both in heterologous and endogenous systems.

      Weaknesses:

      The authors have improved their manuscript after revisions, and some previous concerns have been addressed.

      Still, the main concern about this work is that the current experiments do not quantitatively or mechanistically link the ensembles observed intracellularly (in the endoplasmic reticulum (ER) or Golgi) to those found at the plasma membrane (PM). As a result, it is difficult to fully integrate the findings into a coherent model of trafficking. Specifically, the manuscript does not address what proportion of ensembles detected at the PM originated in the ER. Without data on the turnover or halflife of these ensembles at the PM, it remains unclear how many persist through trafficking versus forming de novo at the membrane. The authors report the percentage of PLApositive ensembles localized to various compartments, but this only reflects the distribution of pre-formed ensembles. What remains unknown is the proportion of total BK and Ca<sub>V</sub>1.3 channels (not just those in ensembles) that are engaged in these complexes within each compartment. Without this, it is difficult to determine whether ensembles form in the ER and are then trafficked to the PM, or if independent ensemble formation also occurs at the membrane. To support the model of intracellular assembly followed by coordinated trafficking, it would be important to quantify the fraction of the total channel population that exists as ensembles in each compartment. A comparable ensemble-to-total ratio across ER and PM would strengthen the argument for directed trafficking of pre-assembled channel complexes.

      We appreciate the reviewer’s thoughtful comment and agree that quantitatively linking intracellular hetero-clusters to those at the plasma membrane is an important and unresolved question. Our current study does not determine what proportion of ensembles at the plasma membrane originated during trafficking. It also does not quantify the fraction of total BK and Ca<sub>V</sub>1.3 channels engaged in these complexes within each compartment. Addressing this requires simultaneous measurement of multiple parameters—total BK channels, total Ca<sub>V</sub>1.3 channels, hetero-cluster formation (via PLA), and compartment identity—in the same cell. This is technically challenging. The antibodies used for channel detection are also required for the proximity ligation assay, which makes these measurements incompatible within a single experiment.

      To overcome these limitations, we are developing new genetically encoded tools to enable real-time tracking of BK and Ca<sub>V</sub>1.3 dynamics in live cells. These approaches will enable us to monitor channel trafficking and the formation of hetero-clusters, as detected by colocalization. This kind of experiments will provide insight into their origin and turnover. While these experiments are beyond the scope of the current study, the findings in our current manuscript provide the first direct evidence that BK and CaV channels can form hetero-clusters intracellularly prior to reaching the plasma membrane. This mechanistic insight reveals a previously unrecognized step in channel organization and lays the foundation for future work aimed at quantifying ensemble-to-total ratios and determining whether coordinated trafficking of pre-assembled complexes occurs.

      This limitation is acknowledged in the discussion section, page 23. It reads: “Our findings highlight the intracellular assembly of BK-Ca<sub>V</sub>1.3 hetero-clusters, though limitations in resolution and organelle-specific analysis prevent precise quantification of the proportion of intracellular complexes that ultimately persist on the cell surface.”

      Reviewer #2 (Public review):

      Summary:

      The co-localization of large conductance calcium- and voltage activated potassium (BK) channels with voltage-gated calcium channels (CaV) at the plasma membrane is important for the functional role of these channels in controlling cell excitability and physiology in a variety of systems.

      An important question in the field is where and how do BK and CaV channels assemble as 'ensembles' to allow this coordinated regulation - is this through preassembly early in the biosynthetic pathway, during trafficking to the cell surface or once channels are integrated into the plasma membrane. These questions also have broader implications for assembly of other ion channel complexes

      Using an imaging based approach, this paper addresses the spatial distribution of BKCaV ensembles using both overexpression strategies in tsa201 and INS-1 cells and analysis of endogenous channels in INS-1 cells using proximity ligation and superesolution approaches. In addition, the authors analyse the spatial distribution of mRNAs encoding BK and Cav1.3.

      The key conclusion of the paper that BK and Ca<sub>V</sub>1.3 are co-localised as ensembles intracellularly in the ER and Golgi is well supported by the evidence.However, whether they are preferentially co-translated at the ER, requires further work. Moreover, whether intracellular pre-assembly of BK-Ca<sub>V</sub>1.3 complexes is the major mechanism for functional complexes at the plasma membrane in these models requires more definitive evidence including both refinement of analysis of current data as well as potentially additional experiments.

      The reviewer raises the question of whether BK and Ca<sub>V</sub>1.3 channels are preferentially co-translated. In fact, I would like to propose that co-translation has not yet been clearly defined for this type of interaction between ion channels. In our current work, we 1) observed the colocalization between BK and Ca<sub>V</sub>1.3 mRNAs and 2) determined that 70% of BK mRNA in active translation also colocalizes with Ca<sub>V</sub>1.3 mRNA. We think these results favor the idea of translational complexes that can underlie the process of co-translation. However, and in total agreement with the Reviewer, the conclusion that the mRNA for the two ion channels is cotranslated would require further experimentation. For instance, mRNA coregulation is one aspect that could help to define co-translation. 

      To avoid overinterpretation, we have revised the manuscript to remove references to “co-translation” in the Results section and included the word “potential” when referring to co-translation in the Discussion section. We also clarified the limitations of our evidence in the Discussion that can be found on page 25: “It is important to note that while our data suggest mRNA coordination, additional experiments are required to directly assess co-translation.”

      Strengths & Weaknesses

      (1) Using proximity ligation assays of overexpressed BK and CaV1.3 in tsa201 and INS1 cells the authors provide strong evidence that BK and CaV can exist as ensembles (ie channels within 40 nm) at both the plasma membrane and intracellular membranes, including ER and Golgi. They also provide evidence for endogenous ensemble assembly at the Golgi in INS-1 cells and it would have been useful to determine if endogenous complexes are also observe in the ER of INS-1 cells. There are some useful controls but the specificity of ensemble formation would be better determined using other transmembrane proteins rather than peripheral proteins (eg Golgi 58K).

      We thank the reviewer for their thoughtful feedback and for recognizing the strength of our proximity ligation assay data supporting BK–Ca<sub>V</sub>1.3 hetero-clusters formation at both the plasma membrane and intracellular compartments. As for specificity controls, we appreciate the suggestion to use transmembrane markers. To strengthen our conclusion, we have performed an additional experiment comparing the number of PLA puncta formed by the interaction of Ca<sub>V</sub>1.3 and BK channels with the number of PLA puncta formed by the interaction of Ca<sub>V</sub>1.3 channels and ryanodine receptors in INS-1 cells. As shown in the figure below, the number of interactions between Ca<sub>V</sub>1.3 and BK channels is significantly higher than that between Ca<sub>V</sub>1.3 and RyR<sub>2</sub>. Of note, RyR<sub>2</sub> is a protein resident of the ER. These results provide additional evidence of the existence of endogenous complex formation in INS-1 cells. We have added this figure as a supplement.

      (2) Ensemble assembly was also analysed using super-resolution (dSTORM) imaging in INS-1 cells. In these cells only 7.5% of BK and CaV particles (endogenous?) co-localise that was only marginally above chance based on scrambled images. More detailed quantification and validation of potential 'ensembles' needs to be made for example by exploring nearest neighbour characteristics (but see point 4 below) to define proportion of ensembles versus clusters of BK or Cav1.3 channels alone etc. For example, it is mentioned that a distribution of distances between BK and Cav is seen but data are not shown.

      We thank the reviewer for this comment. To address the request for more detailed quantification and validation of ensembles, we performed additional analyses:

      Proportion of ensembles vs isolated clusters: We quantified clusters within 200 nm and found that 37 ± 3% of BK clusters are near one or more CaV1.3 clusters, whereas 15 ± 2% of CaV1.3 clusters are near BK clusters. Figure 8– Supplementary 1A

      Distance distribution: As shown in Figure 8–Supplementary 1B, the nearestneighbor distance distribution for BK-to-CaV1.3 in INS-1 cells (magenta) is shifted toward shorter distances compared to randomized controls (gray), supporting preferential localization of BK–CaV1.3 hetero-clusters.

      Together, these analyses confirm that BK–CaV1.3 ensembles occur more frequently than expected by chance and exhibit an asymmetric organization favoring BK proximity to CaV1.3 in INS-1 cells. We have included these data and figures in the revised manuscript, as well as description in the Results section. 

      (3) The evidence that the intracellular ensemble formation is in large part driven by cotranslation, based on co-localisation of mRNAs using RNAscope, requires additional critical controls and analysis. The authors now include data of co-localised BK protein that is suggestive but does not show co-translation. Secondly, while they have improved the description of some controls mRNA co-localisation needs to be measured in both directions (eg BK - SCN9A as well as SCN9A to BK) especially if the mRNAs are expressed at very different levels. The relative expression levels need to be clearly defined in the paper. Authors also use a randomized image of BK mRNA to show specificity of co-localisation with Cav1.3 mRNA, however the mRNA distribution would not be expected to be random across the cell but constrained by ER morphology if cotranslated so using ER labelling as a mask would be useful?

      We thank the reviewer for these constructive suggestions. We measured mRNA colocalization in both directions as recommended. As shown in the figure below, colocalization between KCNMA1 and SCN9A transcripts was comparable in both directions, with no statistically significant difference, supporting the specificity of the observed associations. We decided not to add this to the original figure to keep the figure simple. 

      We agree that co-localization of BK protein with BK mRNA is not conclusive evidence of co-translation, and we do not intend to mislead readers in our conclusion. Consequently, we were careful in avoiding the use of co-translation in the result section and added the word “potential” when referring to co-translation in the Discussion section. We added a sentence in the discussion to caution our interpretation: “It is important to note that while our data suggest mRNA coordination, additional experiments are required to directly assess cotranslation.”

      Author response image 1.

      (4) The authors attempt to define if plasma membrane assemblies of BK and CaV occur soon after synthesis. However, because the expression of BK and CaV occur at different times after transient transfection of plasmids more definitive experiments are required. For example, using inducible constructs to allow precise and synchronised timing of transcription. This would also provide critical evidence that co-assembly occurs very early in synthesis pathways - ie detecting complexes at ER before any complexes 

      We appreciate the reviewer’s insightful suggestion regarding the use of inducible constructs to synchronize transcription timing. This is an excellent approach and would allow direct testing of whether co-assembly occurs early in the synthesis pathway, including detection of complexes at the ER prior to plasma membrane localization. These experiments are beyond the scope of the present work but represent an important direction for future studies.

      We have added the following sentence to the Discussion section (page 24) to highlight this idea. “Future experiments using inducible constructs to precisely control transcription timing will enable more precise quantification of heterocluster formation in the ER compartment prior to plasma membrane insertion and reduce the variability introduced by differences in expression timing after plasmid transfection.” 

      (5) While the authors have improved the definition of hetero-clusters etc it is still not clear in superesolution analysis, how they separate a BK tetramer from a cluster of BK tetramers with the monoclonal antibody employed ie each BK channel will have 4 binding sites (4 subunits in tetramer) whereas Cav1.3 has one binding site per channel. Thus, how do authors discriminate between a single BK tetramer (molecular cluster) with potential 4 antibodies bound compared to a cluster of 4 independent BK channels.

      We appreciate the reviewer’s thoughtful comment regarding the interpretation of super-resolution data. We agree that distinguishing a single BK tetramer from a cluster of multiple BK channels is challenging when using an antibody that can bind up to four sites per channel. To clarify, our analysis does not attempt to resolve individual subunits within a tetramer; rather, it focuses on the nanoscale spatial proximity of BK and Ca<sub>V</sub>1.3 signals.

      We want to note that this limitation applies only to the super-resolution maps in Figures 8C and 9D and does not affect Airyscan-based analyses or measurements of BK–Ca<sub>V</sub>1.3 proximity.

      To address how we might distinguish between a single BK tetramer and a cluster of multiple BK channels, we considered two contrasting scenarios. In the first case, we assume that all four α-subunits within a tetramer are labeled. Based on cryoEM structures, a BK tetramer measures approximately 13 nm × 13 nm (≈169 nm²). Adding two antibody layers (primary and secondary) would increase the footprint by ~14 nm in each direction, resulting in an estimated area of ~41 nm × 41 nm (≈1681 nm²). Under this assumption, particles smaller than ~1681 nm² would likely represent individual tetramers, whereas larger particles would correspond to clusters of multiple tetramers. 

      In the second scenario, we propose that steric constraints at the S9–S10 segment, where the antibody binds, limit labeling to a single antibody per tetramer. If true, the localization precision would approximate 14 nm × 14 nm—the combined size of the antibody complex and the channel—close to the resolution limit of the microscope. To test this, we performed a control experiment using two antibodies targeting the BK C-terminal domain, raised in different species and labeled with distinct fluorophores. Super-resolution imaging revealed that only ~12% of particles were colocalized, suggesting that most channels bind a single antibody.

      If multiple antibodies could bind each tetramer, we would expect much greater colocalization.

      Although these data are not included in the manuscript, we have added the following clarification to the Results section (page 19): “It is important to note that this technique does not allow us to distinguish between labeling of four BK αsubunits within a tetramer and labeling of multiple BK channel clusters. Hence, particles smaller than ~1680 nm² may represent either a single tetramer or a cluster. This limitation applies to Figures 8C and 9D and does not affect measurements of BK–Ca<sub>V</sub>1.3 proximity.”

      Author response image 2.

      (6) The post-hoc tests used for one way ANOVA and ANOVA statistics need to be defined throughout

      We thank the reviewer for highlighting the need for clarity regarding our statistical analyses. We have now specified the post-hoc tests used for all one-way ANOVA and ANOVA comparisons throughout the manuscript, and updated figure legends.

      Reviewer #3 (Public review):

      Summary:

      The authors present a clearly written and beautifully presented piece of work demonstrating clear evidence to support the idea that BK channels and Cav1.3 channels can co-assemble prior to their assertion in the plasma membrane.

      Strengths:

      The experimental records shown back up their hypotheses and the authors are to be congratulated for the large number of control experiments shown in the ms.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The authors have sufficiently addressed the specific points previously raised and the manuscript has improved clarity in those aspects. My main concern, which still remains, is stated in the public review.

      Reviewer #3 (Recommendations for the authors):

      I am content that the authors have attempted to fully address my previous criticisms.

      I have only three suggestions

      (1) I think the word Homo-clusters at the bottom right of Figure 1 is erroneously included.

      We thank the reviewer for bringing this to our attention. The figure has been corrected accordingly.

      (2) The authors should, for completeness, to refer to the beta, gamma and LINGO subunit families in the Introduction and include appropriate references:

      Knaus, H. G., Folander, K., Garcia-Calvo, M., Garcia, M. L., Kaczorowski, G. J., Smith, M., & Swanson, R. (1994). Primary sequence and immunological characterization of betasubunit of high conductance Ca2+-activated K+ channel from smooth muscle. The Journal of Biological Chemistry, 269(25), 17274-17278.

      Brenner, R., Jegla, T. J., Wickenden, A., Liu, Y., & Aldrich, R. W. (2000a). Cloning and functional characterization of novel large conductance calcium-activated potassium channel beta subunits, hKCNMB3 and hKCNMB4. The Journal of Biological Chemistry, 275(9), 6453-6461.

      Yan, J & R.W. Aldrich. (2010) LRRC26 auxiliary protein allows BK channel activation at resting voltage without calcium. Nature. 466(7305):513-516

      Yan, J & R.W. Aldrich. (2012) BK potassium channel modulation by leucine-rich repeatcontaining proteins. Proceedings of the National Academy of Sciences 109(20):7917-22

      Dudem, S, Large RJ, Kulkarni S, McClafferty H, Tikhonova IG, Sergeant, GP, Thornbury, KD, Shipston, MJ, Perrino BA & Hollywood MA (2020). LINGO1 is a novel regulatory subunit of large conductance, Ca2+-activated potassium channels. Proceedings of the National Academy of Sciences 117 (4) 2194-2200

      Dudem, S., Boon, P. X., Mullins, N., McClafferty, H., Shipston, M. J., Wilkinson, R. D. A., Lobb, I., Sergeant, G. P., Thornbury, K. D., Tikhonova, I. G., & Hollywood, M. A. (2023). Oxidation modulates LINGO2-induced inactivation of large conductance, Ca2+-activated potassium channels. The Journal of Biological Chemistry, 299 (3) 102975.

      We agree with the reviewer’s suggestion and have revised the Introduction to include references to the beta, gamma, and LINGO subunit families. Appropriate citations have been added to ensure completeness and contextual relevance.

      Additionally, BK channels are modulated by auxiliary subunits, which fine-tune BK channel gating properties to adapt to different physiological conditions. The β, γ, and LINGO1 subunits each contribute distinct structural and regulatory features: β-subunits modulate Ca²⁺ sensitivity and can induce inactivation; γ-subunits shift voltage-dependent activation to more negative potentials; and LINGO1 reduces surface expression and promotes rapid inactivation (18-24). These interactions ensure precise control over channel activity, allowing BK channels to integrate voltage and calcium signals dynamically in various cell types.

      (3) I think it may be more appropriate to include the sentence "The probes against the mRNAs of interest and tested in this work were designed by Advanced Cell Diagnostics." (P16, right hand column, L12-14) in the appropriate section of the Methods, rather than in Results.

      We thank the reviewer for this helpful suggestion. In response, we have relocated the sentence to the appropriate section of the Methods, where it now appears with relevant context.

    1. Author response:

      Before providing a brief provisional response to the two reviews, it is important to reiterate a few key points about our work. First, our paper is largely a computational biophysics paper, augmented by experimental results. Generally speaking, computational biophysics work intends to achieve one of two things (or both). One is to provide more molecular level insight into various behaviors of biomolecular systems that have not been (or cannot be) provided by qualitative experimental results alone. The second general goal of computational biophysics it to formulate new hypotheses to be tested subsequently by experiment. In our paper, we have achieved both of these goals and then confirmed the key computational results by experiment..

      The first reviewer has some valuable points, which can be addressed as follows (and will be emphasized in the revised version of the paper): (1) Yes the simulations of capsid rupture in the NPC and capsid-only are directly comparable as both have approximately the same number of bound LEN, as determined by following the LEN-capsid interaction protocol described in the main text (around Fig 6) and in the SI section S3; (2) While we have stressed this point in several places in the manuscript, here again we stress that coarse-grained (CG) MD time is not the same as real time. The point of CG simulations is to accelerate the timescale of the MD and the associated sampling, so the CG “time” from the MD integrator needs to be rescaled to associate a real time to it. As such, our CG simulation is not representing a microsecond of real time but rather something much longer. We will emphasize this again in the revised text. (3) Actually, we think that the parameterization of the LEN model and the LEN-capsid interactions is well described in the text associated with Fig 6 and in SI section S3. It is true that this one part of the CG model was parameterized “top-down” given the good experimental structures of bound LEN to capsid and other data, but the rest of the CG model is “bottom-up” (meaning developed from well-defined coarse-graining statistical mechanics as applied to molecular level structures and interactions, see also below). 

      As for the second reviewer, this review is quite problematic in our view as the reviewer seems to think that quoting a number of qualitative experimental results is sufficient to undermine the impact of our paper (they are not) and, furthermore, the reviewer appears to have a very minimal understanding of “bottom-up” CG modeling, which we have utilized. This modeling does not in fact rely on the “assumptions” this reviewer alleges we have relied on. (As an aside, it could be helpful for this reviewer to study the review by Jin et al, https://doi.org/10.1021/acs.jctc.2c00643) in order to become more familiar with the field and our approach before criticizing it.) We also note that our main HIV capsid-NPC docking model is already published in PNAS (https://doi.org/10.1073/pnas.2313737121), where it underwent rigorous peer review. In our forthcoming full response to the reviews and in the revised paper we will attempt to address a number of this reviewers comments, but the number, extent, and tone of this collection of criticisms, for us, calls into question the objectivity of this reviewer, not to mention the reviewer’s rather weak understanding of what we have done and how we have done it.

      Finally, while we certainly appreciate the overall positive eLife assessment, we are disappointed by the statement “some mechanistic interpretations rely on assumptions embedded in the simulations, leaving parts of the evidence incomplete”. Of course, all simulations (and experiments) rely on certain assumptions, but we have gone to great length to provide a “bottomup” approach to our modeling, based on underlying molecular level structures and interactions, and we have provided experimental validation of the main simulation predictions. It seems that the comments of the second reviewer may have influenced this point of view, but we do not feel it is justified.

    1. Author response:

      Reviewer #1 (Public review):

      This manuscript provides several important findings that advance our current knowledge about the function of the gustatory cortex (GC). The authors used high-density electrophysiology to record neural activity during a sucrose/NaCl mixture discrimination task. They observed population-based activity capable of representing different mixtures in a linear fashion during the initial stimulus sampling period, as well as representing the behavioral decision (i.e., lick left or right) at a later time point. Analyzing this data at the single neuron level, they observed functional subpopulations capable of encoding the specific mixture (e.g., 45/55), tastant (e.g., sucrose), and behavioral choice (e.g., lick left). To test the functional consequences of these subpopulations, they built a recurrent neural network model in order to "silence" specific functional subpopulations of GC neurons. The virtual ablation of these functional subpopulations altered virtual behavioral performance in a manner predicted by the subpopulation's presumed contribution.

      Strengths:

      Building a recurrent neural network model of the gustatory cortex allows the impact of the temporal sequence of functionally identifiable populations of neurons to be tested in a manner not otherwise possible. Specifically, the author's model links neural activity at the single neuron and population level with perceptual ability. The electrophysiology methods and analyses used to shape the network model are appropriate. Overall, the conclusions of the manuscript are well supported.

      Weaknesses:

      One potential concern is the apparent mismatch between the neural and behavioral data. Neural analyses indicate a clear separation of the activity associated with each mixture that is independent of the animal's ultimate choice. This would seemingly indicate that the animals are making errors despite correctly encoding the stimulus. Based solely on the neural data, one would expect the psychometric curve to be more "step-like" with a significantly steeper slope. One potential explanation for this observation is the concentration of the stimuli utilized in the mixture discrimination task. The authors utilize equivalent concentrations, rather than intensity-matched concentrations. In this case, a single stimulus can (theoretically) dominate the perception of a mixture, resulting in a biased behavioral response despite accurate concentration coding at the single neuron level. Given the difficulty of isointensity matching concentrations, this concern is not paramount. However, the apparent mismatch between the neural and behavioral data should be acknowledged/addressed in the text.

      We thank the Reviewer for the insightful comments and thoughtful suggestions. Our electrophysiological recordings show that GC dynamically encodes stimulus concentration of mixture elements, dominant perceptual quality, and decisions of directional lick. With regard to the encoding of mixtures, the clear separation of activity associated with each mixture (Figure 3) is present at a trial-averaged pseudo-population level, and average activities associated with more similar, intermediate mixtures are closer to each other in this space. In fact, at a single trial level activity evoked by similar, intermediate mixtures can be hard to separate. This increased similarity can lead to behavioral errors resulting from either incorrect encoding of the stimulus or from the inability to interpret the stimuli to guide the correct decision.

      The psychometric function, which shows that more distinct stimuli (100/0 vs 0/100) lead to fewer mistakes than more ambiguous, intermediate mixtures (55/45 vs 55/45), is consistent with the increased ambiguity of responses to intermediate mixtures and with the possibility that, compared to pure stimuli, intermediate mixtures lead to more trials in which the binary choice component of neural activity is inverted, resulting in more directional errors.

      The Reviewer is correct that there could be a slight mismatch in the perceived intensity of the mixture components. This mismatch could be the reason for the slight asymmetry in our psychometric function (Figure 1B). However, it is not uncommon for mice in these 2AC tasks to also have a motor laterality bias in their responses that manifests itself for the more ambiguous stimuli. We chose not to model this bias given its subtlety and its unknown origin. Rather, we chose to model an ideal scenario in which stimuli have matched intensity and no motor bias exists. In the revised version we will discuss this issue.

      Reviewer #2 (Public review):

      Lang et al. investigate the contribution of individual neuronal encoding of specific task features to population dynamics and behavior. Using a taste-based decision-making behavioral task with electrophysiology from the mouse gustatory cortex and computational modeling, the authors reveal that neurons encoding sensory, perceptual, and decision-related information with linear and categorical patterns are essential for driving neural population dynamics and behavioral performance. Their findings suggest that individual linear and categorical coding units have a significant role in cortical dynamics and perceptual decision-making behavior.

      Overall, the experimental and analytical work is of very high quality, and the findings are of great interest to the taste coding field, as well as to the broader systems neuroscience field.

      I have a couple of suggestions to further enhance the authors' important conclusions:

      My main comment is the distinction between constrained and unconstrained units. The authors train a small percentage of units to match the real neural data (constrained units), and then find some unconstrained units that are similar to the real neural data and some that are not. As far as I could tell, the relative fraction of constrained and unconstrained units in the trained RNN is not reported; I assume the constrained ones are a much smaller population, but this is unclear. The selection of different groups of neurons for the RNN ablation experiments appears to be based on their response profiles only. Therefore, if I understood correctly, both constrained and unconstrained units and ablated together for a given response category (e.g., linear or step-perception). It would be useful, therefore, to separately compare the effects of constrained vs. unconstrained RNN units.

      We thank the Reviewer for the constructive feedback and are pleased that the work is considered of broad interest. The Reviewer is correct that ablations were carried out with respect to response categories only and included both constrained and unconstrained units.

      The ratio of total units to constrained units is fixed at 5.88, thus constrained units are ~17% of the network and unconstrained units are ~83%. This value is specified in the Methods (RNN: Components and dynamics), but we will report it in the Results of the revised manuscript as well for clarity.

      Specifically:

      (1) For the analyses in the initial version of the manuscript, the authors should specify how many units in each ablation category are constrained and unconstrained.

      In the revised manuscript, we will specify the fractions of constrained and unconstrained units within each response category. For convenience, they are reported here: Linear = 194 constrained and 691 unconstrained units; Step-perception = 147 constrained and 840 unconstrained units; Step-choice = 129 constrained and 814 unconstrained units; Other = 353 constrained and 1739 unconstrained units.

      (2) The authors should repeat Figure 6, but only for unconstrained units to test how much of the effects in the initial version of Figure 6 are driven by constrained vs. unconstrained RNN units.

      In the revised version we will add a Supplemental Figure in which the contribution of constrained vs unconstrained units is addressed.

      (3) The authors should repeat Figure 7, but performing ablations separately on the constrained and unconstrained units to examine how the network behaves in each case and the resulting "behavioral" effect.

      The revised version will include a Supplemental Figure with these simulations.

      Reviewer #3 (Public review):

      Primary taste cortex neurons show a variety of dynamic response profiles during taste decision-making tasks, reflecting both sensory and decision variables. In the present study, Lang et al. set out to determine how neurons with distinct response profiles contribute to perceptual decisions about taste stimuli.

      The methods,with reference to the behavioral task and electrophysiological recordings/data analysis, are straightforward, solid, and appropriate. The computational model is presented in a clear and conceptually intuitive manner, although the details are outside of my area of expertise.

      The experimental design features a simple 2-alternative forced-choice design that yielded clear psychometric curves across a range of stimuli. In vivo recordings were performed using Neuropixels and yielded an appropriate sample of single neuron responses. The strength of the model lies in the fact that it consists of single neurons whose response profiles mimic those recorded in vivo, and allows neuron-selective manipulation.By virtually lesioning specific subsets of neurons in the network, the authors demonstrate that a relatively small population of neurons with specific tuning profiles was sufficient to produce the observed neural dynamics and behavioral responses. This effect was selective as lesioning other responsive neurons did not affect overall response dynamics or performance.These findings provide new insight into the relation between the response profiles of single neurons in sensory cortex, their population-level activity dynamics, and the perceptual decisions they inform.

      The approach is particularly innovative as it uses computational modeling to target functionally-defined "cell types", which cannot necessarily be targeted by more conventional genetic approaches.

      We thank the Reviewer for the positive assessment of our study.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      In this paper, the authors develop a biologically plausible recurrent neural network model to explain how the hippocampus generates and uses barcode-like activity to support episodic memory. They address key questions raised by recent experimental findings: how barcodes are generated, how they interact with memory content (such as place and seed-related activity), and how the hippocampus balances memory specificity with flexible recall. The authors demonstrate that chaotic dynamics in a recurrent neural network can produce barcodes that reduce memory interference, complement place tuning, and enable context-dependent memory retrieval, while aligning their model with observed hippocampal activity during caching and retrieval in chickadees.

      Strengths:

      (1) The manuscript is well-written and structured.

      (2) The paper provides a detailed and biologically plausible mechanism for generating and utilizing barcode activity through chaotic dynamics in a recurrent neural network. This mechanism effectively explains how barcodes reduce memory interference, complement place tuning, and enable flexible, context-dependent recall.

      (3) The authors successfully reproduce key experimental findings on hippocampal barcode activity from chickadee studies, including the distinct correlations observed during caching, retrieval, and visits.

      (4) Overall, the study addresses a somewhat puzzling question about how memory indices and content signals coexist and interact in the same hippocampal population. By proposing a unified model, it provides significant conceptual clarity.

      Weaknesses:

      The recurrent neural network model incorporates assumptions and mechanisms, such as the modulation of recurrent input strength, whose biological underpinnings remain unclear. The authors acknowledge some of these limitations thoughtfully, offering plausible mechanisms and discussing their implications in depth.

      One thread of questions that authors may want to further explore is related to the chaotic nature of activity that generates barcodes when recurrence is strong. Chaos inherently implies sensitivity to initial conditions and noise, which raises questions about its reliability as a mechanism for producing robust and repeatable barcode signals. How sensitive are the results to noise in both the dynamics and the input signals? Does this sensitivity affect the stability of the generated barcodes and place fields, potentially disrupting their functional roles? Moreover, does the implemented plasticity mitigate some of this chaos, or might it amplify it under certain conditions? Clarifying these aspects could strengthen the argument for the robustness of the proposed mechanism.

      In our model, chaos is used to produce a random barcode when forming memories, but memory retrieval depends on attractor dynamics. Specifically, the plasticity update at the end of the cache creates an attractor state, and then afterwards for successful memory retrieval the network activity must settle into this attractor rather than remaining chaotic. This attractor state is a conjunction of memory content (place and seed activity) and memory index (barcode activity). Thus a barcode is ‘reactivated’ when network dynamics during retrieval settle into this cache attractor, or in other words chaotic dynamics do not need to generate the same barcode twice.

      The reviewer raises an important point, which is how sensitivity to initial conditions and noise would affect the reliability of our proposed mechanism. The key question here is how noise will affect the network’s dynamics during retrieval. Would adding noise to the dynamics make memory retrieval more difficult? We thank the reviewer for suggesting we investigate this further, and below describe our experiments and changes to the manuscript to better address this topic.

      We first experimented with adding independent gaussian distributed noise into each unit, drawn independently at each timestep. We analyzed recall accuracy using the same task and methods as Fig. 4F while varying the magnitude of noise. Memory recall was quite robust to this form of noise, even as the magnitude of noise approached half of the signal amplitude. This first experiment added noise into the temporal dynamics of the network. We subsequently examined adding static noise into the network inputs, which can also be thought of as introducing noise into initial conditions. Specifically, we added independent gaussian distributed noise into each unit, with the random value held constant for the extent of temporal dynamics. This perturbation decreased the likelihood of memory recall in a graded manner with noise magnitude, without dramatically changing the spatial profile. Examination of dynamics on individual trials revealed that the network failed to converge onto a cache attractor on some random fraction of trials, with other trials appearing nearly identical to noiseless results. We now include these results in the text and as a new supplementary figure, Figure S4AB.

      To clarify the network dynamics and the purpose of chaos in our model, we make the following modifications in text:

      Section 2.3, paragraph 2 (starting at “To store memories…”):

      “…place inputs arrive into the RNN, recurrent dynamics generate an essentially random barcode, seed inputs are activated, and then Hebbian learning binds a particular pattern of barcode activity to place- and seed-related activity.”

      Section 2.3, paragraph 3 (starting at “Memory recall in our network…”): As an example, consider a scenario in which an animal has already formed a memory at some location l, resulting in the storage of an attractor \vec{a} into the RNN. The attractor \vec{a} can be thought of as a linear combination of place input-driven activity $p(l)$, seed input-driven activity $s$, and a recurrent-driven barcode component $b$. Later, the animal returns to the same location and attempts recall (i.e. sets r \= 1, Figure 3B). Place inputs for location l drive RNN activity towards $p(l)$, which is partially correlated with attractor \vec{a}, and the recurrent dynamics cause network activity to converge onto attractor \vec{a}. In this way, barcode activity $b$ is reactivated, along with the place and seed components stored in the attractor state, $p(l)$ and $s$. The seed input can also affect recall, as discussed in the following section.

      Section 2.4, final paragraph (starting “We further examined how model hyperparameters affected performance on these tasks”), added the following describing new results on adding noise: We found that adding noise to the network's temporal dynamics had little effect on memory recall performance (Figure S4A). However, large static noise vectors added to the network's input and initial state decreased the overall probability of memory recall, but not its spatial profile (Figure S4B).

      It may also be worth exploring the robustness of the results to certain modeling assumptions.  For instance, the choice to run the network for a fixed amount of time and then use the activity  at the end for plasticity could be relaxed.

      As described above, chaotic dynamics are necessary to generate a barcode during a cache, but not to reactivate that barcode during retrieval. During a successful memory retrieval, network activity settles into an attractor state and thus does not depend on the duration of simulated dynamics. The choice of duration to run dynamics during caching is important, but only insofar as activity significantly decorrelates from the initial state. We show in Figure S1B that decorrelation saturates ~t=25, and thus any random time point t > 25 would be similarly effective. We used a fixed duration runtime for caches only to avoid introducing unnecessary complication into our model.

      Reviewer #2 (Public review):

      Summary:

      Striking experimental results by Chettih et al 2024 have identified high-dimensional, sparse patterns of activity in the chickadee hippocampus when birds store or retrieve food at a given site. These barcode-like patterns were interpreted as "indexes" allowing the birds to retrieve from memory the locations of stored food.

      The present manuscript proposes a recurrent network model that generates such barcode activity and uses it to form attractor-like memories that bind information about location and food. The manuscript then examines the computational role of barcode activity in the model by simulating two behavioral tasks, and by comparing the model with an alternate model in which barcode activity is ablated.

      Strengths of the study:

      Proposes a potential neural implementation for the indexing theory of episodic memory - Provides a mechanistic model of striking experimental findings: barcode-like, sparse patterns of activity when birds store a grain at a specific location

      A particularly interesting aspect of the model is that it proposes a mechanism for binding discrete events to a continuous spatial map, and demonstrates the computational advantages of this mechanism.

      Weaknesses:

      The relation between the model and experimentally recorded activity needs some clarification

      The relation with indexing theory could be made more clear

      The importance of different modeling ingredients and dynamical mechanisms could be made more clear

      The paper would be strengthened by focusing on the most essential aspects

      Comments:

      The model distinguishes between "barcode activity" and "attractors". Which of the two corresponds to experimentally-recorded barcodes? I would presume the attractors. A potential issue is that the attractors are, as explained in the text (l.137), conjunctions of place activity, barcode activity and "seed" inputs. The fact that the seed activity is shared across attractors seems to imply that they have a non-zero correlation independent of distance. Is that the case in the model? If I understand correctly, Fig 3D shows correlations between an attractor and barcodes at different locations, but correlations between attractors at different locations are not shown. Fig 1 F instead shows that correlations between recorded retrieval activities decay to zero with distance.

      More generally, the fact that the expression "barcode" is apparently used with different meanings in the model and in the experiments is potentially confusing (in the model they correspond to activity generating during caching, and this activity is distinct from the memories; my understanding is that in the experiments barcodes correspond to both caching and retrieval, but perhaps I am mistaken?).

      Our intent is to use the expression “barcode” as similarly as possible between model and experimental work. The reviewer points out that the connection between barcodes in experimental and modeling work is unclear, as well as the relation of “attractors” in our model to previous experimental results. The meaning of ‘barcode’ is absolutely critical—we clarify below our intended meaning, and then describe changes to the manuscript to highlight this.

      In experiments, we observed that activity during caching looked different than ordinary hippocampal activity (i.e. typical “place activity” observed during visits). Empirically there were two major differences. First, there was a pattern of neural activity which was present during every cache . This pattern was also present when birds visually inspected sites containing a cached seed, but not when visually inspecting an empty site. This is what we refer to as “seed activity”. Second, there was a pattern of neural activity which was unique to each cache. This pattern re-occurred during retrieval, and was orthogonal to place activity (see Fig. 1E-F). This is what we refer to as “barcode activity”. In summary, activity during a cache (or retrieval) contains a combination of three components: place activity, seed activity, and barcode activity.

      These experimental findings are recapitulated in our model, as activity during a cache contains a combination of three components: place activity driven by place inputs, seed activity driven by seed inputs, and barcode activity generated by recurrent dynamics. Cache activity in the model corresponds to cache activity in experiments, and barcodes in the model correspond to barcodes in experiments. Our model additionally has “attractors”, meaning that network connectivity changes so that the activity generated during a simulated cache becomes an attractor state of network dynamics. “Attractors” refers to a feature of network dynamics, not a distinct activity state, and we do not yet know if these attractors exist in experimental data.

      Figure 3D, as described in the figure legend, is a correlation of activity during cache and retrieval (in purple), for cache-retrieval pairs at the same or at different sites. We believe this is what the reviewer asks to see: the correlation between attractor states for different cache locations. The reviewer makes an important point: seed activity is shared across all attractors, so then why are correlations not high for all locations? This is because attractors also have a place component, which is anti-correlated for distant locations. This is evident in Fig. 3D by noticing that visit-visit correlations (black line, corresponding to place activity only) are negative for distant locations, and the correlation between attractors (purple line, cache-retrieval pairs) is subtly shifted up relative to the black line (place code only) for these distant locations. The size of this shift is due to the relative magnitude of place and seed inputs. For example, if we increase the strength of the seed input during caching (blue line), we can further increase the correlation between attractors even for quite distant sites:

      Author response image 1.

      To clarify the manuscript, we made the following modifications:

      Section 2.2, first paragraph: We model the hippocampus as a recurrent neural network (RNN) (Alvarez and Squire, 1994; Tsodyks, 1999; Hopfield, 1982) and propose that recurrent dynamics can generate barcodes from place inputs. As in experiments, the model’s population activity during a cache should exhibit both place and barcode activity components.

      Section 2.3, paragraph 3 (starting at “Memory recall in our network…”): As an example, consider a scenario in which an animal has already formed a memory at some location l , resulting in the storage of an attractor \vec{a} into the RNN . The attractor \vec{a} can be thought of as a linear combination of place input-driven activity $p(l)$, seed input-driven activity $s$, and a recurrent-driven barcode component $b$. Later, the animal returns to the same location and attempts recall (i.e. sets r \= 1, Figure 3B). Place inputs for l drive RNN activity towards $p(l)$, which is partially correlated with attractor \vec{a}, and the recurrent dynamics cause network activity to converge onto attractor \vec{a}. In this way, barcode activity $b$ is reactivated as part of attractor \vec{a}, along with the place and seed components stored in the attractor state, $p(l)$ and $s$. The seed input can also affect recall, as discussed in the following section.

      The insights obtained from the network model for the computational role of barcode activity could be explained more clearly. The introduction starts by laying out the indexing theory, which proposes that the hippocampus links an index with each memory so that the memory is reactivated when the index is presented. The experimental paper suggests that the barcode activations play the role of indexes. Yet, in the model reactivations of memories are driven not by presenting bar-code activity, but by presenting place activity (Cache Presence task) or seed activity (Cache Location task). So it seems that either place activity and seed activity play the role of indexes. Section 2.5 nicely shows that ultimately the role of barcode activity is to decorrelate attractors, which seems different from playing the role of indexes. I feel it would be useful that the Discussion reassess more critically the relationship between barcodes, indexing theory, and key-value architectures.

      The reviewer highlights a failure on our part to clearly identify the connection between our findings on barcodes, indexing theory, and key-value architectures. This is another major component of the paper, and below we propose changes to the manuscript to clarify these concepts and their relationships. First, we will summarize the key points that were unclear in our original manuscript.

      The reviewer equates the concept of an ‘index’ with that of a ‘query’: the signal that drives memory reactivation. This may be intuitive, but it is not how a memory index was defined in indexing theory (e.g. Teyler & DiScenna 1986). In indexing theory, the index is a pattern of hippocampal activity that is (a) generated during memory formation, (b) separate from the activity encoding memory content, and (c) linked to memory content via associative plasticity. After memory formation, a memory might be queried by activating a partial set of the memory contents, which would then drive reactivation of the hippocampal index, leading to pattern completion of memory contents. See, for example, figure 1 of Teyler and DiScenna 1986. The ‘index’ is thus not the same as the ‘query’ that drives recall.

      We propose in this work that barcode activity is such an index. Indexing theory originally posited that memory content was encoded by neocortex, and memory index was encoded by hippocampus. However the experiments of Chettih et al. 2024 revealed that the hippocampus contained both memory content and memory index signals, and furthermore there was no division of cells into ‘content’ and ‘index’ subtypes. Thus our model drops the assumption of earlier work that index and content signals correspond to different neurons in different brain areas—a significant advance of our work. Otherwise, the experimentally observed barcodes and the barcodes generated by our computational model play the role of indices as originally defined.

      Our original manuscript was unclear on the relationship of indexing theory and key-value systems. Our work connects diverse areas of memory models, including attractor dynamics, key-value memory systems, and memory indexing. A full account of these literatures and their relationships may be beyond the scope of this manuscript, and we note that a recent review article (Gershman, Fiete, and Irie, 2025) further clarifies the relationship between key-value memory, indexing theory, and the hippocampus. We will cite this work in our discussion as a source for the interested reader.

      Briefly, a key-value memory system distinguishes between the address where a memory is stored, the ‘key’, and the content of that memory, the ‘value’. An advantage of such systems is that keys can be optimized for purposes independent of the value of each memory. The use of barcodes in our model to decorrelate memories is related to this optimization of keys in key-value memory systems. By generating barcodes and adding this to the attractor state corresponding to a cache memory, the ‘address’ of the memory in population activity is differentiated from other memories. Our work is thus consistent with the idea that hippocampus generates keys and implements a key storage system. However it is not so straightforward to equate barcodes with keys, as they are defined in key-value memory. As the reviewer points out, memory recall can be driven by location and seed inputs, i.e. it is content-addressable. We think of the barcode as modifying the memory address to better separate similar memories, without changing memory content, and the resulting memory can be recalled by querying with either content or barcode. Given the complex and speculative nature of these relationships, we prefer to note the salient connection of our work with ongoing efforts applying the key-value framework to biological memory, and leave the precise details of this connection to future work.

      We make the following changes in the manuscript to clarify these ideas:

      Introduction, first paragraph: In this scheme, during memory formation the hippocampus generates an index of population activity, and the neurons representing this index are linked with the neurons representing memory content by associative plasticity . Later, re-experience of partial memory contents may reactivate the index, and reactivation of the index drives complete recall of the memory contents.

      Discussion, 4th paragraph on key-value: Interestingly, prior theoretical work has suggested neural implementations for both key-value memory and attention mechanisms, arguing for their usefulness in neural systems such as long term memory (Kanerva, 1988; Tyulmankov et al., 2021; Bricken and Pehlevan, 2021; Whittington et al., 2021; Kozachkov et al., 2023; Krotov and Hopfield, 2020; Gershman 2025 ). In this framework, the address where a memory is stored (the key) may be optimized independently of the value or content of the memory. In our model, barcodes improve memory performance by providing a content-independent scaffold that binds to memory content, preventing memories with overlapping content from blurring together. Thus barcodes can be considered as a change in memory address, and our model suggests important connections between recurrent neural activity and key generation mechanisms. However we note that barcodes should not be literally equated with keys in key-value systems as our model’s memory is ‘content-addresable’—it can be queried by place and seed inputs.

      The model includes a number of non-standard ingredients. It would be useful to explain which of these ingredients and which of the described mechanisms are essential for the studied phenomenon. In particular:

      - the dynamics in Eq.2 include a shunting inhibition term. Is it essential and why?

      The shunting inhibition is important as it acts to normalize the network activity to prevent runaway excitation. We hope to clarify this further by amending the following sentence in section 2.2: “g (·) is a leak rate that depends on the average activity of the full network, representing a form of global shunting inhibition that normalizes network activity to prevent runaway excitation from recurrent dynamics.”

      - same question for the global inhibition included in the random connectivity;

      The distribution from which connectivity strengths are drawn has a negative mean (global inhibition). This causes activity during caching (i.e. r = 1) to be sparser than activity during visits (i.e. r = 0), and was chosen to match experimental findings. In figures 2B and S2B we show that our model can transition between a mode with place code only, barcode only, or a mode containing both, by changing the variance of the weight distribution while holding the mean constant. We suggest clarifying this by editing the following in section 2.2, paragraph 2: “We initialize the recurrent weights from a random Gaussian distribution, . where 𝑁<sub>𝑋</sub> is the number of RNN neurons and μ < 0, reflecting global subtractive inhibition that encourages sparse network activity to match experimental findings (Chettih et al. 2024).”

      - the model is fully rate-based, but for certain figures, spikes are randomly generated. This seems superfluous.

      Spikes are simulated for one analysis and one visualization, where it is important to consider noise or variability in neural responses across trials. First, for Fig. 2H,J, we generated spikes to allow a visual comparison to figures that can be easily generated from experimental data. Second, and more significantly, for the analysis underlying Fig. 3D, it is essential to simulate variability in neural responses. Because our rate-based models are noiseless, the RNN’s rate vector at site distance = 0 will always be the same and result in a correlation of 1 for both visit-visit and cache-retrieval. However, we show that, if one interprets the rate as a noisy Poisson spiking process, the correlation at site distance = 0 between a cache-retrieval pair is higher than that of two visits. This is because under a Poisson spiking model, the signal-to-noise ratio is higher for cache-retrieval activity, where rates are higher in magnitude. The greater correlation for a cache-retrieval pair at the same site, relative to visits at the same site, is an experimental finding that was critical for our model to reproduce. We detail clarifications to the manuscript below in response to the reviewer’s following and related question.

      How are the correlations determined in the model (e.g., Fig 2 B)? The methods explain that they are computed from Poisson-generated spikes, but over which time period? Presumably during steady-state responses, but are these responses time-averaged?

      The reviewer points out a lack of clarity in our original manuscript. Correlations for events (caches, retrievals and visits) at different sites are calculated in two sections of the paper (2B, 3D), for different purposes and with slight differences in methods:

      - For figure 2B, no spikes are simulated. Note that the methods mentioning poisson spike generation specify only Fig. 2H,J and Fig. 3D. We simply take the network’s rate vector at timestep t=100 (when the decorrelating effect of chaotic dynamics has saturated, S1A-B) and correlate this vector when generated at different locations. We now clarify this in the legend for Figure 2B: “We show correlation of place inputs (gray) and correlation of the RNN's rate vector at t = 100 (black).”

      - For Figure 3D, we want to compare the model to empirical results from Chettih et al. 2024, and reproduced in this paper in Fig. 1E-F. These empirical results are derived from correlating vectors of spiking activity on pairs of single trials, and are thus affected by noise or variability in neural responses as described in our response to the reviewer’s previous question. We thus took the RNN’s rate vector at t=100 and simulated spiking data by drawing samples from a poisson distribution to get spike counts. Our original manuscript was unclear about this, and we suggest the following changes:

      - Legend for Figure 3D: D. Correlation of Poisson-generated spikes simulated from RNN rate vectors at two sites, plotted as a function of the distance between the two sites.

      - Section 2.3, last paragraph: Population activity during retrieval closely matches activity during caching, and is substantially decorrelated from activity during visits (Figure 3C). To compare our model with the empirical results reproduced in Figure 1E,F, we ran in silico experiments with caches and retrievals at varying sites in the circular arena. We simulated Poisson-generated spikes drawn from our network's underlying rates to match the intrinsic variability in empirical data (see Methods).

      - Methods, subsection Spatial correlation of RNN activity for cache-retrieval pairs at different sites: To calculate correlation values as in Figure \ref{fig3}D, we simulated experiments where 5 sites were randomly chosen for caching and retrieval. To compare model results to the empirical data in Fig. 1E,F, which includes intrinsic neural variability, we sampled Poisson-generated spike counts from the rates output by our model. Specifically, for RNN activity \vec{r_i} at location i, using the rates at t=100 as elsewhere, we first generate a sample vector of spikes…

      I was confused by early and late responses in Fig 2 C. The text says that the activity is initialized at zero, so the response at t=0 should be flat (and zero). More generally, I am not sure I understand why the dynamics matter for the phenomenon at all, presumably the decorrelation shown in Fig 2B depends only on steady state activity (cf previous question).

      Thanks for catching this mistake. The legend has been updated to indicate that the ‘early’ response is actually at t=1, when network activity reflects place inputs without the effects of dynamics. The reviewer is correct that we are primarily interested in the ‘late’ response of the network. All other results in the paper use this late response at t=100. As shown in Fig. S2A,B, this timepoint is not truly a steady state, as activity in the network continues to change, but the decorrelation of network activity with place-driven activity has saturated.

      We include the early response in Fig. 2C for visual comparison of the purely place-driven early activity with the eventual network response. It is also relevant since, as the reviewer points out above, there is a shunting inhibition term in the dynamics that is present during both low and high recurrent strength simulations.

      Related to the previous point, the discussion of decorrelation (l.79 - 97) is somewhat confusing. That paragraph focuses on chaotic activity, but chaos decorrelates responses across different time points. Here the main phenomenon is the decorrelation of responses across different spatial inputs (Fig 2B). This decorrelation is presumably due to the fact that different inputs lead to different non-trivial steady-state responses, but this requires some clarification. If that is correct, the temporal chaos adds fluctuations around these non-trivial steady-state responses, but that alone would not lead to the decorrelation shown in Fig 2B.

      We agree with the reviewer that chaotic activity produces a decorrelation across time points. Because of chaotic dynamics, network activity does not settle into a trivial steady-state, and instead evolves from the initial state in an unpredictable way. The network does not settle into a steady-state pattern, but both the decorrelation of network state with initial state and the rate of change in the network state saturate after ~t=25 timesteps, as shown in Fig. S2A-B.

      The initial activity for nearby states is similar, due to them receiving similar place inputs.

      Because network activity is chaotically decorrelated from this initial state by temporal dynamics, ‘late stage’ network activity between nearby spatial states is less correlated than ‘early stage’ activity. Thus the temporal decorrelation produces a spatial decorrelation. We believe that the changes we have introduced to the manuscript in revision will make this point clearer in our resubmission.

      A key ingredient of the model is that the recurrent interactions are switched on and off between "caching" and "visits". The discussion argues that a possible mechanism for this is recurrent inhibition (l.320), which would need to be added. However two forms of inhibition are already included in the model. The text also says that it is unclear how units in the model should be mapped onto E and I neurons. However the model makes explicit assumptions about this, in particular by generating spikes from individual neurons. Altogether, I did not find that part of the Discussion convincing.

      We agree with the reviewer that this section is a limitation of our current work, and in fact it is an ongoing area of future research. However we think the advances in this current work warrant publication despite this topic requiring further research. We attempted to discuss this limitation explicitly, and note that the other reviewer pointed this section out as particularly helpful. We do not think it is problematic for a realistic model of the brain to ultimately include 3, or even more forms of inhibition. We do not think that poisson-generated spikes commit us to interpreting network units as single neurons. Spikes are not a core part of our model’s mechanism, and were used only as a mechanism of introducing variability on top of deterministic rates for specific analyses. Furthermore one could still view network units as pools of both E and I spiking neurons. We would welcome further recommendations the reviewer believes are important to note in this section on our model’s limitations.

      On lines 117-120 the text briefly mentions an alternate feed-forward model and promptly discards it. The discussion instead says that a "separate possibility is that barcodes are generated in a circuit upstream of where memories are stored, and supplied as inputs to the hippocampal population", and that this possibility would lead to identical conclusions. The two statements seem a bit contradictory. It seems that the alternative possibility would replace the need for switching on and off recurrent interactions, with a mechanism where barcode inputs are switched on and off. This alternate scenario is perhaps more plausible, so it would be useful to discuss it more explicitly.

      We apologize for the confusion here, which seems to be due to our phrasing in the discussion section. We do reject the idea that a simple feed-forward model could generate the spatial correlation profile observed in data, as mentioned in the text and included as Fig. S2. Our statement in the discussion may have seemed contradictory because here we intended to discuss the possibility that an upstream area generates barcodes, for example by the chaotic recurrent dynamics proposed in our work, while a downstream network receives these barcodes as inputs and undergoes plasticity to store memories as attractors. We did not intend to suggest any connection to the feedforward model of barcode generation, and apologize for the confusion. Our claim that this ‘2 network’ solution would lead to similar conclusions is because the upstream network would need an efficient means of barcode generation, and the downstream network would need an efficient means of storing memory attractors, and separating these functions into different networks is not likely to affect for example the advantage of partially decorrelating memory attractors. Moreover, the downstream network would still require some form of recurrent gating, so that during visits it exhibits place activity without activating stored memory attractors!

      We thus chose a 1 network instead of a 2 network solution because it was simpler and, we believe, more interesting. It is challenging in the absence of more data to say which is more plausible, thus we wanted to mention the possibility of a 2 network solution. We suggest the following changes to the manuscript:

      - Discussion, 3rd paragraph: “Alternatively, other mechanisms may be involved in generating barcodes. We demonstrated that conventional feed-forward sparsification (Babadi and Sompolinsky, 2014; Xie et al., 2023) was highly inefficient, but more specialized computations may improve this (Földiak, 1990; Olshausen and Field, 1996; Sacouto and Wichert, 2023; Muscinelli et al., 2023). Another possibility is that barcodes are generated in a separate recurrent network upstream of the recurrent network where memories are stored. In this 2-network scenario, the downstream network receives both spatial tuning and barcodes as inputs. This would not obviate the need for modulating recurrent strength in the downstream network to switch between input-driven modes and attractor dynamics. We suspect separating barcode generation and memory storage in separate networks would not fundamentally affect our conclusions.”

      As a minor note, the beginning of the discussion states that the presented model is similar to previous recurrent network models of the hippocampus. It would be worth noting that several of the cited works assign a very different role to recurrent interactions: they generate place cell activity, while the present model assumes it is inherited from upstream inputs.

      We are not sure how best to modify the paper to address this suggestion. As far as we know, all of the cited models which deal with spatial encoding do assume that the hippocampus receives a spatially-modulated or spatially-tuned input. For example, the Tsodyks 1999 paper cited in this paragraph uses exponentially-decaying place inputs to each neuron highly similar to our model. Furthermore we explore how our model would perform if we change the format of spatial inputs in Fig. S4, and find key results are unchanged. It is unclear how hippocampal place fields could emerge without inputs that differentiate between spatial locations. We think it is appropriate to highlight the similarity of our model to well known hopfield-type recurrent models, where memories are stored as attractor states of the network dynamics.

      On the other hand, we agree that a common line of hippocampal modeling proposes that recurrent interactions reshape spatial inputs to produce place fields. This often arises in the context of hippocampus generating a predictive map, where inputs may be one-hot for a single spatial state, in a grid cell-like format, or a random projection of sensory features. We attempted to address this in section 2.6, using a model which superimposes the random connectivity needed for barcode generation with the structured connectivity needed for predictive map formation. We found that such a model was able to perform both predictive and barcode functions, suggesting a path forward to connecting different lines of hippocampal modeling in future work.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Conceptually, I feel that the authors addressed many concerns. However, I am still not convinced that their data support the strength of their claims. Additionally, I spent considerable time investigating the now freely available code and data and found several inconsistencies that would be critical to rectify. My comments are split into two parts, reflecting concerns related to the responses/methods and concerns resulting from investigation of the provided code/data. The former is described in the public review above. Because I show several figures to illustrate some key points for the latter part, an attached file will provide the second part: https://elife-rp.msubmit.net/elife-rp_files/2025/02/24/00136468/01/136468_1_attach_15_2451_convrt.pdf

      (1) This point is discussed in more detail in the attached file, but there are some important details regarding the identification of the learned trial that require more clarification. For instance, isn’t the original criterion by Gibbon et al. (1977) the first “sequence of three out of four trials in a row with at least one response”? The authors’ provided code for the Wilcoxon signed rank test and nDkl thresholds looks for a permanent exceeding of the threshold. So, I am not yet convinced that the approaches used here and in prior papers are directly comparable.

      We agree that there remain unresolved issues with our two attempts to create criteria that match that used by Gibbon and Balsam for trials to criterion. Therefore, we have decided to remove those analyses and return to our original approach showing trials to acquisition using several different criteria so as to demonstrate that the essential feature of the results—the scaling between learning rate and information—is robust. Figure 2A shows the results for a criterion that identifies the trial after which the cumulative response rate during the CS (=cumulative CS response count from Trial 1 divided by cumulative CS time from Trial 1) is consistently above the cumulative overall response rate across the trial (i.e., including both the CS and ITI). These data compare the CS response rate with the overall response rate, rather than with ITI rate as done in the previous version (in Figure 3A of that submission), to be consistent with the subsequent comparisons that are made using the nDkl. (The nDkl relies on the comparison between the CS rate and the overall rate, rather than between the CS and ITI rates.) Figures 2B and 2C show trials to acquisition when two statistical criteria, based on the nDkl, are applied to the difference between CS and overall response rates (the criteria are for odds >= 4:1 and p<.05). As we now explain in the text, a statistical threshold is useful inasmuch as it provides some confidence to the claim that the animals had learned by a given trial. However, this trial is very likely to be after the point when they had learned because accumulating statistical evidence of a difference necessarily adds trials.

      Also, there’s still no regression line fitted to their data (Fig 3’s black line is from Fig 1,according to the legends). Accordingly, I think the claim in the second paragraph of the Discussion that the old data and their data are explained by a model with “essentially the same parameter value” is not yet convincing without actually reporting the parameters of the regression. Related to this, the regression for their data based on my analysis appears to have a slope closer to -0.6, which does not support strict timescale invariance. I think that this point should be discussed as a caveat in the manuscript.

      We now include regression lines fitted to our data in Figures 2A-C, and their slopes are reported in the figure note. We also note on page 14 of the revision that these regressions fitted to our data diverge from the black regression line (slope -1) as the informativeness increases. On pages 14-15, we offer an explanation for this divergence; that, in groups with high informativeness, the effective informativeness is likely to be lower than the assigned value because the rats had not been magazine trained which means they would not have discovered the food pellet as soon as it was released on the first few trials. On pages 15-16, we go on to note that evidence for a change in response rate during the CS in those very first few trials may have been missed because the initial response rates were very low in rats trained with very long inter-reinforcement intervals (and thus high informativeness). We also propose a solution to this problem of comparing between very low response rates, one that uses the nDkl to parse response rates into segments (clusters of trials with equivalent response rates). This analysis with parsed response rates provides evidence that differential responding to the CS may have been acquired earlier than is revealed using trial-by-trial comparisons.

      (2) The authors report in the response that the basis for the apparent gradual/multiple step-like increases after initial learning remains unclear within their framework. This would be important to point out in the actual manuscript Further, the responses indicating the fact that there are some phenomena that are not captured by the current model would be important to state in the manuscript itself.

      We have included a paragraph (on page 26) that discusses the interpretation of the steady/multi-step increase in responding across continued training.

      (3) There are several mismatches between results shown in figures and those produced by the authors’ code, or other supplementary files. As one example, rat 3 results in Fig 11 and Supplementary Materials don’t match and neither version is reproduced by the authors’ code. There are more concerns like this, which are detailed in the attached review file.

      Addressed next….

      The following is the response to the points raised in Part 2 of Reviewer 1’s pdf.

      (1a) I plotted the calculated nDkl with the provided code for rat 3 (Fig 11), but itlooks different, and the trials to acquisition also didn’t match with the table  provided (average of ~20 trial difference). The authors should revise the provided code and plots. Further, even in their provided figures, if one compares rat 3 in Supplementary Materials to data from the same rat in Fig 11, the curves are different. It is critical to have reproducible results in the manuscript, including the ability to reproduce with the provided code.

      We apologise for those inconsistencies. We have checked the code and the data in the figures to ensure they are all now consistent and match the full data in the nHT.mat file in OSF. Figures 11 and 12 from the previous version are now replaced with Figure 6 in the revised manuscript (still showing data from Rats 3 and 176). The data plotted in Fig 6 match what is plotted in the supplementary figures for those 2 rats (but with slightly different cropping of the x-axes) and all plots draw directly from nHT.mat.

      (1b) I tried to replicate also Fig 3C with the results from the provided code, but I failed especially for nDkl > 2.2. Fig 3A and B look to be OK.

      There was error in the previous Fig 3C which was plotting the data from the wrong column of the Trials2Acquisition Table. We suspect this arose because some changes to the file were not updated in Dropbox. However, that figure has changed (now Figure 2) as already mentioned, and no longer plots data obtained with that specific nDkl criterion. The figure now shows criteria that do not attempt to match the Gibbon and Balsam criterion.

      (1c) The trials to learn from the code do match with those in the  Trials2Acquisition Table, but the authors’ code doesn’t reproduce the reported trials to learn values in the nDkl Acquisition Table. The trials to learn from the code are ~20 trials different on average from the table’s ones, for 1:20, 1:100, and 1:1000 nDkl.

      We agree that discrepancies between those different files were a source of potential confusion because they were using different criteria or different ways of measuring response rate (i.e., the “conventional” calculation of rate as number of responses/time, vs our adjusted calculation in which the 1<sup>st</sup> response in the CS was excluded as well as the time spent in the magazine, vs parsed response rates based on inter-response intervals). To avoid this, there is now a single table called Acquisition_Table.xlsx in OSF that includes Trials to acquisition for each rat based on a range of criteria or estimates of response rate in labelled columns. The data shown in Figure 2 are all based on the conventional calculation of response rate (provided in Columns E to H of Acquisition_Table.xlsx). To make the source of these data explicit, we have provided in OSF the matlab code that draws the data from the nHT.mat file to obtain these values for trials-to-acquisition.

      (1d) The nDkl Acquisition Table has columns with the value of the nDkl statistics at various acquisition landmarks, but the value does not look to be true, especially for rat 19. The nDkl curve provided by the authors (Supplementary Materials) doesn’t match the values in the table. The curve is below 10 until at least 300 trials, while the table reports a value higher than 20 (24.86) at the earliest evidence of learning (~120 trials?).

      We are very grateful to the reviewer for finding this discrepancy in our previous files. The individual plots in the Supplementary Materials now contain a plot of the nDkl computed using the conventional calculation of response rate (plot 3 in each 6-panel figure) and a plot of the nDkl computed using the new adjusted calculation of response rate (plot 4). These correspond to the signed nDkl columns for each rat in the full data file nHT.mat. The nDkl values at different acquisition landmarks included in Acquisition_Table.xlsx (Cols AB to AF) correspond to the second of these nDkl formulations. We point out that, of the acquisition landmarks based on the conventional calculation of response rate (Cols E to J of Acquisition_Tabls.xlsx), only the first two landmarks (CSrate>Contextrate and min_nDkl) match the permanently positive and minimum values of the plotted nDkl values. This is because the subsequent acquisition landmarks are based on a recalculation of the nDkl starting from the trial when CSrate>ContextRate, whereas the plotted nDkl starts from Trial 1.

      (2) The cumulative number of responses during the trial (Total) in the raw data table is not measured directly, but indirectly estimated from the pre-CS period, as (cumNR_Pre*[cumITI/cumT_Pre])+ cumNR_CS (cumNR_Pre: cumulative nose-poke response number during pre-CS period; cumITI: cumulative sum of ITI duration; cumT_Pre: cumulative pre-CS duration; cumNR_CS: cumulative response number during CS), according to ‘Explanation of TbyTdataTable (MATLAB).docx’.Why not use the actual cumulative responses during the whole trial instead of using a noisier measure during a smaller time window and then scaling it for the total period?

      Unfortunately, the bespoke software used to control the experimental events and record the magazine activity did not record data continuously throughout the experiment. The ITI responses were only sampled during a specified time-window (the “pre-CS” period) immediately before each CS onset. Therefore, response counts across the whole ITI had to be extrapolated.

      (3) Regarding the “Matlab code for Find Trials to Criterion.docx”:

      (a) What’s the rationale for not using all the trials to calculate nDkl but starting the cumulative summation from the earliest evidence trial (truncated)? Also, this procedure is not described in the manuscript, and this should be mentioned.

      The procedure was perhaps not described clearly enough in the previous manuscript. We have expanded that text to make it clearer (page 12) which includes the text…

      “We started from this trial, rather than from Trial 1, because response rate data from trials prior to the point of acquisition would dilute the evidence for a statistically significant difference in responding once it had emerged, and thereby increase the number of trials required to observe significant responding to the CS. The data from Rat 1 illustrates this point. The CS response rate of Rat 1 permanently exceeded its overall response rate on Trial 52 (when the nD<sub>KL</sub> also became permanently positive). The nD<sub>KL</sub>, calculated from that trial onwards, surpassed 0.82 (odds 4:1) after a further 11 trials (on Trial 63) and reached 1.92 (p < .05) on Trial 81. By contrast, the nD<sub>KL</sub> for this rat, calculated from Trial 1, did not permanently exceed 0.82 until Trial 83 and did not exceed 1.92 until Trial 93, adding 10 or 20 trials to the point of acquisition.”

      (3b) The authors' threshold is the trial when the nDkl value exceeds the threshold permanently.  What about using just the first pass after the minimum?

      Rat 19 provides one example where the nDkl was initially positive, and even exceeded threshold for odds 4:1 and p<.05, but was followed by an extended period when the nDkl was negative because the CS response rate was less than the overall response rate. It illustrates why the first trial on which the nDkl passes a threshold cannot be used as a reliably index of acquisition.

      (3c) Can the authors explain why a value of 0.5 is added to the cumulative response number before dividing it by the cumulative time?

      This was done to provide an “unbiased” estimate of the response count because responses are integers. For example, if a rat has made 10 responses over 100 s of cumulative CS time, the estimated rate should be at least 10/100 but could be anything up to, but not including, 11/100. A rate of 10.5/100 is the unbiased estimate. However, we have now removed this step when calculating the nDkl to identify trials to acquisition because we recognise that it would represent a larger correction to the rate calculated across short intervals than across long intervals and therefore bias comparison between CS and overall response rates that involve very different time durations. As such, the correction would artefactually inflate evidence that the CS response rate was higher than the contextual response rate. However, as noted earlier in this reply, we have now instituted a similar correction when calculating the pre-CS response rate over the final 5 sessions for rats that did not register a single response (hence we set their response count to 0.5).

      (3d) Although the authors explain that nDkl was set to negative if pre-CS rate is higher than CS rate, this is not included in the code because the code calculates the nDkl using the truncated version, starting to accumulate the poke numbers and time from the earliest evidence, thus cumulative CS rate is always higher than cumulative contextual rate. I expect then that the cumulative CS rate will be always higher than the cumulative pre-CS rate.

      Yes, that is correct. The negative sign is added to the nDkl when it is computed starting from Trial 1. But when it is computed starting from the trial when the CS rate is permanently > the overall rate, there is no need to add a sign because the divergence is always in the positive direction.

      (3e) Regarding the Wilcoxon signed rank test, please clarify in the manuscript that the input ‘rate’ is not the cumulative rate as used for the earliest evidence. Please also clarify if the rates being compared for the signed nDkl are just the instantaneous rates or the cumulative ones. I believe that these are the ‘cumulative’ ones (not as for Wilcoxon signed rank test), because if not, the signed nDkl curve of rat 3 would fluctuate a lot across the x-axis.

      The reviewer is correct in both cases. However, as already mentioned, we have removed the analysis involving the Wilcoxon test. The description of the nDkl already specifies that this was done using the cumulative rates.

      (4) Supplemental table ‘nDkl Acquisition Table.xlsx’ 3rd column (“Earliest”) descriptions are unclear.

      (a) It is described in the supplemental ‘Explanation of Excel Tables.docx’ as the ‘earliest estimate of the onset of a poke rate during the CSs higher than the contextual poke rate’, while the last paragraph of the manuscript’s method section says ‘Columns 4, 5 and 6 of the table give the trial after which conditioned responding appeared as estimated in the above described three different ways— by the location of the minimum in the nDkl, the last upward 0 crossings, and the CS parse consistently greater than the ITI parse, respectively. Column 3 in that table gives the minimum of the three estimates.’ I plotted the data from column 3 (right) and comparing them with Fig 3A (left) makes it clear that there’s an issue in this column. If the description in the ‘Explanation of Excel Tables.docx’ is incorrect, please update it.

      We agree that the naming of these criteria can cause confusion, hence we have changed them. On page 9 we have replaced “earliest” with “first” in describing the criterion plotted in Figure 2A showing the trial starting from which the cumulative CS response rate permanently exceeded the cumulative overall rate. What is labelled as “Earliest” in “Acquisition_Table.xlsx” is, as the explanation says, the minimum value across the 3 estimates in that table.

      (b) Also, the term ‘contextual poke rate’ in the 3rd column’s description isconfusing as in the nDkl calculation it represents the poke rate during all the training time, while in the first paragraph of the ‘Data analysis’ part, the earliest evidence is calculated by comparing the ITI (pre-CS baseline) poke rate.

      Yes, we have kept the term “contextual” response rate to refer to responding across the whole training interval (the ITI and the CS duration). This is used in calculation of the nDkl. For consistency with this comparison, we now take the first estimate of acquisition (in Fig 2A) based on a comparison between the CS rate and the overall (context) rate (not the pre-CS rate).

      Reviewer #2 (Recommendations for the authors):

      In response to the Rebuttal comments:

      Analytical (1) relating to Figure 3C/D

      This is a reasonable set of alternative analyses, but it is not clear that it answers the original comment regarding why the fit was worse when using a theoretically derived measure. Indeed, Figure 3C now looks distinctly different to the original Gibbon and Balsam data in terms of the shape of the relationship (specifically, the Group Median - filled orange circles) diverge from the black regression line.

      As mentioned in response to Reviewer 1, there was a mistake in Figure 3C of the revised manuscript. The figure was actually plotting data using a more stringent criterion of nDkl > 5.4, corresponding to p<0.001. The figure was referencing the data in column J of the public Trials2Acquisition Table. The data previously plotted in Figure 3C are no longer plotted because we no longer attempt to identify a criterion exactly matching that used by Gibbon and Balsam.

      We agree that the data shown in the first 3 panels of Figure 2 do diverge somewhat from the black regression line at the highest levels of informativeness (C/T ratios > 70), and the regression lines fitted to the data have slopes greater than -1. We acknowledge this on page 14 of the revised manuscript. Since Gibbon and Balsam did not report data from groups with such high ratios, we can’t know whether their data too would have diverged from the regression line at this point. We now report in the text a regression fitted to the first 10 groups in our experiment, which have C/T ratios that coincide with those of Gibbon and Balsam, and those regression lines do have slopes much closer to -1 (and include -1 in the 95% confidence intervals). We believe the divergence in our data at the high C/T ratios may be due to the fact that our rats were not given magazine training before commencing training with the CS and food. Because of this, it is quite likely that many rats did not find the food immediately after delivery on the first few trials. Indeed, in subsequent experiments, when we have continued to record magazine entries after CS-offset, we have found that rats can take 90 s or more to enter the magazine after the first pellet delivery. This delay would substantially increase the effective CS-US interval, measured from CS onset to discovery of the food pellet by the rat, making the CS much less informative over those trials. We now make this point on pages 14-15 of the revised manuscript.

      Analytical (2)

      We may have very different views on the statistical and scientific approaches here.

      This scalar relationship may only be uniquely applicable to the specific parameters of an experiment where CS and US responding are measured with the same behavioral response (magazine entry). As such, statements regarding the simplicity of the number of parameters in the model may simply reflect the niche experimental conditions required to generate data to fit the original hypotheses.

      To the extent that our data are consistent with the data reported decades ago by Gibbon and Balsam indicates the scalar relationship they identified is not unique to certain niche conditions since those special conditions must be true of both the acquisition of sign-tracking responses in pigeons and magazine entry responses in rats. How broadly it applies will require further experimental work using different paradigms and different species to assess how the rate of acquisition is affected across a wide range of informativeness, just as we have done here.

    1. Author response:

      Thank you for overseeing the review of our manuscript and for providing the eLife Assessment and Public Reviews. We are highly appreciative of the detailed, constructive feedback from the editors and reviewers.

      We acknowledge the core issues raised and we are committed to undertaking the necessary experiments and textual revisions to address every critique.

      Here is a summary of the key revisions we plan to undertake to address the major points raised:

      (1) Absolute yield comparison and efficiency clarification (eLife Assessment, R#3)

      We will perform new quantitative experiments to provide the absolute protein yield of our optimized eCFPS system and benchmark it against a published, widely recognized high-yield CFPS protocol. This will directly address the central requirement for industry comparison and strengthen the claim of "high efficiency." Furthermore, we will revise the manuscript's terminology, especially in the title and abstract, to accurately reflect the system's success in "streamlining" and "robustness" in addition to performance.

      (2) Mechanistic rationale for simplification (eLife Assessment, R#1)

      We will substantially expand the Discussion to provide a mechanistic explanation for why activity is maintained after removing up to 28 components. This analysis will focus on the retention of endogenous metabolic enzymes and residual factors within the "Fast Lysate," citing relevant literature (e.g., Yokoyama et al., 2010, as suggested by R#1) to support the role of metabolic pathways in compensating for the lack of exogenous tRNA, CTP/UTP, and specific amino acids.

      (3) Transcription-translation coupling (R#3)

      To address the concern that expression changes might be due to transcription rather than translation efficiency, we will perform control experiments to monitor mRNA levels under key optimized conditions. This will help confirm that the observed efficiency changes are primarily attributable to translation.

      (4) Data presentation and completeness (R#2)

      We will revise the presentation of data in figures (e.g., Figure 2) to use appropriate graph types for discrete data and ensure all units, incubation times, and conditions are clearly and consistently specified. Furthermore, we will add a paragraph to the Discussion addressing the study's limitations, specifically the potential implications of DTT removal for certain protein types.

      We are confident that these planned revisions will address the reviewers' recommendations and result in a stronger manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):           

      Summary:

      The authors have created a new model of KCNC1-related DEE in which a pathogenic patient variant (A421V) is knocked into a mouse in order to better understand the mechanisms through which KCNC1 variants lead to DEE.  

      Strengths:

      (1)  The creation of a new DEE model of KCNC1 dysfunction. 

      (2)  In Vivo phenotyping demonstrates key features of the model such as early lethality and several types of electrographic seizures. 

      (3)  The ex vivo cellular electrophysiology is very strong and comprehensive including isolated patches to accurately measure K+ currents, paired recording to measure evoked synaptic transmission, and the measurement of membrane excitability at different time points and in two cell types.

      We thank Reviewer 1 for these positive comments related to strengths of the study.   

      Weaknesses:

      (1) The assertion that membrane trafficking is impaired by this variant could be bolstered by additional data.

      We agree with this comment. However, given the technical challenges of standard biochemical experiments for investigating voltage-gated potassium channels (e.g., antibody quality), the lack of a Kv3.1-A421V specific antibody, and the fact that Kv3.1 is expressed in only a small subset of cells, we did not undertake this approach. However, we did perform additional experiments and analysis to improve the rigor of the experiments supporting our conclusion that membrane trafficking is impaired in the Kcnc1-A421V/+ mouse. 

      Such experiments support a highly significant and robust difference in our (albeit imperfect) measurement of the membrane:cytosol ratio of Kv3.1 immunofluorescence between WT and Kcnc1-A421V/+ mice, which is consistent with lack of membrane trafficking (Figure 3). In the revised manuscript, we have added additional data points to this plot and updated the representative example images using improved imaging techniques to better showcase how Kcnc1-A421V/+ PV-INs differ from age-matched WT littermate controls. We think the result is quite clear. Future biochemical experiments perhaps best performed in a culture system in vitro could provide additional support for this conclusion.

      (2) In some experiments details such as the age of the mice or cortical layer are emphasized, but in others, these details are omitted.

      We apologize for this omission. We have now clarified the age of the mice and cortical layer for each experiment in the Methods and Results sections as well as figure legends.   

      (3) The impairments in PV neuron AP firing are quite large. This could be expected to lead to changes in PV neuron activity outside of the hypersynchronous discharges that could be detected in the 2-photon imaging experiments, however, a lack of an effect on PV neuron activity is only loosely alluded to in the text. A more formal analysis is lacking. An important question in trying to understand mechanisms underlying channelopathies like KCNC1 is how changes in membrane excitability recorded at the whole cell level manifest during ongoing activity in vivo. Thus, the significance of this work would be greatly improved if it could address this question.

      Yes, the impairments in the neocortical PV-IN excitability are notably severe relative to other PV interneuronopathies that we and others have directly investigated (e.g., Kv3.1 or Kv3.2-/- knockout mice; Scn1a+/- mice). In the revised version of the manuscript, we have now added a more thorough in vivo 2P calcium imaging investigation and analysis of our in vivo 2P calcium imaging data of PV-IN (and presumptive excitatory cell) neural activity (Figure 8 and Supplementary Figure 9, Methods- lines 230-271 Results- lines 630-657, and Discussion lines- 795-814). 

      Because of the prominent recruitment of neuropil during presumptive myoclonic seizures, further investigation of individual neuronal excitability in vivo required a slightly different labeling strategy now using a soma-tagged GCaMP8m as well as a separate AAV containing tdTomato driven by the PV-IN-specific S5E2 enhancer. Our new results reveal an increase in the baseline calcium transient frequency in non-PV-INs, and reduced mean transient amplitudes in both non-PV cells and PV-INs. These interesting findings, which are consistent with attenuated PV-IN-mediated perisomatic inhibition leading to disinhibited excitatory cells in the Kcnc1-A421V/+ mice, link our in vivo results to the slice electrophysiology experiments. Of course, there are residual issues with the application of this technique to interneurons and the ability to resolve individual or small numbers of spikes, which likely explains the lack of genotype difference in calcium transient frequency in PV-INs.

      (4) Myoclonic jerks and other types of more subtle epileptiform activity have been observed in control mice, but there is no mention of littermate control analyzed by EEG. 

      We performed additional experiments as requested and did not observe myoclonic jerks or any other epileptic activity in WT control mice. We have included this data in the revised manuscript (Figure 9C).   

      Reviewer #2 (Public review):           

      Summary:

      Wengert et al. generated and thoroughly characterized the developmental epileptic encephalopathy phenotype of Kcnc1A421V/+ knock-in mice. The Kcnc1 gene encodes the Kv3.1 channel subunit. Analogous to the role of BK channels in excitatory neurons, Kv3 channels are important for the recurrent high-frequency discharge in interneurons by accelerating the downward hyperpolarization of the individual action potential. Various Kcnc1 mutations are associated with developmental epileptic encephalopathy, but the effect of a recurrent A421V mutation was somewhat controversial and its influence on neuronal excitability has not been fully established. In order to determine the neurological deficits and underlying disease mechanisms, the authors generated cre-dependent KI mice and characterized them using neonatal neurological examination, high-quality in vitro electrophysiology, and in vivo imaging/electrophysiology analyses. These analyses revealed excitability defects in the PV+ inhibitory neurons associated with the emergence of epilepsy and premature death. Overall, the experimental data convincingly support the conclusion.

      Strengths:

      The study is well-designed and conducted at high quality. The use of the Cre-dependent KI mouse is effective for maintaining the mutant mouse line with premature death phenotype, and may also minimize the drift of phenotypes which can occur due to the use of mutant mice with minor phenotype for breeding. The neonatal behavior analysis is thoroughly conducted, and the in vitro electrophysiology studies are of high quality.

      We appreciate these positive comments from Reviewer 2. 

      Weaknesses:

      While not critically influencing the conclusion of the study, there are several concerns.

      In some experiments, the age of the animal in each experiment is not clearly stated. For example, the experiments in Figure 2 demonstrate impaired K+ conductance and membrane localization, but it is not clear whether they correlated with the excitability and synaptic defects shown in subsequent figures. Similarly, it is unclear how old mice the authors conducted EEG recordings, and whether non-epileptic mice are younger than those with seizures. 

      We have now updated the manuscript to include clear report of age for all experiments including the impaired K<sup>+</sup> conductance (now Figure 3) and EEG (now Figure 9). There was no intention to omit this information. The recordings of K<sup>+</sup> conductance impairments in PV-INs from Kcnc1-A421V/+ mice were completed at P1621. Thus, we interpret the loss of potassium current density to be causally linked with the impairments in intrinsic physiological function at that same time-period in neocortical layer II-IV PV-INs and more subtly in PV-positive cells in the RTN and neocortical layer V PVINs.

      Mice used in the EEG experiments were P24-48, an age range which roughly corresponded with the midpoint on the survival curve for Kcnc1-A421V/+ mice. Although we saw significant mouse-to-mouse variability in seizure phenotype, no Kcnc1-A421V/+ mice completely lacked epilepsy or marked epileptiform abnormalities, neither of which were seen in WT mice. We did not detect a clear relationship between seizure frequency/type and mouse age. 

      The trafficking defect of mutant Kv3.1 proposed in this study is based only on the fluorescence density analysis which showed a minor change in membrane/cytosol ratio. It is not very clear how the membrane component was determined (any control staining?). In addition to fluorescence imaging, an addition of biochemical analysis will make the conclusion more convincing (while it might be challenging if the Kv3.1 is expressed only in PV+ cells).

      This relates to comment 3 of Reviewer 1. We agree that, in the initial submission of the manuscript, the evidence from IHC for Kv3.1 trafficking deficits was somewhat subtle. In the revised version of the paper, we have gathered additional replicates of this original experiment with improved imaging quality and clarify how the membrane component was specified, to now show a robust and highly significant (***P<0.001) decrease in membrane:cytosol Kv3.1 ratio. We have also now provided new example images better showcasing the deficits observed in the Kcnc1-A421V/+ mice (Figure 3). The membrane compartment was defined as the outermost 1 micron of the parvalbumin-defined cell soma (drawn blind to the Kv3.1b signal), and, importantly, all analysis was conducted blinded to mouse genotype. These measures help to ensure that the result is robust and unbiased. Nonetheless, we have added a paragraph in the Discussion section highlighting the limitations of our IHC evidence for trafficking impairment (Lines 868-883). 

      While the study focused on the superficial layer because Kv3.1 is the major channel subunit, the PV+ cells in the deeper cortical layer also express Kv3.1 (Chow et al., 1999) and they may also contribute to the hyperexcitable phenotype via negative effect on Kv3.2; the mutant Kv3.1 may also block membrane trafficking of Kv3.1/Kv3.2 heteromers in the deeper layer PV cells and reduce their excitability. Such an additional effect on Kv3.2, if present, may explain why the heterozygous A421V KI mouse shows a more severe phenotype than the Kv3.1 KO mouse (and why they are more similar to Kv3.2 KO). Analyzing the membrane excitability differences in the deep-layer PV cells may address this possibility.

      We appreciate this thoughtful suggestion. We have now provided data from neocortical layer V PV interneurons in the revised manuscript (Supplementary Figure 5). Abnormalities in intrinsic excitability from neocortical layer V PV-INs in Kcnc1A421V/+ mice were present, but less pronounced than in PV-INs from more superficial cortical layers. These results are consistent with the view that greater relative expression of Kv3.2 “dilutes” the impact of the Kv3.1 A421V/+ variant. More specific determination of whether the A421V/+ variant impairs membrane trafficking and/or gating of Kv3.2 remains unclear. 

      We attempted to assess how the mutant Kv3.1 affects Kv3.2 localization, but were unsuccessful due to the lack of reliable antibodies. After immunostaining mouse brain sections with two different anti-Kv3.2 antibodies, only one produced somewhat promising signal (see below). However, even in this case, Kv3.2 staining was successful only once (out of five independent staining experiments) and the signal varied across cortical regions, showing widespread cellular Kv3.2 signal in some areas (b, top panel), and barely detectable signal in others, regardless of Kv3.1 expression. In the remaining four attempts, we detected only ‘fiber-like’ immunostaining signal, further diminishing our confidence in anti-Kv3.2 antibody, although results could be improved with still further testing and refinement which we will attempt. Consequently, this important question remains unsolved in this study. 

      Author response image 1.

      Immunostaining of Kv3.1 and Kv3.2 in sagittal mouse brain sections. a) An example of intracellular Kv3.2 immunostaining signal, variable across the cortex of a WT mice independent of Kv3.1 expression b) Kv3.2 is detectable intracellularly in most of the cells in the top panel but barely detectable in the lowest panel. c) Representative image of Kv3.2 immunostaining signal in other sagittal mouse brain sections.

      We have discussed these important implications and limitations of our results in the Discussion (Lines 868-883). We agree with the Reviewer’s interpretation that an impact on Kv3.1/Kv3.2 heteromultimers across the neocortex may explain why the Kcnc1A421V/+ mouse exhibits a more severe phenotype than Kv3.1-/- or Kv3.2-/- mice (see below), a view which we have attempted to further clarify in the Conclusion.    

      In Table 1, the A421V PV+ cells show a depolarized resting membrane potential than WT by ~5 mV which seems a robust change and would influence the circuit excitability. The authors measured firing frequency after adjusting the membrane voltage to -65mV, but are the excitability differences less significant if the resting potential is not adjusted? It is also interesting that such a membrane potential difference is not detected in young adult mice (Table 2). This loss of potential compensation may be important for developmental changes in the circuit excitability. These issues can be more explicitly discussed.

      We do not entirely understand this finding and its apparent developmental component. It could be compensatory, as suggested by the Reviewer; however, it is transient and seems to be an isolated finding (i.e., it is not accompanied by compensation in other properties). It is also possible that this change in Kcnc1-A421V/+ PV-INs may reflect impaired/delayed development. We cannot test excitability at a meaningfully later time point as the mice are deceased.

      The revised version of the manuscript contains additional data (Supplementary Figure 4) showing that major deficits in intrinsic excitability are still observed even when the resting membrane potential is left unadjusted. These results are further discussed in the Results section (lines 522-523) and the Discussion section (lines 727-731).   

      Reviewer #3 (Public review):           

      Summary:

      Here Wengert et al., establish a rodent model of KCNC1 (Kv3.1) epilepsy by introducing the A421V mutation. The authors perform video-EEG, slice electrophysiology, and in vivo 2P imaging of calcium activity to establish disease mechanisms involving impairment in the excitability of fast-spiking parvalbumin (PV) interneurons in the cortex and thalamic PV cells.

      Outside-out nucleated patch recordings were used to evaluate the biophysical consequence of the A421V mutation on potassium currents and showed a clear reduction in potassium currents. Similarly, action potential generation in cortical PV interneurons was severely reduced. Given that both potassium currents and action potential generation were found to be unaffected in excitatory pyramidal cells in the cortex the authors propose that loss of inhibition leads to hyperexcitability and seizure susceptibility in a mechanism similar to that of Dravet Syndrome.  

      Strengths: 

      This manuscript establishes a new rodent model of KCNC1-developmental and epileptic encephalopathy. The manuscript provides strong evidence that parvabumin-type interneurons are impaired by the A421V Kv3.1 mutation and that cortical excitatory neurons are not impaired. Together these findings support the conclusion that seizure phenotypes are caused by reduced cortical inhibition.

      We thank Reviewer 3 for their view of the strengths of the study.

      Weaknesses:

      The manuscript identifies a partial mechanism of disease that leaves several aspects unresolved including the possible role of the observed impairments in thalamic neurons in the seizure mechanism. Similarly, while the authors identify a reduction in potassium currents and a reduction in PV cell surface expression of Kv3.1 it is not clear why these impairments would lead to a more severe disease phenotype than other loss-of-function mutations which have been characterized previously. Lastly, additional analysis of videoEEG data would be helpful for interpreting the extent of the seizure burden and the nature of the seizure types caused by the mutation.

      We agree with this comment(s) from Reviewer 3. We studied neurons in the reticular thalamus and layer V neocortical PV-INs since they are also linked to epilepsy pathogenesis and are known to express Kv3.1. However, for most of the study, we focused on neocortical layer II-IV PV-INs, because these cells exhibited the most robust impairments in intrinsic excitability. Cross of our novel Kcnc1-Flox(A421V)/+ mice to a cerebral cortex interneuron-specific driver that would avoid recombination in the thalamus, such as Ppp1r2-Cre (RRID:IMSR_JAX:012686), could assist in determining the relative contribution of thalamic reticular nucleus dysfunction to overall phenotype as used by (Makinson et al., 2017) to address a similar question; however, we have been unable to obtain this mouse despite extensive effort. There are of course other Kv3.1expressing neurons in the brain, including in the hippocampus, amygdala, and cerebellum, and we have provided additional discussion (Lines 731-736) of this issue.

      We further agree with the Reviewer that a major question in the field of KCNC1-related neurological disorders is the mechanistic underpinning of why the KCNC1-A421V variant leads to a more severe disease phenotype than other loss of function KCNC1 variants, and, further, why the mouse phenotype is more severe than the Kcnc1 knockout. Previous results and our own recordings in heterologous systems suggest that the A421V variant is more profoundly loss of function than the R320H variant (Oliver et al., 2017; Cameron et al., 2019; Park et al., 2019), which is consistent with A421V having a more severe disease phenotype. Relative to knockout of Kv3.1, our results are consistent with the view that the A421V exhibits dominant negative activity by reducing surface expression of Kv3.1 and/or Kv3.2 (an effect that would not occur in knockout mice), with a possible additional contribution of impairing gating of those Kv3.1-A421V variant containing Kv3.1/Kv3.2 heteromultimers by inclusion of A421V subunits into the heterotetramer. Our finding that the magnitude of total potassium current was reduced in PV-INs by ~50% is consistent with a combination of these various mechanisms but does not distinguish between them.

      In the revised version of the manuscript, we have provided a more complete discussion of these important remaining questions regarding our interpretation of how the severity of KCNC1 disorders relates to the biophysical features of the ion channel variant (lines 868883).

      Recommendations for the authors

      Reviewer #1 (Recommendations for the authors):          

      Major

      (1) The authors suggest that the reduced K+ current density in Kcnc1-A421V/+ neurons is due in part to impaired trafficking and cell surface expression of Kv3.1 in these neurons. The data supporting this claim aren't completely convincing. First, it's difficult to visualize a difference in Kv3.1 localization in the images shown in panel H, and importantly, it seems problematic that the method to assess Kv3.1 levels in membrane vs. cytosol relied on using PV co-staining to define the membrane compartment as the outermost 1 um of the PV-defined cell soma. This doesn't seem to be the best method to define the membrane compartment, as the PV signal should be largely cytosolic.

      As noted above, we have completed additional data collection to confirm our results, and have performed additional imaging and updated our example images to be more representative of the observed deficits in membrane Kv3.1 expression in the Kcnc1-A421V/+ mice. We attempted to identify a marker to more clearly label the membrane to combine with PV immunocytochemistry but were unable to do so despite some effort. 

      Is it possible that in control neurons, the cytosolic PV signal localizes within the membrane-bound Kv3.1 signal, with less colocalization, whereas in Kcnc1-A421V/+ neurons, there would be more colocalization of the cytosolic PV and improperly trafficked Kv3.1.? Could the data be presented in this way showing altered colocalization of Kv3.1 with PV?

      We do not entirely understand the nature of this concern. In our experiments, we utilized the PV signal to determine the cell membrane and cytosolic compartments in an unbiased manner using a 1-micron shell traced around/outside the edge of the PV signal to define the membrane compartment, with the remainder of the area (minus the nuclear signal defined by DAPI) defined as the cytosol (see Methods 176-186). Because we did not identify any alterations in PV signal or correlation between PV immunohistochemistry and tdTomato expression in Cre reporter strains between WT and Kcnc1-A421V/+ mice, we believe that our strategy for determining membrane:cytosol ratio of Kv3.1 in an unbiased manner is acceptable (albeit of course imperfect). 

      Alternatively, membrane fractionation could be performed on WT vs Kcnc1-A421V/+ neurons, followed by Western blotting with a Kv3.1 antibody to show altered proportions in the cytosolic vs. membrane protein fractions. It's important that these results are convincing, as the findings are mentioned in the Abstract, the Results section, and multiple times in the Discussion, although it is still unclear how much the potential altered trafficking contributes to the decrease in K+ currents versus changes in channel gating.

      Multiple technical barriers made it difficult for us to gain direct biochemical evidence for altered trafficking of the A421V/+ Kv3.1 variant (see above). It is not clear how membrane fractionation techniques could be easily applied in this case (at least by us) when PV-INs constitute 3-5% of all neocortical neurons. We further agree (as noted above) that it is difficult to properly disentangle the relative roles of impaired membrane trafficking vs. gating deficits to the observed effect; however, we think that both phenomena are likely occurring. In the revised version of the manuscript, we have more explicitly discussed these limitations in the Discussion section (Lines 868-883).   

      (2) More information is needed regarding the age of mice used for experiments for the following results (added to the Results section as well as figure legends):

      PV density (Supplementary Figure 1) 

      K+ current data (Figure 2A-G)       

      Kv3.1 localization (Figure 2H and I)        

      RTN electrophysiology (Supplementary Figure 3)

      Excitatory neuron electrophysiology (Figure 4)             

      In vivo 2P calcium imaging (Figure 7) 

      Video-EEG (Figure 8)

      We apologize for omitting this critical information. In the revised manuscript, we have provided the age of mice for each of our experiments in the results section, in the figure legend, and in the methods section.   

      (3) It's unclear why developmental milestones/behavioral assessments were only done at P5-P10. In the previous publication of another Kcnc1 LOF variant (Feng et al. 2024), no differences were found at P5-P10, and it was suggested in the discussion that this finding was "consistent with the known developmental expression pattern of Kv3.1 in mouse, where Kv3.1 protein does not appear until P10 or later". In that paper, they did find behavioral deficits at 2-4 months. Even though this model is more severe than the previous model, it would be interesting to determine if there are any behavioral deficits at a later time point (especially as they find more neurophysiological impairments at P32P42).

      As in our previous study, the lack of clear behavioral deficits in developmental milestones from P5-15 is potentially expected considering the developmental expression of Kv3.1, and we performed these experiments primarily to showcase that the Kcnc1-A421V/+ mice exhibit otherwise normal overall early development (although this could be an artifact of the sensitivity of our testing methods).

      For the revised manuscript, we have conducted additional experiments to investigate behavioral deficits in adult Kcnc1-A421V/+ mice. We found cognitive/learning deficits in both Kcnc1-A421V/+ mice relative to WT in both the Barnes maze (Figure 2A-C) and Ymaze (Figure 2D-F). Other aspects of animal behavior including cerebellar-related motor function are likely also impaired at post-weaning timepoints, and will be included in a forthcoming research study focusing on the motor function in these mice.  

      (4) In the Results section, it should be more clearly stated which cortical layer/layers are being studied. In some cases, it mentions layers 2-4, and in some, only layer 4, and in others, it doesn't mention layers at all. Toward the beginning of the Results section, the rationale for focusing on layers 2-4 to assess the effects of this variant should be well described and then, for each experiment, it should be stated which cortical layers were assessed. Related to this point, it seems electrophysiology was only done in layer 4; the rationale for this should also be included.

      We have now clarified which neocortical layers were under investigation in the study. All PV-INs were targeted in somatosensory layers II-IV, while excitatory neurons were either cortical layer IV spiny stellate cells or pyramidal cells. Paired recordings were also completed in layer IV. We have also more explicitly articulated our rationale for looking at PV-INs in layers II-IV to examine the cellular/circuitlevel impact of Kv3.1 in a model of developmental and epileptic encephalopathy (Lines 487-491). 

      (5) Kcnc1-A421V/+ PV neurons showed more robust impairments in AP shape and firing at P32-42 than at P16-21 (Figure 3), and only showed synaptic neurotransmission alterations at P32-42 (Figure 6). Thus, it's unclear why Kcnc1-A421V/+ excitatory neurons were only assessed at P16-21 (Figure 4 and Supplementary Figure 4 related to Figure 5), particularly if only secondary or indirect effects on this population would be expected.

      We appreciate this excellent point raised by the Reviewer and we have taken the suggestion to examine excitatory neurons at P32-42 in addition to the earlier juvenile timepoint. Our new results from the later timepoint are similar to our results at P16-21: Excitatory neurons show no statistically significant impairments in intrinsic excitability at either of the two timepoints examined (Supplementary Figure 7). This adds support to our original conclusion that PV-INs represent the major driver of disease pathology across development.   

      (6) The 2P calcium imaging experiments are potentially interesting, however, a relationship between these results and the electrophysiology results for PV neurons is lacking. Was there an attempt to assess the frequency and/or amplitude of calcium events specifically in PV neurons, outside of the hypersynchronous discharges, to determine whether there are differences between WT and Kcnc1-A421V/+, as was seen in the electrophysiological analyses? It does seem there are some key differences between the two experiments (age: later timepoint for 2P vs. P16-21 and P32-42, layer: 2/3 vs. 4, and PV marking method: virus vs. mouse line), but the electrophysiological differences reported were quite strong. Thus, it would be surprising if there were no alterations in calcium activity among the Kcnc1-A421V/+ PV neurons.

      In our initial experiments, the prominent neuropil GCaMP signal in Kcnc1-A421V/+ mice rendered it difficult to distinguish and accurately describe baseline neuronal excitability in PV-INs and non-PV cells. In our revised manuscript, we utilized a soma-tagged GCaMP8m and separately labeled PV-INs through S5E2-tdTomato. This strategy made it possible to assess the amplitude and frequency of calcium transients in both PV-positive and PV-negative cells in vivo. We have updated the description of our methods (lines 230-271) and our results (lines 630-657) in the revised manuscript.

      As noted above, our more detailed analysis of somatic calcium transients in PV-IN and non-PV cells during quiet rest (Figure 8 and Supplementary Figure 9) shows that PV-INs from Kcnc1-A421V/+ mice are abnormally excitable- having reduced transient amplitude relative to WT controls. Interestingly, non-PV cells also exhibited an increased calcium transient frequency and reduced amplitude which is potentially consistent with reduced perisomatic inhibition causing disinhibition in cortical microcircuits. We again highlight that the slow kinetics of GCaMP combined with the calcium buffering and brief spikes of PVINs render quantification of action potential frequency and comparisons between groups difficult.  

      (7) As mentioned above, it would be helpful to state the time points or age ranges of these experiments to better understand the results and relate them to each other. For example, the 2P imaging showed apparent myoclonic seizures in 7/7 Kcnc1-A421V/+ mice (recorded for a total of 30-50 minutes/mouse), but the video-EEG showed myoclonic seizures in only 3/11 Kcnc1-A421V/+ mice (recorded for 48-72 hours/mouse). Were these experiments done at very different age ranges, so this difference could be due to some sort of progression of seizure types and events as the mice age? Is it possible these are not the same seizure types (even though they are similarly described)? This discrepancy should be discussed.

      Mice in the EEG experiments were between the ages of P24 and 48, slightly younger than the age in which we carried out the in vivo calcium imaging experiments (>P50). Therefore, an age-related exacerbation in myoclonic jerks is possible. 

      As is highlighted by the Reviewer, it is interesting that the myoclonic seizures were only detected in a portion of the Kcnc1-A421V/+ mice during EEG monitoring (4/12). We believe that the difference is most likely driven by more sensitive detection of the myoclonic jerk activity and behavior in the 2P imaging of neuropil cellular activity compared to our video-EEG monitoring and 2P imaging of soma-tagged GCaMP. We have occasionally observed repetitive myoclonic jerking in mice that appears highly localized (i.e. one forepaw only) suggesting that the myoclonic seizures exist on a spectra of severity from focal to diffuse. It is therefore possible that myoclonic events and electrographic activity may be slightly underestimated in our video-EEG experiments? 

      We have now added a few lines discussing this discrepancy in the Discussion (lines 809814).   

      (8) Myoclonic jerks and other types of more subtle epileptiform activity have been observed in control mice. Was video-EEG performed on control mice? These data should be added to Figure 8.

      We have added recordings in control WT mice (N=4). We did not detect myoclonic jerks or other epileptiform activity in the control mice (Figure 9).  

      Minor

      (1) In the first Results section, Line 365, the P value (P<0.001) is different from that in the legend for Figure 1, line 743 (P<0.0001).

      We have fixed this discrepancy. 

      (2) For Supplementary Figure 1, it would be helpful to show images that span the cortical layers (1-6), as PV and Kv3.1 are both expressed across the cortical layers.

      We have updated Supplementary Figure 1 with better example images that span the cortical layers.    

      (3) Error bars should be added to the line graphs in Supplementary Figure 2, particularly panels B and C. Some of the differences appear small considering the highly significant p-values (i.e. body weight at P7 and brain weight at P21).

      The values shown in Supplementary Figure 2D-E are percentages of mice displaying a particular characteristic, so there is no variance for the data.

      Supplementary Figure 2B-C actually do contain error bars plotted as SEM, however, because of the large number of N and small degree of variance in the measurements, the error bars are not apparent in the graphs. This has been noted in the Supplementary Figure 2 legend for clarity. 

      (4) In Figure 3, although the Kcnc1-A421V/+ neurons have elevated AP amplitudes relative to WT, the representative traces for P16-21 and P32-42 groups appear strikingly opposite (traces in B in G appear to have much higher amplitudes than those in C and H). As this is one of the three AP phenotypes described, it would be nice to have it reflected in the traces.

      We have updated our example traces to better represent our main findings including AP amplitude for both P16-21 and P32-42 timepoints.  

      (5) Were any effects on the AHP assessed in the electrophysiology experiments? As other studies have reported the effects of altered Kv3 channel activity on AHP, this parameter could be interesting to report as well.

      We have now provided data on the afterhyperpolarization for each condition displayed in the Supplementary data tables. Interestingly, we failed to detect significant differences in AHP between WT and Kcnc1-A421V/+ PV-INs, RTN neurons, or pyramidal cells, although we did identify differences in the dV/dt of the repolarization phase of the AP.   

      (6) The figure legend for Figure 7 has errors in the panel labeling (D instead of C, and two Fs).

      This error has been corrected in the revised manuscript.

      Reviewer #3 (Recommendations for the authors):

      Specific comments and questions for the authors:         

      (1) Do the authors provide a reason for why the juvenile animals are unaffected by the A421V mutation? Is it that PV cells have not fully integrated at this early time point or that Kv3.1 expression is low? Is the developmental expression profile of Kv3.1 in PV cells known and if so could the authors update the discussion with this information?

      We interpret the normal early developmental milestones (P5-P15) to reflect that Kcnc1-A421V/+ mice exhibit the onset of their neurological impairment at the same time that PV-INs upregulate Kv3.1, develop a fast-spiking physiological phenotype, and integrate into functional circuits in the third and fourth postnatal weeks. We have updated the discussion (Line 780-782) with this information and more clearly describe our interpretation of these early-life behavioral experiments.   

      (2) I would like to see a more complete analysis of the Video-EEG data that is included in Figure 8. What was the seizure duration and frequency? Were there spike-wave seizure types observed? Were EEG events that involve thalamocortical circuitry affected such as spindles? Was sleep architecture impaired in the model? Were littermate control animals recorded?

      Although classical convulsive seizures represent only part of the overall epilepsy phenotype that this mouse exhibits, we agree that reporting seizure duration and frequency is important. We have now included this in our revised manuscript (line 624-626). We have also now added WT control mice to our dataset, and, as expected, we failed to observe any epileptic features in our WT recordings.

      In our EEG experiments, we did not record EMG activity in the mouse to allow for unambiguous determination of sleep vs. quiet wakefulness. For that reason, and because we believe it beyond the scope of this particular study, we did not examine sleep-related EEG phenomena such as spindles or sleep architecture. We have, however, added a line in the discussion (line 771-774) suggesting that future studies focus on a more thorough investigation of the EEG activity in these animals. 

      (3) The in vivo calcium imaging data shows synchronous bursts in A421V animals which is in agreement with the synchronous bursts observed in the EEG. Overall the analysis of the in vivo calcium imaging data appears to be rudimentary and perhaps this is a missed opportunity. What additional insights were gained from this technically demanding experiment that were not obtained from the EEG recordings?

      As noted above, in the revised version of the manuscript, we have conducted additional experiments which allowed us to separately examine PV-IN and non-PV neuron excitability via 2P in vivo calcium imaging. This required an alternative strategy to label individual neuronal somata without contamination by the robust neuropil signal that we observed in the approach undertaken in the original submission. We’ve described the details of this new approach in methods (Lines 230-271) and results section (lines 630-657).

      Our new results (Figure 8 and Supplementary Figure 9) reveal that, during quiet rest, neocortical PV-INs from Kcnc1-A421V/+ mice exhibit a reduction in calcium transient amplitude during quiet wakefulness and that non-PV cells exhibit altered transient frequency and amplitude. Overall, we believe that these results are consistent with the view that PV-IN-mediated perisomatic inhibition is compromised in Kcnc1-A421V/+ mice which leads to a downstream hyperexcitability in excitatory neurons within cortical microcircuits.  

      (4) The increased severity of seizure phenotypes observed in the A421V model relative to knockout mice is interesting but also confusing given what is known about this mutation. As the authors point out, a possible explanation is that the mutation is acting in a dominant negative manner, where mutant Kv3.1 channels compete with other Kvs that would otherwise be able to partially compensate for the loss of Kv function. Alternatively, the A421V mutation might act by affecting the trafficking of heterotetrameric Kv3 channels to the membrane. Can the authors clarify why a trafficking deficit would produce a different effect than a loss of function mutation? Are the authors proposing that a hypomorphic mutation involving both a partial trafficking deficit and a dominant negative effect of those channels that are properly localized is more severe than a "clean" loss of function? The roughly 50% loss of potassium current absent a change in gating would be expected to behave like a loss-of-function mutation. This might be addressed by comparing the surface expression of the other Kv channels and/or through the use of Kv3.1-selective pharmacology.

      These are excellent points raised by the Reviewer. As noted above, we have endeavored to clarify our hypothesis as to the basis of this phenomenon, although the mechanistic basis for the more severe phenotype in the Kcnc1-A421V/+ mouse relative to the Kv3.1 knockout is not entirely clear. Our physiology results and the evidence presented supporting a trafficking impairment, are consistent with dominant negative action of the Kv3.1 A421V variant at the level of channel gating and/or trafficking. To restate, we think the Kcnc1-A421V/+ heterozygous variant is more severe than a Kv3.1 knockout for (at least) three reasons: variant Kv3.1 is incorporated into Kv3.1/Kv3.2 heterotetramers to (1) impair trafficking to the membrane as well as (2) alter the electrophysiological function of those channels that do successfully traffic to the membrane (while Kv3.1 knockout affects Kv3.1 only), and (3) the heterozygous variant may escape compensatory upregulation of Kv3.2 and which is known to occur in Kv3.1 knockout mice.

      For example, our data suggests and is consistent with the view that heterotetramers of WT Kv3.1 and Kv3.2 potentially come together with the A421V Kv3.1 subunit in the endoplasmic reticulum and then fail to traffic to the membrane due to the presence of one or more A421V subunit(s), as evidenced by increased Kv3.1 staining in the cytosol in the Kcnc1-A421V/+ mouse relative to WT. This is in contrast to what would occur in the Kv3.1knockout mice as there is no subunit produced from the null allele to impair WT Kv3.2 subunits from forming fully functional Kv3.2 homotetramers to then reach the cell surface and function properly. This is one specific possible mechanism for dominant negative activity.

      A non-mutually-exclusive mechanism is that inclusion of one or more Kv3.1 A421V subunits into Kv3 heterotetramers impairs gating and prevents potassium flux such that, even if the tetramer does reach the membrane, that entire tetramer fails to contribute to the total potassium current. This is another possible mechanism for dominant negative function of the A421V subunit.

      Experimental elucidation of the precise mechanism of the dominant negative activity of the A421V Kcnc1 variant is beyond the scope of this study; yet, our lab is continuing to work on this. It will likely require dose-response experiments in which various ratios of WT and Kv3.1 A421V subunits are co-expressed in heterologous cells and then recorded for an overall effect on potassium current similar to (Clatot et al., 2017).

      In the revised manuscript, we have updated our discussion of these mechanistic considerations for KCNC1-related epilepsy syndromes in lines 868-883 in the Discussion. 

      References

      Cameron JM et al. (2019) Encephalopathies with KCNC1 variants: genotype-phenotypefunctional correlations. Annals of Clinical and Translational Neurology 6:1263– 1272.

      Clatot J, Hoshi M, Wan X, Liu H, Jain A, Shinlapawittayatorn K, Marionneau C, Ficker E, Ha T, Deschênes I (2017) Voltage-gated sodium channels assemble and gate as dimers. Nature Communications 8.

      Makinson CD, Tanaka BS, Sorokin JM, Wong JC, Christian CA, Goldin AL, Escayg A, Huguenard JR (2017) Regulation of Thalamic and Cortical Network Synchrony by Scn8a. Neuron 93:1165-1179.e6.

      Oliver KL et al. (2017) Myoclonus epilepsy and ataxia due to KCNC1 mutation: Analysis of 20 cases and K+ channel properties. Annals of Neurology 81.

      Park J et al. (2019) KCNC1-related disorders: new de novo variants expand the phenotypic spectrum. Annals of Clinical and Translational Neurology 6:1319–1326.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      (1) A detailed comparison between this work and the work of Sun et al. on experimental protocols and reagents in the main text will be beneficial for readers to assess critically.

      We have added a Key Reagents Table outlining the key reagents used in our study. In terms of experimental protocols, we replicated those described by Sun et al. in most instances and described any differences when present. With this resubmission, we included additional ZnMP accumulation experiments in liquid media (see point 3 below).

      (2) The GaPP used by Sun et al. (purchased from Frontier Scientific) is more effective in killing the worm than the one used in this study (purchased from Santa Cruz). Is the different outcome due to the differences in reagents? Moreover, Sun et al. examined the lethality after 3-4 days, while this work examined the lethality after 72 hours. Would the extra 24 hours make any difference in the result?

      We now cite product vender differences as a possible reason for the observed difference in worm death, as the reviewer suggests, on page 8 (see text below) and include these differences in the Key Reagents Table. We also now stress the fact that our experiments included different doses of GaPP and the use of eat-2 mutants as an additional control, which we believe adds rigor and demonstrates the potency of GaPP in our experiments. We decided on assessment at 72 hours, as we deemed it a less nebulous time point as compared to 3-4 days. Most of the observed worm death occurred earlier in this interval, so we believe it is unlikely that large group differences would emerge after an additional 24 hours.

      “Exposing worms to GaPP, a toxic heme analog, we observed that nematodes deficient in HRG-9 and HRG-10 displayed increased survival compared to WT worms, consistent with prior work,[13] though the between-group difference was markedly smaller in our study. We required higher GaPP concentrations to induce lethality, potentially due to product vendor differences, but did observe a clear dose-dependent effect across strains. Although it was previously proposed that the survival benefit seen in worms lacking HRG-9 and HRG-10 resulted from reduced transfer from intestinal cells after GaPP ingestion, our data suggest the reduced lethality is more likely due to decreased environmental GaPP uptake. Supporting this notion, DKO worms exhibited lawn avoidance, reduced pharyngeal pumping, and modestly lower intestinal ZnMP accumulation when exposed to this fluorescent heme analog on agar plates. In liquid media, DKO worms demonstrated higher fluorescence, but only in ZnMP-free conditions, suggesting the presence of gut granule autofluorescence. Furthermore, survival following exposure to GaPP was highest in eat-2 mutants, despite heme trafficking being unaffected in this strain.”

      (3) This work reported the opposite result of Sun et al. for the fluorescent ZnMP accumulation assay. However, the experimental protocols used by the two studies are massively different. Sun et al. did the ZnMP staining by incubating the L4-stage worms in an axenic mCeHR2 medium containing 40 μM ZnMP (purchased from Frontier Scientific) and 4 μM heme at 20 ℃ for 16 h, while this work placed the L4-stage worms on the OP50 E. coli seeded NGM plates treated with 40 μM ZnMP (purchased from Santa Cruz) for 16 h. The liquid axenic mCeHR2 medium is bacteria-free, heme-free, and consistent for ZnMP uptake by worms. This work has mentioned that the hrg-9 hrg-10 double null mutant has bacterial lawn avoidance and reduced pharyngeal pumping phenotypes. Therefore, the ZnMP staining protocol used in this work faces challenges in the environmental control for the wild type vs. the mutant. The authors should adopt the ZnMP staining protocol used by Sun et al. for a proper evaluation of fluorescent ZnMP accumulation.

      We agree with this comment. As such, we performed the ZnMP assay in liquid media conditions, as now described on page 13:

      “For liquid media experiments, three generations of worms were cultured in regular heme (20 uM) axenic media, with the first two generations receiving antibiotic-supplemented media (10 mg/ml tetracycline) and the 3<sup>rd</sup> generation cultivated without antibiotic. L4 worms from the 3<sup>rd</sup> generation were placed in media containing 40uM ZnMP for 16 hours before being prepared and mounted for imaging as above. Worms were imaged on Zeiss Axio Imager 2 at 40x magnification, with image settings kept uniform across all images. Fluorescent intensity was measured within the proximal region of the intestine using ImageJ.”

      In heme-free media, both WT and DKO worms invariably entered L1 arrest, thus we were not able to replicate the results reported by Sun et al. Using media containing heme, we did see an increase in fluorescence, but this was only in the ZnMP-free condition, indicating that the increased signal was attributable to autofluorescence. This is a known phenomenon associated with gut granules in C. elegans in the setting of oxidative stress. The results of these experiments are now summarized on page 6:

      “DKO nematodes at the L4 larval stage were previously shown to accumulate the fluorescent heme analog zinc mesoporphyrin IX (ZnMP) in intestinal cells in low-heme (4 µM) liquid media. While attempting to replicate this experiment, we observed that both wildtype and DKO nematodes entered L1 arrest under these conditions. Therefore, to allow for developmental progression, we grew worms on standard OP50 E. coli plates and in media containing physiological levels of heme (20 µM). We then examined whether differences in ZnMP uptake persisted under these basal conditions. DKO worms grown on ZnMP-treated E. coli plates displayed significantly reduced intestinal ZnMP fluorescence compared to N2 (Figure 1B and C). Using basal heme media with ZnMP, there was no significant difference in ZnMP fluorescence between DKO and wildtype nematodes, although DKO worms grown in media without ZnMP exhibited significantly higher autofluorescence (Figure 1D and E). To test whether autofluorescence may have contributed to the higher fluorescent intensities previously reported in heme-deficient DKO worms, we repeated this experiment on agar plates under starved conditions but did not observe a difference between groups (Figure 1B).”

      (4) A striking difference between the two studies is that Sun et al. emphasize the biochemical function of TANGO2 homologs in heme transporting with evidence from some biochemical tests. In contrast, this work emphasizes the physiological function of TANGO2 homologs with evidence from multiple phenotypical observations. In the discussion part, the authors should address whether these observed phenotypes in this study can be due to the loss of heme transporting activities upon eliminating TANGO2 homologs. This action can improve the merit of academic debate and collaboration.

      Thank you for this suggestion. The following text has been added to the Discussion section (page 9):

      “In addition to altered pharyngeal pumping, DKO worms displayed multiple previously unreported phenotypic features, suggesting a broader metabolic impairment and reminiscent of some clinical manifestations observed in patients with TDD. Elucidating the mechanisms underlying this phenotype, and whether they reflect a core bioenergetic defect, is an active area of investigation in our lab. Several C. elegans heme-responsive genes have been characterized, revealing relatively specific defects in heme uptake or utilization rather than broad organismal dysfunction. For example, hrg-1 and hrg-4 mutants exhibit impaired growth only under heme-limited conditions,[23] and hrg-3 loss affects brood size and embryonic viability specifically when maternal heme is scarce.[24] ]By contrast, hrg-9 and hrg-10 mutants exhibit the most severe organismal phenotypes of the hrg family, to date, including reduced pharyngeal pumping, decreased motility, shortened lifespan, and smaller broods, even when fed a heme-replete diet.”

      Reviewer #2 (Public review):

      (1) The manuscript is written mainly as a criticism of a previously published paper. Although reproducibility in science is an issue that needs to be acknowledged, a manuscript should focus on the new data and the experiments that can better prove and strengthen the new claims.

      Thank you for this suggestion. While the primary intent of this study was to replicate key findings from the 2022 publication by Sun et al., the revised manuscript now emphasizes underlying mechanisms more broadly rather than focusing narrowly on that prior publication.

      (2) The current presentation of the logic of the study and its results does not help the authors deliver their message, although they possess great potential.

      We have attempted to rectify this through substantial revision of the Discussion section and other places throughout the manuscript.

      (3) The study is missing experiments to link hrg-9 and hrg-10 more directly to bioenergetic and oxidative stress pathways.

      The reviewer is correct in this assertion, but it was not our intent to definitively prove this link or, indeed, the primary mechanism of TANGO2 in the present manuscript. This said, we are actively engaged in this endeavor in our lab and anticipate these data will be published in a separate, forthcoming publication.

      We have added additional references pertaining to hrg-9 enrichment as part of the mitochondrial unfolded protein response (page 10) and a comparison of the phenotype observed in hrg-9 and hrg-10 deficient worms versus those lacking other proteins in the hrg family (page 9).

      Reviewer #3 (Public review):

      (1) The authors stress - with evidence provided in this paper or indicated in the literature - that the primary role of TANGO2 and its homologues is unlikely to be related to heme trafficking, arguing that observed effects on heme transport are instead downstream consequences of aberrant cellular metabolism. But in light of a mounting body of evidence (referenced by the authors) connecting more or less directly TANGO2 to heme trafficking and mobilization, it is recommended that the authors comment on how they think TANGO2 could relate to and be essential for heme trafficking, albeit in a secondary, moonlighting capacity. This would highlight a seemingly common theme in emerging key players in intracellular heme trafficking, as it appears to be the case for GAPDH - with accumulating evidence of this glycolytic enzyme being critical for heme delivery to several downstream proteins.

      TANGO2 is essential for mitochondrial health, albeit in a yet unknown capacity. In the absence of TANGO2, defects in heme trafficking may be secondary sequelae of mitochondrial dysfunction. We would point out that prior studies that attempted to show that TANGO2 and its homologs are involved in heme trafficking proposed very different mechanisms (direct binding vs. membrane protein interaction) and relied on artificially low or high heme conditions to produce these effects. We have attempted to address these more clearly in the Discussion section and have added a fifth figure to summarize our current unifying theory for how heme levels and mitochondrial stress may be linked.

      (2) The observation - using eat-2 mutants and lawn avoidance behaviour - that survival patterns can be partially explained by reduced consumption, is fascinating. It would be interesting to quantify the two relative contributions.

      We have completed additional ZnMP experiments in liquid media at the reviewers’ request. This experimental condition eliminates lawn avoidance as a factor in consumption. Fluorescent intensity was significantly higher in the DKO worms in media lacking ZnMP, indicating increased autofluorescence in DKO worms, while signal was not significantly different in media with ZnMP.

      (3) In the legend to Figure 1A it's a bit unclear what the differently coloured dots represent for each condition. Repeated measurements, worms, independent experiments? The authors should clarify this.

      The following sentence has been added to the legend for Figure 1:

      “Each dot represents the number of offspring laid by one adult worm on one GaPP-treated plate after 24 hours.”

      (4) It would help if the entire fluorescence images (raw and processed) for the ZnMP treatments were provided. Fluorescence images would also benefit Figure 1B.

      Fluorescent intensity values pertaining to the ZnMP experiments are included in our Extended Data supplement, and we have added representative images to Figure 1, per the reviewer’s request. We thank the reviewer for this helpful suggestion. We would be happy to upload raw images to an open-access repository if deemed necessary by the editorial team.

      (5) Increasingly, the understanding of heme-dependent roles relies on transient or indirect binding to unsuspected partners, not necessarily relying on a tight affinity and outdating the notion of heme as a static cofactor. Despite impressive recent advancements in the detection of these interactions (for example https://doi.org/10.1021/jacs.2c06104; cited by the authors), a full characterisation of the hemome is still elusive. Sandkuhler et al. deemed it possible but seem to question that heme binding to TANGO2 occurs. However, Sun et al. convincingly showed and characterised TANGO2 binding to heme. It is recommended that the authors comment on this.

      We believe it is plausible that TANGO2 binds heme (as do hundreds of other proteins), especially as it has been shown to bind other hydrophobic molecules. However, we also note that a separate paper examining the role of TANGO2 in heme transport posited that GAPDH is the sole heme binding partner for cytoplasmic transport (https://doi.org/10.1038/s41467-025-62819-2), contradicting the originally posited theory of how TANGO2 functions. This is described in the Discussion section and, as noted above, we have added an additional figure to demonstrate our unifying hypothesis for why TANGO2 may be important in the low-heme state, irrespective of any direct effect on heme trafficking.

      Additional comments and revisions:

      (1) It was suggested that a triple mutant (eat-2; hrg-9; hrg-10) be tested to determine the primary driver of GaPP toxicity. We appreciate this suggestion, but we offer the following rationale for why these experiments were not pursued. The eat-2 mutant, which lacks a nicotinic acetylcholine receptor subunit in pharyngeal muscles, was included solely as a dietary restriction control to illustrate that reduced GaPP toxicity in the hrg-9/10 double mutant could arise from poor feeding rather than defective heme transport. Both eat-2 and hrg-9/10 mutants exhibit markedly reduced feeding but via different mechanisms. In our assays, GaPP survival was inversely correlated with ingestion rate: eat-2 animals, which feed the least, showed the highest survival, while hrg-9/10 mutants showed intermediate feeding and intermediate survival. Consistent with this, eat-2 worms also displayed the lowest ZnMP accumulation.

      (2) GaPP solution was added to NGM plates after seeding with OP50. This is now expressly stated in the Methods section (page 15). We would note that Sun et al. mixed GaPP in with NGM in the liquid phase. We would expect that if there were a difference in GaPP exposure due to these different protocols, worms in our experiment would have received higher GaPP concentrations.

      “Standard NGM plates were treated with 1, 2, 5, or 10 µM gallium protoporphyrin IX (GaPP; Santa Cruz) after seeding with OP50. Plates were swirled to ensure an even distribution of GaPP and allowed to dry completely.

      (3) The manuscript has been reworked to read as more of an independent study rather than a rebuttal of prior work, though the primary objective of validating prior work remains unchanged.

      (4) Several technical details of experiments have been moved from the main text to the materials and methods section.

      (5) One reviewer noted that the figure numbering should be adjusted. Numbering does not progress sequentially (i.e., 1A…1B…2A…2B) early in the text, because we have opted to consolidate data pertaining to heme analog experiments in Figure 1 and behavioral data in Figure 2.

      (6) “Kingdoms” has been changed to “domains” (page 4).

      (7) Example images are now included for Figure 1B, as noted above.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment:

      This study introduces an important approach using selection linked integration (SLI) to generate Plasmodium falciparum lines expressing single, specific surface adhesins PfEMP1 variants, enabling precise study of PfEMP1 trafficking, receptor binding, and cytoadhesion. By moving the system to different parasite strains and introducing an advanced SLI2 system for additional genomic edits, this work provides compelling evidence for an innovative and rigorous platform to explore PfEMP1 biology and identify novel proteins essential for malaria pathogenesis including immune evasion.

      Reviewer #1 (Public review):

      One of the roadblocks in PfEMP1 research has been the challenges in manipulating var genes to incorporate markers to allow the transport of this protein to be tracked and to investigate the interactions taking place within the infected erythrocyte. In addition, the ability of Plasmodium falciparum to switch to different PfEMP1 variants during in vitro culture has complicated studies due to parasite populations drifting from the original (manipulated) var gene expression. Cronshagen et al have provided a useful system with which they demonstrate the ability to integrate a selectable drug marker into several different var genes that allows the PfEMP1 variant expression to be 'fixed'. This on its own represents a useful addition to the molecular toolbox and the range of var genes that have been modified suggests that the system will have broad application. As well as incorporating a selectable marker, the authors have also used selective linked integration (SLI) to introduce markers to track the transport of PfEMP1, investigate the route of transport, and probe interactions with PfEMP1 proteins in the infected host cell.

      What I particularly like about this paper is that the authors have not only put together what appears to be a largely robust system for further functional studies, but they have used it to produce a range of interesting findings including:

      Co-activation of rif and var genes when in a head-to-head orientation.

      The reduced control of expression of var genes in the 3D7-MEED parasite line.

      More support for the PTEX transport route for PfEMP1.

      Identification of new proteins involved in PfEMP1 interactions in the infected erythrocyte, including some required for cytoadherence.

      In most cases the experimental evidence is straightforward, and the data support the conclusions strongly. The authors have been very careful in the depth of their investigation, and where unexpected results have been obtained, they have looked carefully at why these have occurred.

      We thank the reviewer for the kind assessment and the comments to improve the paper.

      (1) In terms of incorporating a drug marker to drive mono-variant expression, the authors show that they can manipulate a range of var genes in two parasite lines (3D7 and IT4), producing around 90% expression of the targeted PfEMP1. Removal of drug selection produces the expected 'drift' in variant types being expressed. The exceptions to this are the 3D7-MEED line, which looks to be an interesting starting point to understand why this variant appears to have impaired mutually exclusive var gene expression and the EPCR-binding IT4var19 line. This latter finding was unexpected and the modified construct required several rounds of panning to produce parasites expressing the targeted PfEMP1 and bind to EPCR. The authors identified a PTP3 deficiency as the cause of the lack of PfEMP1 expression, which is an interesting finding in itself but potentially worrying for future studies. What was not clear was whether the selected IT4var19 line retained specific PfEMP1 expression once receptor panning was removed.

      We do not have systematic long-term data for the Var19 line but do have medium-term data. After panning the Var19 line, the binding assays were done within 3 months without additional panning. The first binding assay was 2 months after the panning and the last binding assays three weeks later, totaling about 3 months without panning. While there is inherent variation in these assays that precludes detection of smaller changes, the last assay showed the highest level of binding, giving no indication for rapid loss of the binding phenotype. Hence, we can say that the binding phenotype appears to be stable for many weeks without panning the cells again and there was no indication for a rapid loss of binding in these parasites.

      Systematic long-term experiments to assess how long the Var19 parasites retain binding would be interesting, but given that the binding-phenotype appears to remain stable over many weeks or even months, this would only make sense if done over a much longer time frame. Such data might arise if the line is used over extended times for a specific project in which case it might be advisable to monitor continued binding. We included a statement in the discussion that the binding phenotype was stable over many weeks but that if long-term work with this line is planned, monitoring the binding phenotype might be advisable: “In the course of this work the binding phenotype of the IT4var19 expressor line remained stable over many weeks without further panning. However, given that initial panning had been needed for this particular line, it might be advisable for future studies to monitor the binding phenotype if the line is used for experiments requiring extended periods of cultivation.”

      (2) The transport studies using the mDHFR constructs were quite complicated to understand but were explained very clearly in the text with good logical reasoning.

      We are aware of this being a complex issue and are glad this was nevertheless understandable.

      (3) By introducing a second SLI system, the authors have been able to alter other genes thought to be involved in PfEMP1 biology, particularly transport. An example of this is the inactivation of PTP1, which causes a loss of binding to CD36 and ICAM-1. It would have been helpful to have more insight into the interpretation of the IFAs as the anti-SBP1 staining in Figure 5D (PTP-TGD) looks similar to that shown in Figure 1C, which has PTP intact. The anti-EXP2 results are clearly different.

      We realize the description of the PTP1-TGD IFA data and that of the other TGDs (see also response to Recommendation to authors point 4 and reviewer 2, major points 6 and 7) was rather cursory. The previously reported PTP1 phenotype is a fragmentation of the Maurer’s clefts into what in IFA appear to be many smaller pieces (Rug et al 2014, referenced in the manuscript). The control in Fig. 5D has 13 Maurer’s cleft spots (previous work indicates an average of ~15 MC per parasite, see e.g. the originally co-submitted eLife preprint doi.org/10.7554/eLife.103633.1 and references therein). The control mentioned by the reviewer in Fig. 1C has about 22 Maurer’s clefts foci, at the upper end of the typical range, but not unusual. In contrast, the PTP1-TGD in Fig. 5D, has more than 30 foci with an additional cytoplasmic pool and additional smaller, difficult to count foci. This is consistent with the published phenotype in Rug et al 2014. The EXP1 stained cell has more than 40 Maurer’s cleft foci, again beyond what typically is observed in controls. Therefore, these cells show a difference to the control in Fig. 5 but also to Fig. 1C. Please note that we are looking at two different strains, in Fig. 1 it is 3D7 and in Fig. 5 IT4. While we did not systematically assess this, the Maurer’s clefts number per cell seemed to be largely comparable between these strains (Fig. 10C and D in the other eLife preprint doi.org/10.7554/eLife.103633.1). 

      Overall, as the PTP1 loss phenotype has already been reported, we did not go into more experimental detail. However, we now modified the text to more clearly describe how the phenotype in the PTP1-TGD parasites was different to control: “IFAs showed that in the PTP1-TGD parasites, SBP1 and PfEMP1 were found in many small foci in the host cell that exceeded the average number of ~ 15 Maurer’s clefts typically found per infected RBC [66] (Fig. 5D). This phenotype resembled the previously reported Maurer’s clefts phenotype of the PTP1 knock out in CS2 parasites [39].”

      (4) It is good to see the validation of PfEMP1 expression includes binding to several relevant receptors. The data presented use CHO-GFP as a negative control, which is relevant, but it would have been good to also see the use of receptor mAbs to indicate specific adhesion patterns. The CHO system if fine for expression validation studies, but due to the high levels of receptor expression on these cells, moving to the use of microvascular endothelial cells would be advisable. This may explain the unexpected ICAM-1 binding seen with the panned IT4var19 line.

      We agree with the reviewer that it is desirable to have better binding systems for studying individual binding interactions. As the main purpose of this paper was to introduce the system and provide proof of principle that the cells show binding, we did not move to more complicated binding systems. However, we would like to point out that the CSA binding was done on receptor alone in addition to the CSA-expressing HBEC-5i cells and was competed successfully with soluble CSA. In addition, apart from the additional ICAM1-binding of the Var19 line, all binding phenotypes were conform with expectations. We therefore hope the tools used for binding studies are acceptable at this stage of introducing the system while future work interested in specific PfEMP1 receptor interactions may use better systems, tailored to the specific question (e.g. endothelial organoid models and engineered human capillaries and inhibitory antibodies or relevant recombinant domains for competition).

      (5) The proxiome work is very interesting and has identified new leads for proteins interacting with PfEMP1, as well as suggesting that KAHRP is not one of these. The reduced expression seen with BirA* in position 3 is a little concerning but there appears to be sufficient expression to allow interactions to be identified with this construct. The quantitative impact of reduced expression for proxiome experiments will clearly require further work to define it.

      This is a valid point. Clearly there seems to be some impact on binding when BirA* is placed in the extracellular domain (either through reduced presentation or direct reduction of binding efficiency of the modified PfEMP1; please see also minor comment 10 reviewer 2). The exact quantitative impact on the proxiome is difficult to assess but we note that the relative enrichment of hits to each other is rather similar to the other two positions (Fig. 6H-J). We therefore believe the BioIDs with the 3 PfEMP1-BirA* constructs are sufficient to provide a general coverage of proteins proximal to PfEMP1 and hope this will aid in the identification of further proteins involved in PfEMP1 transport and surface display as illustrated with two of the hits targeted here.

      The impact of placing a domain on the extracellular region of PfEMP1 will have to be further evaluated if needed in other studies. But the finding that a large folded domain can be placed into this part at all, even if binding was reduced, in our opinion is a success (it was not foreseeable whether any such change would be tolerated at all).

      (6) The reduced receptor binding results from the TryThrA and EMPIC3 knockouts were very interesting, particularly as both still display PfEMP1 on the surface of the infected erythrocyte. While care needs to be taken in cross-referencing adhesion work in P. berghei and whether the machinery truly is functionally orthologous, it is a fair point to make in the discussion. The suggestion that interacting proteins may influence the "correct presentation of PfEMP1" is intriguing and I look forward to further work on this.

      We hope future work will be able to shed light on this.

      Overall, the authors have produced a useful and reasonably robust system to support functional studies on PfEMP1, which may provide a platform for future studies manipulating the domain content in the exon 1 portion of var genes. They have used this system to produce a range of interesting findings and to support its use by the research community. Finally, a small concern. Being able to select specific var gene switches using drug markers could provide some useful starting points to understand how switching happens in P. falciparum. However, our trypanosome colleagues might remind us that forcing switches may show us some mechanisms but perhaps not all.

      Point noted! From non-systematic data with the Var01 line that has been cultured for extended periods of time (several years), it seems other non-targeted vars remain silent in our SLI “activation” lines but how much SLI-based var-expression “fixing” tampers with the integrity of natural switching mechanisms is indeed very difficult to gage at this stage. We now added a statement to the discussion that even if mutually exclusive expression is maintained, it is not certain the mechanisms controlling var expression all remain intact: “However, it should be noted that it is not known whether all mechanisms controlling mutually exclusive expression and switching remain intact in parasites with SLI-activated var genes.”

      Reviewer #2 (Public review):

      Summary

      Croshagen et al develop a range of tools based on selection-linked integration (SLI) to study PfEMP1 function in P. falciparum. PfEMP1 is encoded by a family of ~60 var genes subject to mutually exclusive expression. Switching expression between different family members can modify the binding properties of the infected erythrocyte while avoiding the adaptive immune response. Although critical to parasite survival and Malaria disease pathology, PfEMP1 proteins are difficult to study owing to their large size and variable expression between parasites within the same population. The SLI approach previously developed by this group for genetic modification of P. falciparum is employed here to selectively and stably activate the expression of target var genes at the population level. Using this strategy, the binding properties of specific PfEMP1 variants were measured for several distinct var genes with a novel semi-automated pipeline to increase throughput and reduce bias. Activation of similar var genes in both the common lab strain 3D7 and the cytoadhesion competent FCR3/IT4 strain revealed higher binding for several PfEMP1 IT4 variants with distinct receptors, indicating this strain provides a superior background for studying PfEMP1 binding. SLI also enables modifications to target var gene products to study PfEMP1 trafficking and identify interacting partners by proximity-labeling proteomics, revealing two novel exported proteins required for cytoadherence. Overall, the data demonstrate a range of SLI-based approaches for studying PfEMP1 that will be broadly useful for understanding the basis for cytoadhesion and parasite virulence.

      We thank the reviewer for the kind assessment and the comments to improve the paper.

      Comments

      (1) While the capability of SLI to actively select var gene expression was initially reported by Omelianczyk et al., the present study greatly expands the utility of this approach. Several distinct var genes are activated in two different P. falciparum strains and shown to modify the binding properties of infected RBCs to distinct endothelial receptors; development of SLI2 enables multiple SLI modifications in the same parasite line; SLI is used to modify target var genes to study PfEMP1 trafficking and determine PfEMP1 interactomes with BioID. Curiously, Omelianczyk et al activated a single var (Pf3D7_0421300) and observed elevated expression of an adjacent var arranged in a head-to-tail manner, possibly resulting from local chromatin modifications enabling expression of the neighboring gene. In contrast, the present study observed activation of neighboring genes with head-to-head but not head-totail arrangement, which may be the result of shared promoter regions. The reason for these differing results is unclear although it should be noted that the two studies examined different var loci.

      The point that we are looking at different loci is very valid and we realize this is not mentioned in the discussion. We now added to the discussion that it is unclear if our results and those cited may be generalized and that different var gene loci may respond differently

      “However, it is unclear if this can be generalized and it is possible that different var loci respond differently.”

      (2) The IT4var19 panned line that became binding-competent showed increased expression of both paralogs of ptp3 (as well as a phista and gbp), suggesting that overexpression of PTP3 may improve PfEMP1 display and binding. Interestingly, IT4 appears to be the only known P. falciparum strain (only available in PlasmoDB) that encodes more than one ptp3 gene (PfIT_140083100 and PfIT_140084700). PfIT_140084700 is almost identical to the 3D7 PTP3 (except for a ~120 residue insertion in 3D7 beginning at residue 400). In contrast, while the C-terminal region of PfIT_140083100 shows near-perfect conservation with 3D7 PTP3 beginning at residue 450, the N-terminal regions between the PEXEL and residue 450 are quite different. This may indicate the generally stronger receptor binding observed in IT4 relative to 3D7 results from increased PTP3 activity due to multiple isoforms or that specialized trafficking machinery exists for some PfEMP1 proteins.

      We thank the reviewer for pointing this out, the exact differences between the two PTP3s of IT4 and that of other strains definitely should be closely examined if the function of these proteins in PfEMP1 binding is analysed in more detail. 

      It is an interesting idea that the PTP3 duplication could be a reason for the superior binding of IT4. We always assumed that IT4 had better binding because it was less culture adapted but this does not preclude that PTP3(s) is(are) a reason for this. However, at least in our 3D7 PTP3 can’t be the reason for the poor binding, as our 3D7 still has PfEMP1 on the surface while in the unpanned IT4-Var19 line and in the Maier et al., Cell 2008 ptp3 KO (PMID: 18614010)) PfEMP1 is not on the surface anymore. 

      Testing the impact of having two PTP3s would be interesting, but given the “mosaic” similarity of the two PTP3s isoforms, a simple add-on experiment might not be informative. Nevertheless, it will be interesting in future work to explore this in more detail.

      Reviewer #3 (Public review):

      Summary:

      The submission from Cronshagen and colleagues describes the application of a previously described method (selection linked integration) to the systematic study of PfEMP1 trafficking in the human malaria parasite Plasmodium falciparum. PfEMP1 is the primary virulence factor and surface antigen of infected red blood cells and is therefore a major focus of research into malaria pathogenesis. Since the discovery of the var gene family that encodes PfEMP1 in the late 1990s, there have been multiple hypotheses for how the protein is trafficked to the infected cell surface, crossing multiple membranes along the way. One difficulty in studying this process is the large size of the var gene family and the propensity of the parasites to switch which var gene is expressed, thus preventing straightforward gene modification-based strategies for tagging the expressed PfEMP1. Here the authors solve this problem by forcing the expression of a targeted var gene by fusing the PfEMP1 coding region with a drug-selectable marker separated by a skip peptide. This enabled them to generate relatively homogenous populations of parasites all expressing tagged (or otherwise modified) forms of PfEMP1 suitable for study. They then applied this method to study various aspects of PfEMP1 trafficking.

      Strengths:

      The study is very thorough, and the data are well presented. The authors used SLI to target multiple var genes, thus demonstrating the robustness of their strategy. They then perform experiments to investigate possible trafficking through PTEX, they knock out proteins thought to be involved in PfEMP1 trafficking and observe defects in cytoadherence, and they perform proximity labeling to further identify proteins potentially involved in PfEMP1 export. These are independent and complimentary approaches that together tell a very compelling story.

      We thank the reviewer for the kind assessment and the comments to improve the paper.

      Weaknesses:

      (1)  When the authors targeted IT4var19, they were successful in transcriptionally activating the gene, however, they did not initially obtain cytoadherent parasites. To observe binding to ICAM-1 and EPCR, they had to perform selection using panning. This is an interesting observation and potentially provides insights into PfEMP1 surface display, folding, etc. However, it also raises questions about other instances in which cytoadherence was not observed. Would panning of these other lines have been successfully selected for cytoadherent infected cells? Did the authors attempt panning of their 3D7 lines? Given that these parasites do export PfEMP1 to the infected cell surface (Figure 1D), it is possible that panning would similarly rescue binding. Likewise, the authors knocked out PTP1, TryThrA, and EMPIC3 and detected a loss of cytoadhesion, but they did not attempt panning to see if this could rescue binding. To ensure that the lack of cytoadhesion in these cases is not serendipitous (as it was when they activated IT4var19), they should demonstrate that panning cannot rescue binding.

      These are very important considerations. Indeed, we had repeatedly attempted to pan 3D7 when we failed to get the SLI-generated 3D7 PfEMP1 expressor lines to bind, but this had not been successful. The lack of binding had been a major obstacle that had held up the project and was only solved when we moved to IT4 which readily bound (apart from Var19 which was created later in the project). After that we made no further efforts to understand why 3D7 does not bind but the fact that PfEMP1 is on the surface indicates this is not a PTP3 issue because loss of PTP3 also leads to loss of PfEMP1 surface display. Also, as the parent 3D7 could not be panned, we assumed this issue is not easily fixed in the SLI var lines we made in 3D7.

      Panning the TGD lines: we see the reasoning for conducting panning experiments with the TGD lines. However, on second thought, we are unsure this should be attempted. The outcome might not be easily interpretable as at least two forces will contribute to the selection in panning experiments with TGD lines that do not bind anymore:

      Firstly, panning would work against the SLI of the TGD, resulting in a tug of war between the TGD-SLI and binding. This is because a small number of parasites will loop out the TGD plasmid (revert) and would normally be eliminated during standard culturing due to the SLI drug used for the TGD. These revertant cells would bind and the panning would enrich them. Hence, panning and SLI are opposed forces in the case of a TGD abolishing binding. It is unclear how strong this effect would be, but this would for sure lead to mixed populations that complicate interpretations. 

      The second selecting force are possible compensatory changes to restore binding. These can be due to different causes: (i) reversal of potential independent changes that may have occurred in the TGD parasites and that are in reality causing the binding loss (i.e. such as ptp3 loss or similar, the concern of the reviewer) or (ii) new changes to compensate the loss of the TGD target (in this case the TGD is the cause of the binding loss but for instance a different change ameliorates it by for instance increasing PfEMP1 expression or surface display). As both TGDs show some residual binding and have VAR01 on the surface to at least some extent, it is possible that new compensatory changes might indeed occur that indirectly increase binding again. 

      In summary, even if more binding occurs after panning of the lines, it is not clear whether this is due to a compensatory change ameliorating the TGD or reversal of an unrelated change or are counter-selections against the SLI. To determine the cause, the panned TGD lines would need to be subjected to a complex and time-consuming analysis (WGS, RNASeq, possibly Maurer’s clefts phenotype) to find out whether they were SLI-revertants, or had an unrelated chance that was reverted or a new compensatory change that helps binding. This might be further muddled if a mix of cells come out of the selection that have different changes of the options indicated above. In that case, it might even require scRNASeq to make sense of the panning experiment. Due to the envisaged difficulty in interpreting the outcome, we did not attempt this panning.

      To exclude loss of ptp3 expression as the reason for binding loss (something we would not have seen in the WGS if it is only due to a transcriptional change), we now carried out RNASeq with the TGD lines that have a binding phenotype. While we did not generate replicas to obtain quantitative data, the results show that both ptp3 copies were expressed in these TGDs comparable to other parasite lines that do bind with the same SLI-activated var gene, indicating that the effect is not due to ptp3 (see response to point 4 on PTP3 expression in the Recommendations for the authors). While we can’t fully exclude other changes in the TGDs that might affect binding, the WGS did not show any obvious alterations that could be responsible for this. 

      (2) The authors perform a series of trafficking experiments to help discern whether PfEMP1 is trafficked through PTEX. While the results were not entirely definitive, they make a strong case for PTEX in PfEMP1 export. The authors then used BioID to obtain a proxiome for PfEMP1 and identified proteins they suggest are involved in PfEMP1 trafficking. However, it seemed that components of PTEX were missing from the list of interacting proteins. Is this surprising and does this observation shed any additional light on the possibility of PfEMP1 trafficking through PTEX? This warrants a comment or discussion.

      This is an interesting point and we agree that this warrants to be discussed. A likely reason why PTEX components are not picked up as interactors is that BirA* is expected to be unfolded when it passes through the channel and in that state can’t biotinylate. Labelling likely would only be possible if PfEMP1 lingered at the PTEX translocation step before BirA* became unfolded to go through the channel which we would not expect under physiological conditions. We added the following sentences to the discussion: “While our data indicates PfEMP1 uses PTEX to reach the host cell, this could be expected to have resulted in the identification of PTEX components in the PfEMP1 proxiomes, which was not the case. However, as BirA* must be unfolded to pass through PTEX, it likely is unable to biotinylate translocon components unless PfEMP1 is stalled during translocation. For this reason, a lack of PTEX components in the PfEMP1 proxiomes does not necessarily exclude passage through PTEX.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Most of my comments are in the public section. I would just highlight a few things:

      (1) In the binding studies section you talk about "human brain endothelial cells (HBEC-5i)". These cells do indeed express CSA but this is a property of their immortalisation rather than being brain endotheliium, which does not express CSA. I think this could be confusing to readers so I think you might want to reword this sentence to focus on CSA expressing the cell line rather than other features.

      We thank the reviewer for pointing this out, we now modified the sentence to focus on the fact these are CSA expressing cells and provided a reference for it.

      (2) As I said in the public section, CHO cells are great for proof of concept studies, but they are not endothelium. Not a problem for this paper.

      Noted! Please also see our response to the public review.

      (3) I wonder whether your comment about how well tolerated the Bir3* insertion is may be a bit too strong. I might say "Nonetheless, overall the BirA* modified PfEMP1 were functional."

      Changed as requested.

      (4) I'm not sure how you explain the IFA staining patterns to the uninitiated, but perhaps you could explain some of the key features you are looking for.

      We apologise for not giving an explanation of the IFA staining patterns in the first place. Please see detailed response to public review of this reviewer (point 3 on PTP1-TGD phenotype) and to reviewer 2 (Recommendations to the authors, points 6 and 7 on better explaining and quantifying the Maurer’s clefts phenotypes). For this we now also generated parasites that episomally express mCherry tagged SBP1 in the TGD parasites with the reduced binding phenotype. This resulted in amendments to Fig. S7, addition of a Fig. S8 and updated results to better explain the phenotypes. 

      This is a great paper - I just wish I'd had this system before.

      Thank you!

      Reviewer #2 (Recommendations for the authors):

      Major Comments

      (1) Does the RNAseq analysis of 3D7var0425800 and 3D7MEEDvar0425800 (Figure 1G, H) reveal any differential gene expression that might suggest a basis for loss of mutually exclusive var expression in the MEED line?

      We now carried out a thorough analysis of these RNASeq experiments to look for an underlying cause for the phenotype. This was added as new Figure 1J and new Table S3. This analysis again illustrated the increased transcript levels of var genes. In addition, it showed that transcripts of a number of other exported proteins, including members of other gene families, were up in the MEED line. 

      One hit that might be causal of the phenotype was sip2, which was down by close to 8-fold (pAdj 0.025). While recent work in P. berghei found this ApiAP2 to be involved in the expression of merozoite genes (Nishi et al., Sci Advances 2025(PMID: 40117352)), previous work in P. falciparum showed that it binds heterochromatic telomere regions and certain var upstream regions (Flück et al., PlosPath 2010 (PMID: 20195509), now cited in the manuscript). The other notable change was an upregulation of the non-coding RNA ruf6 which had been linked with impaired mono-allelic var expression (Guizetti et al., NAR 2016 (PMID: 27466391), now also cited in the manuscript). While it would go beyond this manuscript to follow this up, it is conceivable that alterations in chromosome end biology due to sip2 downregulation or upregulation of ruf6 are causes of the observed phenotype

      We now added a paragraph on the more comprehensive analysis of the RNA Seq data of the MEED vs non-MEED lines at the end of the second results section.

      (2) Could the inability of the PfEMP1-mDHFR fusion to block translocation (Fig 2A) reflect unique features of PfEMP1 trafficking, such as the existence of a soluble, chaperoned trafficking state that is not fully folded? Was a PfEMP1-BPTI fusion ever tested as an alternative to mDHFR?

      This is an interesting suggestion. The PfEMP1-BPTI was never tested. However, a chaperoned trafficking state would likely also affect BPTI. Given that both domains (mDHFR and BPTI) in principle do the same when folded and would block when the construct is in the PV, it is not so likely that using a different blocking domain would make a difference. Therefore, the scenario where BPTI would block when mDHFR does not, is not that probable. The opposite would be possible (mDHFR blocking while BPTI does not, because only the latter depends on the redox state). However, this would only happen if the block  occurred before the construct reaches the PV.

      At present, we believe the lacking block to be due to the organization of the domains in the construct. In the PfEMP1-mDHFR construct in this manuscript the position of the blocking domain is further away from the TMD compared to all other previously tested mDHFR fusions. Increased distance to the TMD has previously been found to be a factor impairing the blocking function of mDHFR (Mesen-Ramirez et al., PlosPath 2016 (PMID: 27168322)). Hence, our suspicion that this is the reason for the lacking block with the PfEMP1-mDHFR rather than the type of blocking domain. However, the latter option can’t be fully excluded and we might test BPTI in future work.

      (3) The late promoter SBP1-mDHFR is 2A fused with the KAHRP reporter. Since 2A skipping efficiency varies between fusion contexts and significant amounts of unskipped protein can be present, it would be helpful to include a WB to determine the efficiency of skipping and provide confidence that the co-blocked KAHRP in the +WR condition (Fig 2D) is not actually fused to the C-terminus of SBP1-mDHFR-GFP.

      Fortunately, this T2A fusion (crt_SBP1-mDHFR-GFP-2A-KAHRP-mScarlet<sup>epi</sup>) was used before in work that included a Western blot showing its efficient skipping (S3 A Fig in MesenRamirez et al., PlosPath 2016). In agreement with these Western blot result, fluorescence microscopy showed very limited overlap of SBP1-mDHFR-GFP and KAHRP-mCherry in absence of WR (Fig. 3B in Mesen-Ramirez et al., PlosPath 2016 and Fig. 2 in this manuscript) which would not be the case if these two constructs were fused together. Please note that KAHRP is known to transiently localize to the Maurer’s clefts before reaching the knobs (Wickham et al., EMBOJ 2001, PMID: 11598007), and therefore occasional overlap with SBP1 at the Maurer’s clefts is expected. However, we would expect much more overlap if a substantial proportion of the construct population would not be skipped and therefore the co-blocked KAHRP-mCherry in the +WR sample is unlikely to be due to inefficient skipping and attachment to SBP1-mDHFR-GFP.

      (4) Does comparison of RNAseq from the various 3D7 and IT4 lines in the study provide any insight into PTP3 expression levels between strains with different binding capacities? Was the expression level of ptp3a/b in the IT4var19 panned line similar to the expression in the parent or other activated IT4 lines? Could the expanded ptp3 gene number in IT4 indicate that specialized trafficking machinery exists for some PfEMP1 proteins (ie, IT4var19 requires the divergent PTP3 paralog for efficient trafficking)?

      PTP3 in the different IT4 lines that bind:

      In those parasite lines that did bind, the intrinsic variation in the binding assays, the different binding properties of different PfEMP1 variants and the variation in RNA Seq experiments to compare different parasite lines precludes a correlation of binding level vs ptp3 expression. For instance, if a PfEMP1 variant has lower binding capacity, ptp3 may still be higher but binding would be lower than if comparing to a parasite line with a better binding PfEMP1 variant. Studying the effect of PTP3 levels on binding could probably be done by overexpressing PTP3 in the same PfEMP1 SLI expressor line and assessing how this affects binding, but this would go beyond this manuscript.

      PTP3 in panned vs unpanned Var19:

      We did some comparisons between IT4 parent, and the IT4-Var19 panned and unpanned

      (see Author response table 1). This did not reveal any clear associations. While the parent had somewhat lower ptp3 transcript levels, they were still clearly higher than in the unpanned Var19 line and other lines had also ptp3 levels comparable to the panned IT4-Var19 (see Author response table 2) 

      PTP3 in the TGDs and possible reason for binding phenotype:

      A key point is whether PTP3 could have influenced the lack of binding in the TGD lines (see also weakness section and point 1 of public review of reviewer 3: ptp3 may be an indirect cause resulting in lacking binding in TGD parasites). We now did RNA Seq to check for ptp3 expression in the relevant TGD lines although we did not do a systematic quantitative comparison (which would require 3 replicates of RNASeq), but we reasoned that loss of expression would also be evident in one replicate. There was no indication that the TGD lines had lost PTP3 expression (see Author response table 2) and this is unlikely to explain the binding loss in a similar fashion to the Var19 parasites. Generally, the IT4 lines showed expression of both ptp3 genes and only in the Var19 parasites before panning were the transcript levels considerably lower:

      Author response table 1.

      Parent vs IT4-Var19 panned and unpanned

      Author response table 2.

      TGD lines with binding phenotype vs parent

      The absence of an influence of PTP3 on the binding phenotype in the cell lines in this manuscript (besides Var19) is further supported by its role in PfEMP1 surface display. Previous work has shown that KO of ptp3 leads to a loss of VAR2CSA surface display (Maier et al., Cell 2008). The unpanned Var19 parasite also lacked PfEMP1 surface display and panning and the resulting appearance of the binding phenotype was accompanied by surface display of PfEMP1. As both, the EMPIC3 and TryThra-TGD lines had still at least some PfEMP1 on the surface, this also (in addition to the RNA Seq above) speaks against PTP3 being the cause of the binding phenotype. The same applies to 3D7 which despite the poor binding displays PfEMP1 on the host cell surface (Figure 1D). This indicating that also the binding phenotype in 3D7 is not due to PTP3 expression loss, as this would have abolished PfEMP1 surface display. 

      The idea about PTP3 paralogs for specific PfEMP1s is intriguing. In the future it might be interesting to test the frequency of parasites with two PTP3 paralogs in endemic settings and correlate it with the PfEMP1 repertoire, variant expression and potentially disease severity. 

      (5) The IT4var01 line shows substantially lower binding in Figure 5F compared with the data shown in Figure 4E and 6F. Does this reflect changes in the binding capacity of the line over time or is this variability inherent to the assay?

      There is some inherent variability in these assays. While we did not systematically assess this, we had no indication that this was due to the parasite line changing. The Var01 line was cultured for months and was frozen down and thawed more than once without a clear gradual trend for more or less binding. While we can’t exclude some variation from the parasite side, we suspect it is more a factor of the expression of the receptor on the CHO cells the iRBCs bind to. 

      Specifically, the assays in Fig. 6F and 4E mentioned by the reviewer both had an average binding to CD36 of around 1000 iE/mm2, only the experiments in Fig. 5F are different (~ 500 iE/mm2) but these were done with a different batch of CHO cells at a different time to the experiments in Fig. 6F and 4E. 

      (6) In Figure S7A, TryThrA and EMPIC3 show distinct localization as circles around the PfEMP1 signal while PeMP2 appears to co-localize with PfEMP1 or as immediately adjacent spots (strong colocalization is less apparent than SBP1, and the various PfEMP1 IFAs throughout the study). Does this indicate that TryThrA and EMPIC3 are peripheral MC proteins? Does this have any implications for their function in PfEMP1 binding? Some discussion would help as these differences are not mentioned in the text. For the EMPIC3 TGD IFAs, localization of SBP1 and PfEMP1 is noted to be normal but REX1 is not mentioned (although this also appears normal).

      We apologise for the lacking description of the candidate localisations and cursory description of the Maurer’s clefts phenotypes (next point). Our original intent was to not distract too much from the main flow of the manuscript as almost every part of the manuscript could be followed up with more details. However, we fully agree that this is unsatisfactory and now provided more description (this point) and more data (next point).

      Localisation of TryThrA and EMPIC3 compared to PfEMP1 at the Maurer’s clefts: the circular pattern is reminiscent of the results with Maurer’s clefts proteins reported by McMillan et al using 3D-SIM in 3D7 parasites (McMillan et al., Cell Microbiology 2014 (PMID: 23421990)). In that work SBP1 and MAHRP1 (both integral TMD proteins) were found in foci but REX1 (no TMD) in circular structures around these foci similar to what we observed here for TryThrA and EMPIC3 which both also lack a TMD. The SIM data in McMillan et al indicated that also PfEMP1 is “more peripheral”, although it did only partially overlap with REX1. The conclusion from that work was that there are sub-compartments at the Maurer’s clefts. In our IFAs (Fig. S7A) PfEMP1 is also only partially overlapping with the TryThrA and EMPIC3 circles, potentially indicating similar subcompartments to those observed by 3D-SIM. We agree with the reviewer that this might be indicative of peripheral MC proteins, fitting with a lack of TMD in these candidates, but we did not further speculate on this in the manuscript.

      We now added enlargements of the ring-like structures to better illustrate this observation in Fig. S7A. In addition, we now specifically mention the localization data and the ring like signal with TryThrA and EMPIC3 in the results and state that this may be similar to the observations by McMillan et al., Cell Microbiology 2014.

      We also thank the reviewer for pointing out that we had forgotten to mention REX1 in the EMPIC3-TGD, this was amended.  

      (7) The atypical localization in TryThrA TGD line claimed for PfEMP1 and SBP1 in Fig S7B is not obvious. While most REX1 is clustered into a few spots in the IFA staining for SBP1 and REX1, SBP1 is only partially located in these spots and appears normal in the above IFA staining for SBP1 and HA. The atypical localization of PfEMP1-HA is also not obvious to me. The authors should clarify what is meant by "atypical" localization and provide support with quantification given the difference between the two SBP1 images shown.

      We apologise for the inadequate description of these IFA phenotypes. The abnormal signal for SBP1, REX1 and PfEMP1 in the TryThrA-TGD included two phenotypes found with all 3 proteins: 

      (1) a dispersed signal for these proteins in the host cell in addition to foci (the control and the other TGD parasites have only dots in the host cell with no or very little detectable dispersed signal). 

      (2) foci of disproportionally high intensity and size, that we assumed might be aggregation or enlargement of the Maurer’s clefts or of the detected proteins.

      The reason for the difference between the REX1 (aggregation) phenotype and the PfEMP1 and SBP1 (dispersed signal, more smaller foci) phenotypes in the images in Fig. S7B is that both phenotypes were seen with all 3 proteins but we chose a REX1 stained cell to illustrate the aggregation phenotype (the SBP1 signal in the same cell is similar to the REX1 signal, illustrating that this phenotype is not REX1 specific; please note that this cell also has a dispersed pool of REX1 and SBP1). 

      Based on the IFAs 66% (n = 106 cells) of the cells in the TryThrA-TGD parasites had one or both of the observed phenotypes. We did not include this into the previous version of the manuscript because a description would have required detouring from the main focus of this results section. In addition, IFAs have some limitations for accurate quantifications, particularly for soluble pools (depending on fixing efficiency and agent, more or less of a soluble pool in the host cell can leak out). 

      To answer the request to better explain and quantify the phenotype and given the limitations of IFA, we now transfected the TryThrA-TGD parasites with a plasmid mediating episomal expression of SBP1-mCherry, permitting live cell imaging and a better classification of the Maurer’s clefts phenotype. Due to the two SLI modifications in these parasites (using up 4 resistance markers) we had to use a new selection marker (mutated lactate transporter PfFNT, providing resistance to BH267.meta (Walloch et al., J. Med. Chem. 2020 (PMID: 32816478))) to transfect these parasites with an additional plasmid. 

      These results are now provided as Fig. S8 and detailed in the last results section. The new data shows that the majority of the TryThrA-TGD parasites contain a dispersed pool of SBP1 in the host cell. About a third of the parasites also showed disproportionally strong SBP1 foci that may be aggregates of the Maurer’s clefts. We also transfected the EMPIC3-TGD parasites with the FNT plasmid mediating episomal SBP1-mCherry expression and observed only few cells with a cytoplasmic pool or aggregates (Fig. S8). Overall these findings agree with the previous IFA results. As the IFA suggests similar results also for REX1 and PfEMP1, this defect is likely not SBP1 specific but more general (Maurer’s clefts morphology; association or transport of multiple proteins to the Maurer’s clefts). This gives a likely explanation for the cytoadherence phenotype in the TryThrA-TGD parasites. The reason for the EMPIC3-TGD phenotype remains to be determined as we did not detect obvious changes of the Maurer’s clefts morphology or in the transport of proteins to these structures in these experiments. 

      Minor comments

      (1) Italicized numbers in parenthesis are present in several places in the manuscript but it is not clear what these refer to (perhaps differently formatted citations from a previous version of the manuscript). Figure 1

      legend: (121); Figure S3 legend: (110), (111); Figure S6 legend: (66); etc.

      We thank the reviewer for pointing out this issue with the references, this was amended.

      (2) Figure 5A and legend: "BSD-R: BSD-resistance gene". Blasticidin-S (BS) is the drug while Blasticidin-S deaminase (BSD) is the resistance gene.

      We thank the reviewer for pointing this out, the legend and figure were changed.

      (3) Figure 5E legend: µ-SBP1-N should be α-SBP1-N.

      This was amended.

      (4) Figure S5 legend: "(Full data in Table S1)" should be Table S3.

      This was amended.

      (5) Figure S1G: The pie chart shows PF3D7_0425700 accounts for 43% of rif expression in 3D7var0425800 but the text indicates 62%.

      We apologize for this mistake, the text was corrected. We also improved the citations to Fig. S1G and H in this section.

      (6) "most PfEMP1-trafficking proteins show a similar early expression..." The authors might consider including a table of proteins known to be required for EMP1 trafficking and a graph showing their expression timing. Are any with later expressions known?

      Most exported proteins are expressed early, which is nicely shown in Marti et al 2004 (cited for the statement) in a graph of the expression timing of all PEXEL proteins (Fig. 4B in that paper). PNEPs also have a similar profile (Grüring et al 2011, also cited for that statement), further illustrated by using early expression as a criterion to find more PNEPs (Heiber et al., 2013 (PMID: 23950716)). Together this includes most if not all of the known PfEMP1 trafficking proteins. The originally co-submitted paper (Blancke-Soares & Stäcker et al., eLife preprint doi.org/10.7554/eLife.103633.1) analysed several later expressed exported proteins

      (Pf332, MSRP6) but their disruption, while influencing Maurer’s clefs morphology and anchoring, did not influence PfEMP1 transport. However, there are some conflicting results for Pf332 (referenced in Blancke-Soares & Stäcker et al). This illustrates that it may not be so easy to decide which proteins are bona fide PfEMP1 trafficking proteins. We therefore did not add a table and hope it is acceptable for the reader to rely on the provided 3 references to back this statement.

      (7)  Figure S1J: The predominate var in the IT4 WT parent is var66 (which appears to be syntenic with Pf3D7_0809100, the predominate var in the 3D7 WT parent). Is there something about this locus or parasite culture conditions that selects for these vars in culture? Is this observed in other labs as well?

      This is a very interesting point (although we are not certain these vars are indeed syntenic, they are on different chromosomes). As far as we know at least Pf3D7_0809100 is commonly a dominant var transcribed in other labs and was found expressed also in sporozoites (Zanghì et al. Cell Rep. 2018). However, it is unclear how uniform this really is. For IT4 we do not know in full but have also here commonly observed centromeric var genes to be dominating transcripts in unselected parasite cultures. It is possible that transcription drifts to centromeric var genes in cultured parasites. However, given the anecdotal evidence, it is unknown to which extent this is related to an inherent switching and regulation regiment or a consequence of faulty regulation following prolonged culturing.

      (8) Figure 4B, C: Presumably the asterisks on the DNA gels indicate non-specific bands but this is not described in the legend. Why are non-specific bands not consistent between parent and integrated lanes?

      We apologize for not mentioning this in the legend, this was amended.

      It is not clear why the non-specific bands differ between the lines but in part this might be due to different concentrations and quality of DNA preps. A PCR can also behave differently depending on whether the correct primer target is present or not. If present, the PCR will run efficiently and other spurious products will be outcompeted, but in absence of the correct target, they might become detectable.  

      Overall, we do not think the non-specific bands are indications of anything untoward with the lines, as for instance in Fig. 4B the high band in the 5’ integration in the IT4 line (that does not occur anywhere else) can’t be due to a genomic change as this is the parental line and does not contain the plasmid for integration. In the same gel, the ori locus band of incorrect size (likely due to crossreaction of the primers to another var gene which due to the high similarity of the ATS region is not always fully avoidable), is present in both, the parent IT4 and the integrant line which therefore also is not of concern. In C there are a couple of bands of incorrect size in the Integration line. One of these is very faint and both are too large and again therefore are likely other vars that are inefficiently picked up by these primers. The reason they are not seen in the parent line is that there the correct primer binding site is present, which then efficiently produces a product that outcompetes the product derived from non-optimal matching primer products and hence appear in the Int line where the correct match is not there anymore. For these reasons we believe these bands are not of any concern.  

      (9) Figure 4C: Is there a reason KAHRP was used as a co-marker for the IFA detecting IT4var19 expression instead of SBP1 which was used throughout the rest of the study?

      This is a coincidence as this line was tested when other lines were tested for KAHRP. As there were foci in the host cell we were satisfied that the HA-tagged PfEMP1 is produced and the localization deemed plausible. 

      (10) Figure 6: Streptavidin labeling for the IT4var01-BirA position 3 line is substantially less than the other two lines in both IFA and WB. Does the position 3 fusion reduce PfEMP1 protein levels or is this a result of the context or surface display of the fusion? Interestingly, the position 3 trypsin cleavage product appears consistently more robust compared with the other two configurations. Does this indicate that positioning BirA upstream of the TM increases RBC membrane insertion and/or makes the surface localized protein more accessible to trypsin?

      It is possible that RBC membrane insertion or trypsin accessibility is increased for the position 3 construct. But there could also be other explanations:

      The reason for the more robustly detected protected fragment for the position 3 construct in the WB might also be its smaller size (in contrast to the other two versions, it does not contain BirA*) which might permit more efficient transfer to the WB membrane. In that case the more robust band might not (only) be due to better membrane insertion or better trypsin accessibility.

      The lower biotinylation signal with the position 3 construct might also be explained by the farther distance of BirA* to the ATS (compared to position 1 and 2), the region where interactors are expected to bind. The position 1 and 2 constructs may therefore generally be more efficient (as closer) to biotinylate ATS proximal proteins. Further, in the final destination (PfEMP1 inserted into the RBC membrane) BirA* would be on the other side of the membrane in the position 3 construct while in the position 1 and 2 constructs BirA* would be on the side of the membrane where the ATS anchors PfEMP1 in the knob structure. In that case, labelling with position 3 would come from interactions/proximities during transport or at the Maurer’s clefts (if there indeed PfEMP1 is not membrane embedded) and might therefore be less.

      Hence, while alterations in trypsin accessibility and RBC membrane insertion are possible explanations, other explanations exist. At present, we do not know which of these explanations apply and therefore did not mention any of them in the manuscript. 

      Reviewer #3 (Recommendations for the authors):

      (1) In the abstract and on page 8, the authors mention that they generate cell lines binding to "all major endothelial receptors" and "all known major receptors". This is a pretty allencompassing statement that might not be fully accepted by others who have reported binding to other receptors not considered in this paper (e.g. VCAM, TSP, hyaluronic acid, etc). It would be better to change this statement to something like "the most common endothelial receptors" or "the dominant endothelial receptors", or something similar.

      We agree with the reviewer that these statements are too all-encompassing and changed them to “the most common endothelial receptors” (introduction) and “the most common receptors” (results).

      (2) The authors targeted two rif genes for activation and in each case the gene became the most highly expressed member of the family. However, unlike var genes, there were other rif genes also expressed in these lines and the activated copy did not always make up the majority of rif mRNAs. The authors might wish to highlight that this is inconsistent with mutually exclusive expression of this gene family, something that has been discussed in the past but not definitively shown.

      We thank the reviewer for highlighting this, we now added the following statement to this section: “While SLI-activation of rif genes also led to the dominant expression of the targeted rif gene, other rif genes still took up a substantial proportion of all detected rif transcripts, speaking against a mutually exclusive expression in the manner seen with var genes.”

      (3) In Figure 6, H-J, the authors display volcano plots showing proteins that are thought to interact with PfEMP1. These are labeled with names from the literature, however, several are named simply "1, 2, 3, 4, 5, or 6". What do these numbers stand for?

      We apologize for not clarifying this and thank the reviewer for pointing this out. There is a legend for the numbered proteins in what is now Table S4 (previously Table S3). We now amended the legend of Figure 6 to explain the numbers and pointing the reader to Table S4 for the accessions.

    1. Author response:

      The following is the authors’ response to the original reviews.

      The parts of the text that have been changed.The major changes are as follows:

      We re-analyzed the dataset and improved the local resolution of the extracellular region (Author response image 1).

      We re-modeled based on the improved density and canceled the bicarbonate model based on comments from all reviewers.

      We performed calcium assay using cell lines stably expressing the mutants, whose surface expression levels were analyzed by fluorescence-activated cell sorting (FACS)<br /> (Figure 3F, G and Figure 3–figure supplement 1-3).

      Thus, we significantly revised our discussion of the extracellular binding pocket and the result of the mutational study. In the revised manuscript, we speculate that H307 is a candidate for the bicarbonate binding site.

      Author response image 1.

      Figure Comparison of local resolution between re-analyzed and previous maps.A Side and top view of the re-analyzed receptor-focused map of GPR30 colored by local resolution. B Side and top view of the previous receptor-focused map of GPR30 colored by local resolution

      Reviewer #1 (Public Review):

      Summary:

      This study resolves a cryo-EM structure of the GPCR, GPR30, which was recently identified as a bicarbonate receptor by the authors' lab. Understanding the ligand and the mechanism of activation is of fundamental importance to the field of receptor signaling. However, the main claim of the paper, the identification of the bicarbonate binding site, is only partly supported by the structural and functional data, leaving the study incomplete.

      Strengths:

      The overall structure, and proposed mechanism of G-protein coupling seem solid. The authors perform fairly extensive unbiased mutagenesis to identify a host of positions that are important to G-protein signaling. To my knowledge, bicarbonate is the only physiological ligand that has been identified for GPR30, making this study a particularly important contribution to the field.

      Weaknesses:

      Without higher resolution structures and/or additional experimental assessment of the binding pocket, the assignment of the bicarbonate remains highly speculative. The local resolution is especially poor in the ECL loop region where the ligand is proposed to bind (4.3 - 4 .8 Å range). Of course, sometimes it is difficult to achieve high structural resolution, but in these cases, the assignment of ligands should be backed up by even more rigorous experimental validation.The functional assay monitors activation of GPR30, and thus reports on not only bicarbonate binding, but also the integrity of the allosteric network that transduces the binding signal across the membrane. Thus, disruption of bicarbonate signaling by mutagenesis of the putative coordinating residues does not necessarily mean that bicarbonate binding has been disrupted. Moreover, the mutagenesis was apparently done prior to structure determination, meaning that residues proposed to directly surround bicarbonate binding, such as E218, were not experimentally validated. Targeted mutagenesis based on the structure would strengthen the story.

      Moreover, the proposed bicarbonate binding site is surprising in a chemical sense, as it is located within an acidic pocket. The authors cite several other structural studies to support the surprising observation of anionic bicarbonate surrounded by glutamate residues in an acidic pocket (references 31-34). However, it should be noted that in general, these other structures also possess a metal ion (sodium or calcium) and/or a basic sidechain (arginine or lysine) in the coordination sphere, forming a tight ion pair. Thus, the assigned bicarbonate binding site in GPR30 remains an anomaly in terms of the chemical properties of the proposed binding site.

      Thank you for your insightful comments. Based on the weaknesses you pointed out, we reconstructed the receptor based on the improved density and removed the bicarbonate model. We performed calcium assays using cell lines stably expressing the variant based on the structure.

      Reviewer #2(Public Review):

      Summary:

      In this manuscript, "Cryo-EM structure of the bicarbonate receptor GPR30," the authors aimed to enrich our understanding of the role of GPR30 in pH homeostasis by combining structural analysis with a receptor function assay. This work is a natural development and extension of their previous work (PMID: 38413581). In the current body of work, they solved the first cryo-EM structure of the human GPR30-G-protein (mini-Gsqi) complex in the presence of bicarbonate ions at 3.21 Å resolution. From the atomic model built based on this map, they observed the overall canonical architecture of class A GPCR and also identified 4 extracellular pockets created by extracellular loops (ECLs) (Pockets A-D). Based on the polarity, location, and charge of each pocket, the authors hypothesized that pocket D is a good candidate for the bicarbonate binding site. To verify their structural observation, on top of the 10 mutations they generated in the previous work, the authors introduced another 11 mutations to map out the essential residues for the bicarbonate response on hGPR30. In addition, the human GPR30-G-protein complex model also allowed the authors to untangle the G-protein coupling mechanism of this special class A GPCR that plays an important role in pH homeostasis.

      Strengths:

      As a continuation of their recent Nature Communication publication (PMID: 38413581), this study was carefully designed, and the authors used mutagenesis and functional studies to confirm their structural observations. This work provided high-resolution structural observations for the receptor in complex with G-protein, allowing us to explore its mechanism of action, and will further facilitate drug development targeting GPR30. There were 4 extracellular pockets created by ECLs (Pockets A-D). The authors were able to filter out 3 of them and identified that pocket D was a good candidate for the bicarbonate binding site based on the polarity, location, and charge of each pocket. From there, the authors identified the key residues on GPR30 for its interaction with the substrate, bicarbonate. Together with their previous work, they carefully mapped out nine amino acids that are critical for receptor reactivity.

      Weaknesses:

      It is unclear how novel the aspects presented in the new paper are compared to the most recent Nature Communications publication (PMID: 38413581). Some areas of the manuscript appear to be mixed with the previous publication. The work is still impactful to the field. The new and novel aspects of this manuscript could be better highlighted.

      I also have some concerns about the TGFα shedding assay the authors used to verify their structural observation. I understand that this assay was also used in the authors' previous work published in Nature Communications. However, there are still several things in the current data that raised concerns:

      Thank you for your insightful comments. Based on the weaknesses you pointed out, we highlighted the new and novel aspects of this manuscript could be better highlighted.l. We performed calcium assays using cell lines stably expressing the variant based on the structure.

      (1) The authors confirmed the "similar expression levels of HA-tagged hGPR30" mutants by WB in Supplemental Figure 1A and B. However, compared to the hGPR30-HA (~6.5 when normalized to the housekeeping gene, Na-K-ATPase), several mutants of the key amino acids had much lower surface expression: S134A, D210A, C207A had ~50% reduction, D125A had ~30% reduction, and Q215A and P71A had ~20% reduction. This weakens the receptor reactivity measured by the TGFα shedding assay.

      Since the calcium assay data is included in the main figure, the TGFα shedding assay and WB expression quantification data are Figure 3. –– supplement figure 1-4, but we included an explanation of the expression levels in the figure caption.

      (2) In the previous work, the authors demonstrated that hGPR30 signals through the Gq signaling pathway and can trigger calcium mobilization. Given that calcium mobilization is a more direct measurement for the downstream signaling of hGPR30 than the TGFα shedding assay, pairing the mutagenesis study with the calcium assay will be a better functional validation to confirm the disruption of bicarbonate signaling.

      According to the suggestion, we performed calcium assay using cell lines stably expressing the mutants (Figure 3F, G and Figure 3–figure supplement 1-3).

      (3) It was quite confusing for Figure 4B that all statistical analyses were done by comparing to the mock group. It would be clearer to compare the activity of the mutants to the wild-type cell line.

      Thank you for your comment. As you mentioned, the comparisons are made between wild-type GPR30 and mutants in the revised manuscript (Figure 3G, Figure 3.—figure supplement 4B)

      Additional concerns about the structural data include

      (1) E218 was in close contact with bicarbonate in Figure 4D. However, there is no functional validation for this observation. Including the mutagenesis study of this site in the cell-based functional assay will strengthen this structural observation.

      We cancelled the bicarbonate model, and we performed mutation analysis targeting all residues facing the binding pocket using cell lines that stably express variants including E218A.

      (2) For the flow chart of the cryo-EM data processing in Supplemental data 2, the authors started with 10,148,422 particles after template picking, then had 441,348 Particles left after 2D classification/heterogenous refinement, and finally ended with 148,600 particles for the local refinement for the final map. There seems to be a lot of heterogeneity in this purified sample. GPCRs usually have flexible and dynamic loop regions, which explains the poor resolution of the ECLs in this case. Thus, a solid cell-based functional validation is a must to assign the bicarbonate binding pocket to support their hypothesis.

      We re-analyzed the dataset and improved the local resolution of the extracellular region (Author response image 1) and cancelled the bicarbonate model. Yet, as suggested by the reviewer, solid cell-based functional validation is efficient to analyze the receptor function response to bicarbonate. Thus, we performed mutation analysis targeting all residues facing the binding pocket using cell lines stably expressing the mutants, whose surface expression levels were analyzed by FACS (Figure 3F, G and Figure 3.––figure supplement 1-3).

      Reviewer #3 (Public Review):

      Summary:

      GPR30 responds to bicarbonate and regulates cellular responses to pH and ion homeostasis. However, it remains unclear how GPR30 recognizes bicarbonate ions. This paper presents the cryo-EM structure of GPR30 bound to a chimeric mini-Gq in the presence of bicarbonate. The structure together with functional studies aims to provide mechanistic insights into bicarbonate recognition and G protein coupling.

      Strengths:

      The authors performed comprehensive mutagenesis studies to map the possible binding site of bicarbonate.

      Weaknesses:

      Owing to the poor resolution of the structure, some structural findings may be overclaimed.

      Based on EM maps shown in Figure 1a and Figure Supplement 2, densities for side chains in the receptor particularly in ECLs (around 4 Å) are poorly defined. At this resolution, it is unlikely to observe a disulfide bond (C130ECL1-C207ECl2) and bicarbonate ions. Moreover, the disulfide between ECL1 and ECL2 has not been observed in other GPCRs and the published structure of GPR30 (PMID: 38744981). The density of this disulfide bond could be noise.

      The authors observed a weak density in pocket D, which is accounted for by the bicarbonate ions. This ion is mainly coordinated by Q215 and Q138. However, the Q215A mutation only reduced but not completely abolished bicarbonate response, and the author did not present the data of Q138A mutation. Therefore, Q215 and Q138 could not be bicarbonate binding sites. While H307A completely abolished bicarbonate response, the authors proposed that this residue plays a structural role. Nevertheless, based on the structure, H307 is exposed and may be involved in binding bicarbonate. The assignment of bicarbonate in the structure is not supported by the data.

      Thank you for your insightful comments. Based on the weaknesses you pointed out, we reconstructed the receptor based on the improved density and removed the bicarbonate model. We performed calcium assays using cell lines stably expressing the variant based on the structure.

      Reviewer #1 (Recommendations For The Authors):

      (1) The experimental validation of the bicarbonate binding could be strengthened by developing an assay that directly monitors bicarbonate binding (rather than GPCR signaling)

      We agree that a direct binding assay for bicarbonate would be highly attractive (i.e. Filter binding assay using 14C-HCO₃⁻). However, the weak affinity of bicarbonate ions (in the mM range) would make reliable radioisotope-based detection impossible due to minimal specific receptor occupancy and high non-specific background and thus it is highly challenging and there are limitations to what can be done in this structural paper.

      and determining a structure at comparable resolution in the absence of bicarbonate. In addition, all residues that are proposed to be located adjacent to the bicarbonate should be mutated and functionally validated.

      We re-modeled the receptor based on the improved density and canceled the bicarbonate model. We performed calcium assay using cell lines stably expressing the mutants (Figure 3F, G and Figure 3.–figure supplement 1-3).

      (2) What are the maps contoured in Figure 4D? The legend should describe this. Is 218 within the map region shown, or is there no density for its sidechain?

      We removed the corresponding figure and cancelled the bicarbonate model.

      (3) The contour level of the maps in Figure 1 - Figure Supplement 2 should also be indicated. Are these all contoured at the same level?

      Thank you for your comment. We re-analyzed the same data set and obtained new density maps and models. We reworked Figure 1 and Figure 1. figure supplement 2; the contour level of the map for Figure 1 and composite map for the Figure 1. figure supplement 2 is the same, 7.65. 

      (4) Regarding the cited structures of bicarbonate-binding proteins, for three of the four cited structures, the bicarbonate is actually coordinated by positive ligands, with the Asp/Glu playing a more peripheral role:

      Capper et al: Overall basic cavity with tight bidentate coordination by Arg. The Glu is 5-6 Å away.

      Koropatkin et al: Two structures. The first, solved at pH 5, is proposed to have carbonic acid bound. The second, solved at pH 8, shows carbonate in a complex with calcium, with the calcium coordinated by carboxylates.

      Wang et al: The bicarbonate is coordinated by a lysine and a sodium ion. The sodium is coordinated by carboxylates.

      The authors should more thoughtfully discuss the unusual properties of this binding site with regard to the previous literature. Is it possible that bicarbonate binds in complex with a metal ion? Could this possibility be experimentally tested?

      We cancelled the bicarbonate model.

      (5) As a structure of GPR30 has been recently published by another group (PMID: 38744981), it would be valuable to discuss structural similarities and differences and discuss how bicarbonate activation and activation by the chloroquine ligand identified by the other group might both be accommodated by this structure.

      Thank you for your valuable comment. We compared the structure presented by another group and added our discussion, as “During the revision of this manuscript, the structures of apo-GPR30-G<sub>q</sub> (PDB 8XOG) and the exogenous ligand Lys05-bound GPR30-G<sub>q</sub> (PDB 8XOF) were reported [42]. We compared our structure of GPR30 in the presence of bicarbonate with these structures. In the extracellular region, the position of TM5 in GPR30 in the presence of bicarbonate is similar to that in apo-GPR30. In contrast, the position of TM6 is shifted outward relative to that of apo-GPR30, resembling the conformation observed in Lys05-bound GPR30 (Figure 6A, B). Additionally, the position of ECL1 is also shifted outward compared to that of apo-GPR30 (Figure 6B). In the GPR30 structure in the presence of bicarbonate, ECL2 was modeled, suggesting differences in structural flexibility. These findings indicate that the structure of GPR30 in the presence of bicarbonate is different from both the apo structure and the Lys05-bound structure, demonstrating that the structure and the flexibility of the extracellular domain of GPR30 change depending on the type of ligand. Furthermore, focusing on the interaction with G<sub>q</sub>, the αN helix of G<sub>q</sub> is not rotated in the structure bound to Lys05, in contrast to the characteristic bending of the αN helix in our structure (Figure 6C, D). Although it is necessary to consider variations in experimental conditions, such as salt concentration, the differences in the G<sub>q</sub> binding modes suggest that the downstream signals may change in a ligand-dependent manner.” (lines 249-266).

      Reviewer #2 (Recommendations For The Authors):

      (1) It is highly recommended that the authors carefully go through the "insights into bicarbonate binding" section. The results of the new findings in this paper were blended in with the results from the previous work: the importance of E115, Q138, and H307 in the receptor-bicarbonate interaction was shown in the Nature Communication paper but the authors didn't make it clear, which added a little confusion.

      We emphasized this fact in the main text (lines 130-132).

      (2) It would be nice for the authors to add some content about the physiological concentration of HCO3 or refer more to their previous work about the rationale for selecting the bicarbonate dose in their functional assay.

      Thank you for your comment. The physiological concentration of bicarbonate is 22-26 mM in the extracellular fluid, including interstitial fluid and blood, and 10-12 mM in the intracellular fluid. The bicarbonate concentration alters in various physiological and pathological conditions – metabolic acidosis in chronic kidney disease causes a drop to 2-3 mM, and metabolic alkalosis induced by severe vomiting increases HCO<sub>3</sub><sup>-</sup> concentrations more than 30 mM. Thus, our present and previous works clearly show that GPR30 is activated by physiological concentrations of bicarbonate, whether it is localized intracellularly or on the membrane, and that GPR30 can be deactivated or reactivated in various pathophysiological conditions. We added this in the discussion section (lines 267-278).

      (3) In Figure 3A, in the legend, the authors mentioned: "black dashed lines indicate hydrogen bonds". No hydrogen bond was noted in the figure.

      We totally corrected Figure 3.

      (4) Figure 3B, it would be helpful for the authors to denote the meaning of the blue-white-red color coding in the legend.

      We removed the figure.

      (5) Supplemental Figure 3: since AF3 was released on May 3rd, it would be awesome in the revision version if the authors would update this to the AF3 model.

      The AF2 model has been replaced with the AF3. (Figure 2–figure supplement 2A-C). The AF2 and AF3 models are almost identical, and they form incorrect disulfide bonds. This confirms the usefulness of the experimental structural determination in this study.

      (6) Supplemental Figure 4: it wasn't clear to me if the expression experiments were repeated multiple times or if there was any statistical analysis for the expression level was done in this study.

      We performed the expression experiment by western blotting once and did not perform statistical analyses. We performed repeated FACS analyses of HEK cells stably expressing N-terminally HA-tagged wild-type or mutant GPR30s to analyze their membrane and whole-cell expressions during revision (Figure 3.–figure supplement 1-3). Using these stable cells, we performed calcium assays using cell lines stably expressing the mutants (Figure 3F, G and Figure 3–figure supplement 1-3).

      (7) Supplemental Figure 4: Also, is there a reason for the authors to compare the expression level of hGPR30 to the housekeeping gene NA-K-ATPase rather than the total loaded protein? Traditionally housekeeping genes have been used as loading controls to semiquantitatively compare the expression of target proteins in western blots. However, numerous recent studies show that housekeeping proteins can be altered due to experimental conditions, biological variability across tissues, or pathologies. A consensus has developed for using total protein as the internal control for loading. An editorial from the Journal of Biological Chemistry reporting on "Principles and Guidelines for Reporting Preclinical Research" from the workshop held in June 2014 by the NIH Director's Office, Nature Publishing Group, and Science stated, "It is typically better to normalize Western blots using total protein loading as the denominator".

      Thank you for your instructive comment. We evaluated western blotting with the same amount of total protein loaded 20 µg for whole-cell lysate and 1.5 µg for cell surface protein (Figure 3.–figure supplement 3C-F).

      Reviewer #3 (Recommendations For The Authors):

      The claim about this disulfide should be removed unless the authors can provide mass spec evidence.

      Thank you for your crucial comments. Firstly, C130 is a residue of TM3, not ECL1, so our misprint has been corrected to C130<sup>3.25</sup>. C207<sup>ECL2</sup>, located at position 45.50, is the most conserved residue in ECL2, and it forms a disulfide bond with cysteine at position 3.25 (PMID: 35113559). The paper was additionally cited regarding the preservation of the bond of C130<sup>3.25</sup>-C207<sup>ECL2</sup> (line 103). Indeed, disruption of this disulfide bond by the C207<sup>ECL2</sup> A mutation resulted in a marked reduction in receptor activity. In addition, the data set was re-analyzed to improve the local resolution of the extracellular region, and it was shown that the density of ECL2 is not noise (Figure 2. ––figure supplement 2). We are confident about the presence of the disulfide bond, based on the structural analysis data and the conservation.

      The highly flexible extracellular region is greatly affected by experimental conditions and ligands, so we speculate that the ECL2 and the disulfide bond was not observed in other reported structures of GPR30. Then, we have added the following content to the discussion, as “In the GPR30 in the presence of bicarbonate, ECL2 was modelled, suggesting differences in structural flexibility.” (lines 256-257).

      The authors should remove the assignment of bicarbonate in the structure, and tone down the binding site of bicarbonate.

      We cancelled the bicarbonate model.

      Minor:

      (1) The potency of bicarbonate for GPR30 is in the mM range. Although the concentration of bicarbonate in the serum can reach mM range, how about its concentration in the tissues? Given its low potency, it may be not appropriate to claim GPR30 is a bicarbonate receptor at this point, but the authors can claim that GPR30 can be activated by or responds to bicarbonate.

      The physiological concentration of bicarbonate is 22-26 mM in the extracellular fluid, including interstitial fluid and blood, and 10-12 mM in the intracellular fluid. Therefore, GPR30 is activated by physiological concentrations of bicarbonate in the tissues. Also, the bicarbonate concentration alters in various physiological and pathological conditions – metabolic acidosis in chronic kidney disease causes a drop to 2-3 mM, and metabolic alkalosis induced by severe vomiting increases HCO3- concentrations more than 30 mM. Thus, our work clearly shows that GPR30 is activated by physiological concentrations of bicarbonate, whether it is localized intracellularly or on the membrane, and that GPR30 can be deactivated or reactivated in various pathophysiological conditions. According to the reasons above, we claim GPR30 is a bicarbonate receptor (lines 267-278).

      (2) The description that there is no consensus on a drug that targets GPR30 is not accurate, since lys05 has been reported as an agonist of GPR30 and their structure is published (PMID: 38744981). The published structures of GPR30 should be introduced in the paper.

      We added the discussion about the structural comparison with the Lys05-bound structure (Figure 6, lines 249-266)

      (3) BW numbers in Figure 4A should be shown.

      We added BW numbers in the figures of the mutational studies.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study presents a new Bayesian approach to estimate importation probabilities of malaria, combining epidemiological data, travel history, and genetic data through pairwise IBD estimates. Importation is an important factor challenging malaria elimination, especially in low-transmission settings. This paper focuses on Magude and Matutuine, two districts in southern Mozambique with very low malaria transmission. The results show isolation-by-distance in Mozambique, with genetic relatedness decreasing with distances larger than 100 km, and no spatial correlation for distances between 10 and 100 km. But again, strong spatial correlation in distances smaller than 10 km. They report high genetic relatedness between Matutuine and Inhambane, higher than between Matutuine and Magude. Inhambane is the main source of importation in Matutuine, accounting for 63.5% of imported cases. Magude, on the other hand, shows smaller importation and travel rates than Matutuine, as it is a rural area with less mobility. Additionally, they report higher levels of importation and travel in the dry season, when transmission is lower. Also, no association with importation was found for occupation, sex, and other factors. These data have practical implications for public health strategies aiming for malaria elimination, for example, testing and treating travelers from Matutuine in the dry season.

      Strengths:

      The strength of this study lies in the combination of different sources of data - epidemiological, travel, and genetic data - to estimate importation probabilities, and the statistical analyses.

      Weaknesses:

      The authors recognize the limitations related to sample size and the biases of travel reports.

      We appreciate the review and comment about the manuscript.

      Reviewer #2 (Public review):

      Summary:

      Based on a detailed dataset, the authors present a novel Bayesian approach to classify malaria cases as either imported or locally acquired.

      Strengths:

      The proposed Bayesian approach for case classification is simple, well justified, and allows the integration of parasite genomics, travel history, and epidemiological data. The work is well-written, very organized, and brings important contributions both to malaria control efforts in Mozambique and to the scientific community. Understanding the origin of cases is essential for designing more effective control measures and elimination strategies.

      Weakness:

      While the authors aim to classify cases as imported or locally acquired, the work lacks a quantification of the contribution of each case type to overall transmission.

      The method presented here allows for classifying individual cases according to whether the infection occurred locally or was imported during a trip. By definition, it does not look to secondary infections after an importation event. Our next step is to conduct outbreak investigation to quantify the impact of importation events on the overall transmission, but this activity goes beyond the scope of this manuscript. We clarify this in the discussion section.

      The Bayesian rationale is sound and well justified; however, the formulation appears to present an inconsistency that is replicated in both the main text and the Supplementary Material.

      Thank you for pointing out the inconsistency in the final formula. In fact, the final formula corresponds to P(IA | G), instead of P(IA), so:

      instead of

      We have now corrected this error in the new version of the manuscript.

      Reviewer #3 (Public review):

      The authors present an important approach to identify imported P. falciparum malaria cases, combining genetic and epidemiological/travel data. This tool has the potential to be expanded to other contexts. The data was analyzed using convincing methods, including a novel statistical model; although some recognized limitations can be improved. This study will be of interest to researchers in public health and infectious diseases.

      Strengths:

      The study has several strengths, mainly the development of a novel Bayesian model that integrates genomic, epidemiological, and travel data to estimate importation probabilities. The results showed insights into malaria transmission dynamics, particularly identifying importation sources and differences in importation rates in Mozambique. Finally, the relevance of the findings is to suggest interventions focusing on the traveler population to help efforts for malaria elimination.

      Weaknesses:

      The study also has some limitations. The sample collection was not representative of some provinces, and not all samples had sufficient metadata for risk factor analysis, which can also be affected by travel recall bias. Additionally, the authors used a proxy for transmission intensity and assumed some conditions for the genetic variable when calculating the importation probability for specific scenarios. The weaknesses were assessed by the authors.

      We acknowledge the limitations commented by the reviewer. We have the following plans to address the limitations. We will repeat the study for our data collected in 2023, which this time contains a good representation of all the provinces of Mozambique, and completeness of the metadata collection was ensured by implementing a new protocol in January 2023. Regarding the proxy for transmission intensity, we will refine the model by integrating monthly estimates of malaria incidence (previously calibrated to address testing and reporting rates) from the DHIS2 data, taking also into account the date of the reported cases in the analysis.

      Reviewing Editor Comments:

      The reviewers have made specific suggestions that could improve the clarity and accuracy of this report.

      Reviewer #1 (Recommendations for the authors):

      (1) Abstract, lines 36, 37 and 38: "Spatial genetic structure and connectivity were assessed using microhaplotype-based genetic relatedness (identity-by-descent) from 1605 P. falciparum samples collected (...)", but only 540 samples were successfully sequenced, therefore used in spatial genetic structure and connectivity analysis.

      The 540 samples refer to those from Maputo province and are described in Fig. 1. The Spatial and connectivity analyses also included the samples from the rest of the provinces from the multi-cluster sampling scheme. Sample sizes from these provinces are described in Suppl. Table 2, and the total between them and the 540 samples from Maputo are the 1605 samples mentioned in the abstract. We specify this number in the caption of Sup. Fig. 4, and add it now into Fig. 3

      (2) In the Introduction, some epidemiological context about Magude and Matutuine could be added. It is only mentioned in the Discussion section (lines 265-269).

      We have added some context about both districts in the introduction now.

      (3) In the Discussion, lines 241-244, could the lack of structure mean no barriers for gene flow due to high mobility in short distances? Maybe it could only be resolved with a large number of samples.

      This could be an explanation (we mention it in the new version), although it is not something we can prove, or at least in this study.

      Reviewer #2 (Recommendations for the authors):

      The work is well written, very organized, and brings important contributions both to malaria control efforts in Mozambique and to the scientific community. Based on detailed datasets from Mozambique, the authors present a novel Bayesian approach to classify malaria cases as either imported or locally acquired. Understanding the origin of cases is essential for designing more effective control measures and elimination strategies. My review focuses on the Bayesian approach as well as on a few aspects of the presentation of results.

      The authors combine travel history, parasite genetic relatedness, and transmission intensity from different areas to compute the probability of infection occurring in the study area, given the P. falciparum genome. The Bayesian rationale is sound and well justified; however, the formulation appears to present an inconsistency that is replicated in both the main text and the Supplementary Material. According to Bayes' Rule:

      P(I_A |G) = (P(I_A) ∙ P(G|I_A)) / (P(G)),

      with

      P(I_A) = K ∙ T_A ∙ PR_A,

      P(G│I_A) = R'_A,

      and assuming

      P(I_A│G) + P(I_B│G) = 1,

      the expression,

      (T_A ∙ PR_A ∙ R'_A) / (T_A ∙ PR_A ∙ R'_A + T_B ∙ PR_B ∙ R'_B)

      appears to refer to P(I_A│G), not to P(I_A) (as indicated in the main text and Supplementary Material).

      P(I_A│G) + P(I_B│G) = (P(I_A) ∙ P(G|I_A) + P(I_B) ∙ P(G|I_B)) / P(G) = 1

      ⇒P(G) = P(I_A) ∙ P(G|I_A) + P(I_B) ∙ P(G|I_B)

      ⇒P(G) = K ∙ T_A ∙ PR_A ∙ R'_A + K ∙ T_B ∙ PR_B ∙ R'_B

      ⇒P(I_A│G) = (T_A ∙ PR_A ∙ R'_A) / (T_A ∙ PR_A ∙ R'_A + T_B ∙ PR_B ∙ R'_B)

      Please clarify this.

      As mentioned in a previous comment, we acknowledge this point from the reviewer.  In fact, the final formula corresponds to P(IA | G), instead of P(IA), so:

      instead of

      We have now corrected this error in the new version of the manuscript and in the supplementary information.

      Additional comments:

      (1) Figure 3A has a scale that includes negative values, which is not reasonable for R.

      We agree that R estimates are not compatible with negative values. The intention of this scale was to show the overall mean R in the centre, in white, so that blue colours represented values below the average and red values above the average. However, we proceeded to update the figures according to your recommendations.

      (2) I suggest using a common scale from 0 to 0.12 (maximum values among panels) across panels A, C, and D, as well as in Sup Fig 3, to facilitate comparison.

      We updated the figures according to the recommendations.

      (3) The x-axis labels in Figure 3A and Supplementary Figure 2A are not aligned with the x-axis ticks.

      We updated the figures so that the alignment in the x-axis is clear.

      (4) Supplementary Figure 5 would be better presented if the data were divided into four separate panels.

      We have divided the figure into four separate panels.

      (6) Figure 5D is not referenced in the main text.

      We missed the mention, which is now fixed in the new version.

      (7) The authors state: "No significant differences in R were found comparing parasite samples from Magude and the rest of the districts." However, Supplementary Figure 3 shows statistically significant relatedness between parasites from Magude and Matutuine. Please clarify this.

      Answer: we added clarity to this sentence which was indeed confusing.

      Reviewer #3 (Recommendations for the authors):

      (1) Introduction: More background info about malaria in Mozambique would be appreciated.

      We included some contextualisation about malaria in Mozambique and our study districts.

      (2) Why were most of the samples collected from children? Is malaria most prevalent in that group? Information could be added in the introduction.

      Children are usually considered an appropriate sentinel group for malaria surveillance for several reasons. First, most malaria cases reported from symptomatic outpatient visits are children, especially in areas with moderate to high burden. Second (and probably the cause for the first reason), their lower immunity levels, due to lower time of exposure, and their immature system, provides a cleaner scenario of the effects of malaria, since the body response is less adapted from past exposures. Finally, as a vulnerable population, they deserve a stronger focus in surveillance systems. We added a comment in the introduction referring to them as a common sentinel group for surveillance.

      (3) Minor: Check spaces in the text (for example, line 333 and the start of the Discussion).

      Thank you for noticing, we fixed in in the new version

      (4) Minor: In my case, the micro (u) symbol can be observed in Word, but not in PDF.

      One of the symbols produced an error, we hope that the new version is correct now.

      (5) Were COI calculations with MOIRE performed across provinces and regions, or taking all samples as one population?

      Wwe took all samples as one population. However, we validated that the same results (reaching equivalent numbers and the same conclusions) were obtained when run across different populations (regions or provinces). We mention this in the manuscript now.

      (6) Have you tested lower values than 0.04 for PR in Maputo?

      This would not have had any impact in the classification. Only two individuals reported a trip to Maputo city (where we assumed PR=0.04), and none of them were classified as imported. If lower values of PR were assumed, their probabilities of importation would have reduced, so that we would still obtain no imported cases.

      (7) Map (Supplementary Figure 1): Please, improve the resolution (like in the zoom in) and add a scale and a compass rose.

      We improved the resolution of the map. We did not add a scale and a compass rose, but labelled the coordinates as longitude and latitude to clarify the scale and orientation of the map. We added this in the rest of the maps of the manuscript as well.

      (8) In this work, Pimp values were bimodal to 0 or 1, making the classification easy. I wonder in other scenarios, where Pimp values are more intermediate (0.4-0.6), is the threshold at 0.5 still useful? Is there another way, like having a confidence interval of Pimp, to ensure the final classification? A discussion on this topic may be appreciated.

      In this case, we would recommend doing probabilistic analyses, keeping the probability of being imported as the final outcome, and quantifying the importation rates from the weighted sum of probabilities across individuals. We added this clarification in the Methods section: “ In case of obtaining a higher fraction of intermediate values (0.4-0.6), weighted sums of individual probabilities would be more appropriate to better quantify importation rates.”

      (9) Results: More details per panel, not as the whole figure (Figure 2B, Figure 3A, etc) in the manuscript would be appreciated.

      We appreciate the comment and added more details

      (10) Figure 3: Please, add a color legend in panel B (not only in the caption, but in the panel, such as in A, C, D).

      We added a color legend in panel B.

      (11) Do the authors recommend routine surveillance to detect importation in Mozambique, or are these results solid enough to propose strategies? How possible is it that importation rates vary in the future in the south? If so, how feasible is it to implement all this process (including the amplicon sequencing) routinely?

      We added the following text in the discussion: “While these results propose programmatic strategies for the two study districts, routine surveillance to detect importation in Mozambique would allow for identifying new strategies in other districts aiming for elimination, as well as monitoring changes in importation rates in Magude and Matutuine in the future. If scaling molecular surveillance is not feasible, travel reports could be integrated in the routing surveillance to extrapolate the case classification based on the results of this study. “

      (12) Which other proxies of transmission intensity could have been used?

      Better proxies of transmission intensity could be malaria incidence at the monthly level from national surveillance systems, or estimates of force of infection, for example from the use of molecular longitudinal data if available. We added this text in the discussion.

      (13) Can this strategy be applied to P. vivax-endemic areas outside Africa?

      This new method can also be applied to P. vivax-endemic areas outside Africa. Symptomatic P. vivax cases are not necessarily reflecting recent infections, so that travel reports might need to cover longer time periods, which does not require any essential adaptation to the method. We added this text to the discussion.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      Colorectal cancer (CRC) is the third most common cancer globally and the second leading cause of cancer-related deaths. Colonoscopy and fecal immunohistochemical testing are among the early diagnostic tools that have significantly enhanced patient survival rates in CRC. Methylation dysregulation has been identified in the earliest stages of CRC, offering a promising avenue for screening, prediction, and diagnosis. The manuscript entitled "Early Diagnosis and Prognostic Prediction of Colorectal Cancer through Plasma Methylation Regions" by Zhu et al. presents that a panel of genes with methylation pattern derived from cfDNA (27 DMRs), serving as a noninvasive detection method for CRC early diagnosis and prognosis.

      Strengths:

      The authors provided evidence that the 27 DMRs pattern worked well in predicting CRC distant metastasis, and the methylation score remarkably increased in stage III-IV.

      Weaknesses:

      The major concerns are the design of DMR screening, the relatively low sensitivity of this DMR pattern in detecting early-stage CRC, the limited size of the cohorts, and the lack of comparison with the traditional diagnosis test.

      We sincerely thank the reviewer for their thorough evaluation and constructive feedback on our manuscript. We are encouraged that the reviewer found our 27-DMR panel promising for predicting distant metastasis and for its performance in late-stage CRC. We have carefully considered the weaknesses pointed out and have made revisions to address these concerns, which we believe have significantly strengthened our paper.

      We agree with the reviewer that achieving high sensitivity for early-stage disease is the ultimate goal for any noninvasive screening test. Detecting the minute quantities of cfDNA shed from early-stage tumors is a well-recognized challenge in the field. Although the sensitivity of our current panel for early-stage CRC is modest, its core strengths, lie in its capability to also detect advanced adenomas and its excellent performance in assessing CRC metastasis and prognosis. Furthermore, we have now added a direct comparative analysis of our 27-DMR panel against the most widely used clinical serum biomarker for CRC, carcinoembryonic antigen (CEA), using samples from the same patient cohorts. Our results demonstrate that 27-DMR methylation score significantly outperforms CEA in diagnostic accuracy for early-stage CRC (64% vs. 18%) (Table s7). And in the Discussion section, we have also acknowledged our limitations and suggest that future studies are warranted to combine the cfDNA methylation model with commonly used clinical markers, such as CEA and CA19-9, with the aim of improving the sensitivity for early diagnosis.

      We acknowledge the reviewer's concern regarding the cohort size and validation in larger, prospective, multi-center cohorts is essential before this panel can be considered for clinical application. We have explicitly stated this as a limitation of our study in the Discussion section and have highlighted the need for future large-scale validation studies (Page 18, Lines 367-373). We once again thank the reviewer for their insightful comments, which have allowed us to substantially improve our manuscript. We hope that the revised version is now suitable for publication.

      Reviewer #2 (Public review):

      This work presents a 27-region DMR model for early diagnosis and prognostic prediction of colorectal cancer using plasma methylation markers. While this non-invasive diagnostic and prognostic tool could interest a broad readership, several critical issues require attention.

      Major Concerns:

      (1) Inconsistencies and clarity issues in data presentation

      (a) Sample size discrepancies

      The abstract mentions screening 119 CRC tissue samples, while Figure 1 shows 136 tissues. Please clarify if this represents 119 CRC and 17 normal samples.

      We sincerely thank the reviewer for this careful observation and for pointing out the inconsistency. We apologize for the error and the confusion it caused. Regarding Figure 1: The reviewer is correct. The number 136 in the original Figure 1 was an error. This was due to an inadvertent double-counting of the tumor samples that were used in the differential analysis against adjacent normal tissues. The actual number of tissue samples used in this analysis is 89. We have now corrected this value in the revised Figure 1.

      Regarding the Abstract: The 119 CRC tissue samples mentioned in the abstract represents the total number of unique tumor samples analyzed across all stages of our study. This number is composed of two cohorts: the initial 15 pairs of tissues used for preliminary screening, and the subsequent 89 tissue samples used for validation, totaling 119 samples. We have ensured all sample numbers are now consistent throughout the revised manuscript.

      The plasma sample numbers vary across sections: the abstract cites 161 samples, Figure 1 shows 116 samples, and the Supplementary Methods mentions 77 samples (13 Normal, 15 NAA, 12 AA, 37 CRC).

      We sincerely thank the reviewer for their meticulous review and for identifying these inconsistencies in the plasma sample numbers. We apologize for this oversight and the lack of clarity.

      Figure 1 & Supplementary Methods (77 samples): The number 116 in the original Figure 1 was a clerical error. The correct number is 77, which is the cohort used for our differential methylation analysis. This number is now consistent with the Supplementary Methods. This cohort is composed of 13 Normal, 15 NAA, 12 AA, and 37 CRC samples. The figure has been revised accordingly.

      Abstract (161 samples): The total of 161 plasma samples mentioned in the abstract is the sum of two distinct sample sets used for different stages of our analysis: The 77 samples (13 Normal, 15 NAA, 12 AA, 37 CRC) used for the differential analysis.  An additional 84 samples (33 Normal, 51 CRC) which served as the training set for the LASSO regression model. We have now clarified these distinctions in the text and ensured consistency across the abstract, figures, and methods sections.

      (b) Methodological inconsistencies

      The Supplementary Material reports 477 hypermethylated sites from TCGA data analysis (Δβ>0.20, FDR<0.05), but Figure 1 indicates 499 sites.

      The manuscript states that analyzing TCGA data across six cancer types identified 499 CRC-specific methylation sites, yet Figure 1 shows 477. Please also explain the rationale for selecting these specific cancer types from TCGA.

      We sincerely thank the reviewer for their sharp observation and for highlighting these inconsistencies. We apologize for this clerical error, which occurred when labeling the figure. The numbers 477 and 499 in Figure 1 were inadvertently swapped and the text in Supplementary Material is correct. We have now corrected this error throughout the manuscript to ensure clarity and consistency. We deeply regret the confusion this has caused.

      Regarding the rationale for selecting the cancer types:

      The selection of colorectal, esophageal, gastric, lung, liver, and breast cancers was based on the following strategic criteria to ensure the stringent identification of CRC-specific markers. Firstly, esophageal, gastric, liver, and colorectal cancers all originate from the gastrointestinal tract and share developmental and functional similarities. Comparing CRC against these closely related cancers allowed us to filter out general GI-tract-related methylation patterns and isolate those that are truly unique to colorectal tissue. Secondly, we included lung and breast cancer as they are two of the most common non-GI malignancies worldwide with distinct tissue origins. This helps ensure our identified markers are not just pan-cancer methylation events but are specific to CRC, even when compared against highly prevalent cancers from different lineages. Finally, these six cancer types have some of the largest and most complete datasets available in the TCGA database, including high-quality methylation data. This provided a robust statistical foundation for a reliable cross-cancer comparison. We hope this explanation clarifies our methodology. Thank you again for your valuable feedback.

      "404 CRC-specific DMRs" mentioned in the main text while "404 MCBs" in Figure 1, the authors need to clarify if these terms are interchangeable or how MCBs are defined.

      We sincerely thank the reviewer for pointing out this important inconsistency in terminology. We apologize for the confusion this has caused and for the error in Figure 1. The two terms are closely related in our study. The final 404 markers are technically DMRs that were identified through an analysis of MCBs. To avoid confusion, we have decided to unify the terminology. The manuscript has now been revised to consistently use "DMRs", which is the most accurate final descriptor. The label in Figure 1 has been corrected accordingly.

      (2) Methodological documentation

      The Results section requires a more detailed description of marker identification procedures and justification of methodological choices.

      Figure 3 panels need reordering for sequential citation.

      We thank the reviewer for this valuable suggestion. We agree that the original Results section lacked sufficient detail regarding the marker identification procedures and the justification for our methodological choices. To address this, we have substantially rewritten the "Methylation markers selection" subsection. This revised section provides a clear, step-by-step narrative of our marker discovery. The revised text now integrates the specific methodological details and statistical criteria. For instance, we now explicitly describe the three-pronged approach for the initial TCGA data mining and the specific criteria (Δβ, FDR, log2FC) for each, and the analysis methodology such as Wilcoxon test and LASSO regression analysis. We believe this detailed narrative now provides the necessary description and justification for our methodological choices directly within the results, significantly improving the clarity and logical flow of our manuscript. This revision can be found on (Page 9-11, Lines 180-195, 202-213). We hope these changes fully address the reviewer's concerns.

      We thank the reviewer for pointing out the citation order of the panels in Figure 3. This was a helpful suggestion for improving the clarity of our manuscript. We have now reordered the panels in Figure 3 to ensure they are cited sequentially within the text. These adjustments have been made in the "Development and validation of the CRC diagnosis model" subsection of the Results (Page 11, lines 224-230). We appreciate the reviewer's attention to detail.

      (3) Quality control and data transparency

      No quality control metrics are presented for the in-house sequencing data (e.g., sequencing quality, alignment rate, BS conversion rate, coverage, PCA plots for each cohort).

      The analysis code should be publicly available through GitHub or Zenodo.

      At a minimum, processed data should be made publicly accessible to ensure reproducibility.

      We sincerely thank the reviewer for their valuable and constructive feedback regarding quality control and data transparency. We fully agree that these elements are crucial for ensuring the robustness and reproducibility of our research. As the reviewer suggested, we have made all processed data and the key quality control metrics for each sample including sequencing quality scores, bisulfite (BS) conversion rates, and sequencing coverage publicly available to ensure the reproducibility of our findings. The analysis was performed using standard algorithms as detailed in the Methods section. While we are unable to host the code in a public repository at this time, all analysis scripts are available from the corresponding author upon reasonable request. The data has been deposited in the National Genomics Data Center (NGDC) and is accessible under the accession number OMIX009128. This information is now clearly stated in the "Data and Code Availability" section of the manuscript. We thank the reviewer again for pushing us to improve our manuscript in this critical aspect.

      Reviewer #3 (Public review):

      Summary:

      This article provides a model for early diagnosis and prognostic prediction of Colorectal Cancer and demonstrates its accuracy and usability. However, there are still some minor issues that need to be revised and paid attention to.

      Strengths:

      A large amount of external datasets were used for verification, thus demonstrating robustness and accuracy. Meanwhile, various influencing factors of multiple samples were taken into account, providing usability.

      Weaknesses:

      There are notable language issues that hinder readability, as well as a lack of some key conclusions provided.

      We are very grateful to the reviewer for their positive assessment of our study and for the constructive feedback provided. We are particularly encouraged that the reviewer recognized the strengths of our work, especially the robustness demonstrated through extensive external validation and the practical usability of our model. Regarding the weaknesses, we have taken the comments very seriously and have thoroughly revised the manuscript. We sincerely apologize for the language issues that hindered readability in our initial submission. To address this, the entire manuscript has undergone a comprehensive round of professional language polishing and editing. We have carefully reviewed and revised the text to improve clarity, flow, and grammatical accuracy. Besides, we agree that the conclusions could be stated more explicitly. To rectify this, we have substantially revised the final paragraph of the Discussion and the Conclusion section (Page 14-18, lines 279-305, 319-334, 346-348, 358-360, 367-379). We now more clearly summarize the main findings of our study, emphasize the clinical significance and potential applications of our model, and provide clear take-home messages. We thank you again for your time and insightful comments, which have been invaluable in improving the quality of our paper. We hope the revised manuscript now meets the standards for publication.

      Reviewer #1 (Recommendations for the authors):

      Detail comments are outlined below:

      (1) In this study, the authors have highlighted methylated cfDNA as a noninvasive approach for CRC early diagnosis. However, the small size of cohorts for plasma screening, particularly the sample number of NAA and AA , may cause bias in the selection of DMRs. This bias may lead to inappropriate DMRs for early diagnosis. Furthermore, the similar issues for the training set with a high percentage of late-stage CRC, no AA or NAA samples were included. This absence may be the key factor in screening changed methylated cfDNA that can predict the early stages of CRC.

      We are very grateful to the reviewer for this insightful methodological critique. We agree that cohort composition and sample size are critical factors in the development of robust biomarkers, and we appreciate the opportunity to clarify our study design and the interpretation of our results.

      We agree with the reviewer that the number of precancerous lesion samples (NAA and AA) in our initial plasma screening cohort was limited. This is a valid point. However, it is important to contextualize the role of this step within our overall multi-stage marker selection funnel. The markers evaluated in this plasma cohort were not discovered from this small sample set alone. They were the result of a rigorous pre-selection process based on large-scale public TCGA data and our own tissue-level sequencing. This robust, tissue-based validation ensured that only the most promising CRC-specific markers were advanced for plasma testing. Therefore, while the plasma cohort was modest in size, its purpose was to confirm the circulatory detectability of markers already known to have a strong tissue-of-origin signal, thereby mitigating the potential bias from a smaller discovery set.

      Our primary aim was to first build a model that could robustly and accurately identify a definitive cancer-specific methylation signal. By training the model on clear-cut invasive cancer cases versus healthy controls, we could isolate the most powerful and specific markers for established malignancy. Our working hypothesis was that these strong cancer-specific methylation patterns are initiated during the precursor stages and would therefore be detectable, albeit at lower levels, in precancerous lesions.  Unfortunately, the panel could only identify a limited proportion of precancerous lesions (48.4% in the NAA group and 52.2% in the AA group). We fully agree with the reviewer's sentiment that including a larger and more balanced set of precancerous lesions in future training cohorts could potentially optimize a model specifically for adenoma detection. We have now explicitly added this point to our Discussion section, highlighting it as an important direction for future research (Page 18, lines 367-373).

      (2) The sensitivity of 27 DMRs in the external validation set (for NAA, AA and CRC 0-Ⅱare 48.4%. 52.2% and 66.7%, respectively) were much lower compared with previously published studies, like ColonES assay (DOI: 10.1016/j.eclinm.2022.101717) and ColonSecure test (DOI: 10.1186/s12943-023-01866-z). The 27 DMRs from the layered screening process did not show superior performance in a small population of an external validation cohort. Therefore, it is unlikely that this DMR pattern will be applicable to the general population in the future.

      We sincerely thank the reviewer for their insightful comments and for providing a thorough comparison with the highly relevant ColonES and ColonSecure assays. This has given us an important opportunity to clarify the unique contributions and specific clinical applications of our 27-DMR panel.

      We acknowledge the reviewer's point that the sensitivities of our panel for precancerous lesions (NAA: 48.4%, AA: 52.2%), while substantial, are numerically lower than those reported by the excellent ColonES assay (AA: 79.0%). However, it is important to clarify that while the ColonES and ColonSecure tests are outstanding benchmarks designed primarily for early detection and screening, the primary objective and contribution of our study were slightly different. Our model demonstrated an exceptional ability to predict distant metastasis with an AUC of 0.955 and a strong capacity for predicting overall prognosis with an AUC of 0.867. Our goal was to develop a multi-functional, biologically-rooted biomarker panel that not only contributes to early detection but, more importantly, provides crucial information for post-diagnosis patient management, including staging, risk stratification, and prognostication, from a single preoperative sample. We believe this ability to preoperatively identify high-risk patients who may require more aggressive treatment or intensive surveillance is the key contribution of our work. It provides a distinct clinical utility that complements, rather than directly competes with, pure screening assays.

      We agree with the reviewer that our external validation was performed on a limited cohort, and we have acknowledged this as a limitation in our Discussion section. However, the purpose of this validation was to provide a proof-of-concept for the panel's performance across its multiple functions. The promising and exceptionally high-performing results in the prognostic domain strongly warrant further validation in larger, prospective, multi-center cohorts.

      (3) The 27 DMRs pattern worked well in predicting CRC distant metastasis, and the methylation score remarkably increased in stage III-IV. In contrast, the increase of AA and 0-II groups was very mild in the validation cohort. This observation raises concerns regarding the study design, particularly in the context of the layered screening process and sample assigning.

      We sincerely thank the reviewer for this insightful and critical comment. We agree with the reviewer's observation that the methylation score increased more remarkably in late-stage (III-IV) CRC compared to the milder increase in adenoma (AA) and early-stage (0-II) CRC in the validation cohort. However, the observed pattern is biologically plausible and consistent with the nature of colorectal cancer progression. Carcinogenesis is a multi-step process involving the gradual accumulation of genetic and epigenetic alterations. The methylation changes we identified are likely associated with tumor progression and metastasis. Therefore, it is expected that advanced, metastatic cancers (Stage III-IV), which have undergone significant biological changes, would exhibit a much stronger and more robust methylation signal compared to pre-cancerous lesions (adenomas) or early-stage, non-metastatic cancers (Stage 0-II). The "mild" increase in early stages reflects the initial, more subtle epigenetic alterations, while the "remarkable" increase in late stages reflects the extensive changes required for invasion and metastasis. We believe this graduated increase actually strengthens the validity of our methylation signature, as it mirrors the underlying biological progression of the disease. We hope this response and the corresponding revisions address the reviewer's comments.

      (4) The authors did not provide the 27 DMRs prediction efficacy comparison with other noninvasive CRC assays, like a CEA and a FIT test.

      Thank you for this valuable suggestion. We agree that comparing our model with established non-invasive assays is crucial for demonstrating its clinical potential. Following your advice, we have now included a direct comparison of the diagnostic performance between our model and the traditional tumor marker, carcinoembryonic antigen (CEA), using the external validation cohort. The results show that our model has a significantly higher sensitivity for detecting early-stage colorectal cancer and adenomas compared to CEA. This detailed comparison has been added as Table s7 in the supplementary materials, and the corresponding description has been incorporated into the Results section of our manuscript (Page 12, lines 234-236). Regarding the Fecal Immunochemical Test (FIT), we unfortunately could not perform a direct statistical comparison because very few individuals in our cohort had undergone FIT. A comparison based on such a small sample size would lack statistical power and might not yield meaningful conclusions. We have acknowledged this as a limitation of our study in the Discussion section.We believe these additions and clarifications have substantially strengthened our manuscript. Thank you again for your constructive feedback.

      (5) The authors did not explicitly describe how they assigned the plasma samples to the distinct sets, nor did they specify the criteria for the plasma screen set, training set, and validation set. The detailed information for the patient grouping should be listed.

      Responce: Thank you for this essential feedback. We agree that a transparent and detailed description of the sample allocation process is crucial for the manuscript. We apologize for the previous lack of clarity and have now revised the Methods section to address this. Our patient cohorts were assigned to the screening, training, and validation sets based on a chronological splitting strategy. Specifically, samples were allocated based on the date of collection in a consecutive manner. This approach was chosen to minimize selection bias and to provide a more realistic, forward-looking assessment of the model's performance, simulating a prospective validation scenario. The screening set comprised 89 tissue samples and 77 plasma samples collected between June to December 2020. The primary purpose of this set was for the initial discovery and screening of potential methylation markers. The training set and validation set included 165 plasma samples collected from December 2020 to July 2022. The external validation cohort comprised 166 plasma samples collected from from July 2022 to December 2022. The subsection titled "Study design and samples" within the Methods section of the revised manuscript, which now contains all of this detailed information (Page 6, lines 116-133). We believe this detailed explanation now makes our study design clear and transparent. Thank you again for helping us improve our manuscript.

      Reviewer #2 (Recommendations for the authors):

      The manuscript requires significant language editing to improve clarity and readability. We recommend that the authors seek professional editing services for revision.

      Thank you for your constructive comments on the language of our manuscript. We apologize for any lack of clarity in the previous version. To address this, we have performed a thorough revision of the manuscript. The text has been carefully reviewed and edited by a native English-speaking colleague who is an expert in our research field. We have focused on correcting all grammatical errors, improving sentence structure, and refining the phrasing throughout the document to enhance readability. We are confident that these extensive revisions have significantly improved the clarity of the manuscript. We hope you will find the current version much easier to read and understand.

      Reviewer #3 (Recommendations for the authors):

      (1) However, I think the abstract part of the article is too detailed and should be more concise and shortened. It is not necessary to show detailed values but to summarize the results.

      Thank you for this valuable suggestion. We agree that the previous version of the abstract was overly detailed and that a more concise summary would be more effective for the reader. Following your advice, we have substantially revised the abstract. We have removed the specific numerical values (such as detailed statistics) and have instead focused on summarizing the key findings and their broader implications (Page 3, lines 54-60, 64-66, 70-72). The revised abstract is now shorter and provides a clearer, high-level overview of our study's background, methods, main results, and conclusions. We believe these changes have significantly improved its readability and impact. We hope you will find the current version more appropriate.

      (2) Figure 4, the color in the legend and plot are not the same, and should be revised.

      Thank you for your careful attention to detail and for pointing out the color inconsistency in Figure 4. We apologize for this oversight. We have now corrected the figure as you suggested, ensuring that the colors in the legend perfectly match those in the plot. The revised Figure 4 has been updated in the manuscript. We appreciate your help in improving the quality of our figures.

      (3) Please pay attention to the article format, such as the consistency of fonts and punctuation marks. (For example, Lines 75 and Line 230).

      Thank you for your meticulous review and for pointing out the inconsistencies in our manuscript's formatting. We sincerely apologize for these oversights and any inconvenience they may have caused. Following your feedback, we have carefully corrected the specific issues you highlighted. Furthermore, we have conducted a thorough proofread of the entire manuscript to ensure consistency in all fonts, punctuation marks, and overall adherence to the journal's formatting guidelines. We appreciate your help in improving the presentation and professionalism of our paper.

    1. Author response:

      (1) General Statements

      We thank the Reviewers for a fair review of our work and helpful suggestions. We have significantly revised the manuscript in response to these suggestions. We provide a point-by-point response to the Reviewers below but wanted to highlight in our response a recurring concern related to the strong cell cycle arrest observed upon the acute FAM53C knock-down being different than the limited phenotypes in other contexts, including the knockout mice and DepMap data.

      First, we now show that we can recapitulate the strong G1 arrest resulting from the FAM53C knock-down using two independent siRNAs in RPE-1 cells, supporting the specificity of the effects.

      Second, the G1 arrest that results from the FAM53C knock-down is also observed in cells with inactive p53, suggesting it is not due to a non-specific stress response due to “toxic” siRNAs. In addition, the arrest is dependent on RB, which fits with the genetic and biochemical data placing FAM53C upstream of RB, further supporting a specific phenotype.

      Third, we have performed experiments in other human cells, including cancer cell lines. As would be expected for cancer cells, the G1 arrest is less pronounced but is still significant, indicating that the G1 arrest is not unique to RPE-1 cells.

      Fourth, it is not unexpected that compensatory mechanisms would be activated upon loss of FAM53C during development or in cancer – which may explain the lack of phenotypes in vivo or upon long-term knockout. This has been true for many cell cycle regulators, either because of compensation by other family members that have overlapping functions, or by a larger scale rewiring of signaling pathways. 

      (2) Point-by-point description of the revisions

      Reviewer #1 (Evidence, reproducibility and clarity): 

      Summary: 

      Taylar Hammond and colleagues identified new regulators of the G1/S transition of the cell cycle.

      They did so by screening public available data from the Cancer Dependency Map, and identified FAM53C as a positive regulator of the G1/S transition. Using biochemical assays they then show that FAM53 interacts with the DYRK1A kinase to inhibit its function. DYRK1A in its is known to induce degradation of cyclin D, leading the authors to propose a model in which DYRK1Adependent cyclin D degradation is inhibited by FAM53C to permit S-phase entry. Finally the authors assess the effect of FAM53C deletion in a cortical organoid model, and in Fam53c knockout mice. Whereas proliferation of the organoids is indeed inhibited, mice show virtually no phenotype.  

      Major comments: 

      The authors show convincing evidence that FAM53C loss can reduce S-phase entry in cell cultures, and that it can bind to DYRK1A. However, FAM53 has multiple other binding partners and I am not entirely convinced that negative regulation of DYRK1A is the predominant mechanism to explain its effects on S-phase entry. Some of the claims that are made based on the biochemical assays, and on the physiological effects of FAM53C are overstated. In addition, some choices made methodology and data representation need further attention. 

      (1) The authors do note that P21 levels increase upon FAM53C. They show convincing evidence that this is not a P53-dependent response. But the claim that " p21 upregulation alone cannot explain the G1 arrest in FAM53C-deficient cells (line 138-139) is misleading. A p53-independent p21 response could still be highly relevant. The authors could test if FAM53C knockdown inhibits proliferation after p21 knockdown or p21 deletion in RPE1 cells. 

      The Reviewer raises a great point. Our initial statement needed to be clarified and also need more experimental support. We have performed experiments where we knocked down FAM53C and p21 individually, as well as in combination, in RPE-1 cells. These experiment show that p21 knock-down is not sufficient to negate the cell cycle arrest resulting from the FAM53C knockdown in RPE-1 cells (Figure 4B,C and Figure S4C,D).

      We now extended these experiments to conditions where we inhibited DYRK1A, and we also compared these data to experiments in p53-null RPE-1 cells. Altogether, these experiments point to activation of p53 downstream of DYRK1A activation upon FAM53C knock-down, and indicate that p21 is not the only critical p53 target in the cell cycle arrest observed in FAM53C knock-down cells (Figure 4 and Figure S4).

      (2) The authors do not convincingly show that FAM53C acts as a DYRK1A inhibitor in cells. Figures 4B+C and S4B+C show extremely faint P-CycD1 bands, and tiny differences in ratios. The P values are hovering around the 0.05, so n=3 is clearly underpowered here. Total CycD1 levels also correlate with FAM53C levels, which seems to affect the ratios more than the tiny pCycD1 bands. Why is there still a pCycD1 band visible in 4B in the GFP + BTZ + DYRK1Ai condition? And if I look at the data points I honestly don't understand how the authors can conclude from S4C that knockdown of siFAM53C increases (DYRK1A dependent) increases in pCycD1 (relative to total CycD1). In figure 5C, no blot scans are even shown, and again the differences look tiny. So the authors should either find a way to make these assays more robust, or alter their claims appropriately. 

      We appreciate these comments from the Reviewer and have significantly revised the manuscript to address them.

      The analysis of Cyclin D phosphorylation and stability are complicated by the upregulation of p21 upon FAM53C knock-down, in particular because p21 can be part of Cyclin D complexes, which may affect its protein levels in cells (as was nicely showed in a previous study from the lab of Tobias Meyer – Chen et al., Mol Cell, 2013). Instead of focusing on Cyclin D levels and stability, we refocused the manuscript on RB and p53 downstream of FAM53C loss.

      We removed previous panel 4B from the revised manuscript. For panels 4E and S4B (now panels S3J and S3K)), we used a true “immunoassay” (as indicated in the legend – not an immunoblot), which is much more quantitative and avoids error-prone steps in standard immunoblots (“Western blots”). Briefly, this system was developed by ProteinSimple. It uses capillary transfer of proteins and ELISA-like quantification with up to 6 logs of dynamic range (see their web site https://www.proteinsimple.com/wes.html). The “bands” we show are just a representation of the luminescence signals in capillaries. We made sure to further clarify the figure legends in the revised manuscript.

      The representative Western blot images for 5C-D (now 5F-G) in the original submission are shown in Figure 5E, we apologize if this was not clear. The differences are small, which we acknowledge in the revised manuscript. Note that several factors can affect Cyclin D levels in cells, including the growth rate and the stage of the cell cycle. Our FACS analysis shows that normal organoids have ~63% of cells in G1 and ~13% in S phase; the overall lower proportion of S-phase cells in organoids may make the immunoblot difference appear smaller, with fewer cycling cells resulting in decreased Cyclin D phosphorylation.

      Nevertheless, the Reviewer brings up a good point and comments from this Reviewer and the others made us re-think how to best interpret our results. As discussed above, we re-read carefully the Meyer paper and think that FAM53C’s role and DYRK1A activity in cells may be understood when considering levels of both CycD and p21 at the same time in a continuum. While our genetic and biochemical data support a role for FAM53C in DYRK1A inhibition, it is likely that the regulation of cell cycle progression by FAM53C is not exclusively due to this inhibition. As discussed above and below, we noted an upregulation of p21 upon FAM53C knock-down, and activation of p53 and its targets likely contributes significantly to the phenotypes observed. We added new experiments to support this more complex model (Figure 4 and Figure S4, with new model in S4L).

      (3) The experiments to test if DYRK1A inhibition could rescue the G1 arrest observed upon FAM53C knockdown are not entirely convincing either. It would be much more convincing if they also perform cell counting experiments as they have done in Figures 1F and 1G, to complement the flow cytometry assays. I suggest that the authors do these cell counting experiments in RPE1 +/- P53 cells as well as HCT116 cells. In addition, did the authors test if P21 is induced by DYRK1Ai in HCT116 cells? 

      We repeated the experiments with the DYRK1A inhibitor and counted the cells. In p53-null RPE1 cells, we found that cell numbers do not increase in these conditions where we had observed a cell cycle re-entry (Fig. 4E), which was accompanied by apoptotic cell death (Fig. S4I). Thus, cells re-enter the cell cycle but die as they progress through S-phase and G2/M. We note that inhibition of DYRK1A has been shown to decrease expression of G2/M regulators (PMID: 38839871), which may contribute to the inability of cells treated to DYRK1Ai to divide. Because our data in RPE-1 cells showed that p21 knock-down was not sufficient to allow the FAM53C knock-down cells to re-enter the cell cycle, we did not further analyze p21 in HCT-116 cells.

      (4) The data in Figure 5C and 5D are identical, although they are supposed to represent either pCycD1 ratios or p21 levels. This is a problem because at least one of the two cannot be true. Please provide the proper data and show (representative) images of both data types.

      We apologize for these duplicated panels in the original submission. We now replaced the wrong panel with the correct data (Fig. 5F,G). 

      (5) Line 246: "Fam53c knockout mice display developmental and behavioral defects." I don't agree with this claim. The mutant mice are born at almost the expected Mendelian ratios, the body weight development is not consistently altered. But more importantly, no differences in adult survival or microscopic pathology were seen. The authors put strong emphasis on the IMPC behavioral analysis, but they should be more cautious. The IMPC mouse cohorts are tested for many other phenotypes related to behavior and neurological symptoms and apparently none of these other traits were changed in the IMPC Famc53c-/- cohort. Thus, the decreased exploration in a new environment could very well be a chance finding. The authors need to take away claims about developmental and behavioral defects from the abstract, results and discussion sections; the data are just too weak to justify this. 

      We agree with the Reviewer that, although we observed significant p-values, this original statement may not be appropriate in the biological sense. We made sure in the revised manuscript to carefully present these data.

      Minor comments: 

      (6) Can the authors provide a rationale for each of the proteins they chose to generate the list of the 38 proteins in the DepMap analysis? I looked at the list and it seems to me that they do not all have described functions in the G1/S transition. The analysis may thus be biased. 

      To address this point, we updated Table S1 (2nd tab) to provide a better rationale for the 38 factors chosen. Our focus was on the canonical RB pathway and we included RB binding proteins whose function had suggested they may also be playing a role in the G1/S transition. We do agree that there is some bias in this selection (e.g., there are more RB binding factors described) but we hope the Reviewer will agree with us that this list and the subsequent analysis identified expected factors, including FAM53C. Future studies using this approach and others will certainly identify new regulators of cell cycle progression.

      (7) Figure 1B is confusing to me. Are these just some (arbitrarily) chosen examples? Consider leaving this heatmap out altogether, of explain in more detail. 

      We agree with the Reviewer that this panel was not necessarily useful and possibly in the wrong place, and we removed it from the manuscript. We replaced it with a cartoon of top hits in the screen.

      (8) The y-axes in Figures 2C, 2D, 2E, and 4D are misleading because they do not start at 0. Please let the axis start at 0, or make axis breaks. 

      We re-graphed these panels.

      (9) Line 229: " Consequences ... brain development." This subheader is misleading, because the in vitro cortical organoid system is a rather simplistic model for brain development, and far away from physiological brain development. Please alter the header. 

      We changed the header to “Consequences of FAM53C inactivation in human cortical organoids in culture”.

      (10) Figure S5F: the gating strategy is not clear to me. In particular, how do the authors know the difference between subG1 and G1 DAPI signals? Do they interpret the subG1 as apoptotic cells? If yes, why are there so many? Are the culturing or harvesting conditions of these organoids suboptimal? Perhaps the authors could consider doing IF stainings on EdU or BrdU on paraffin sections of organoids to obtain cleaner data?

      Thank you for your feedback. The subG1 population in the original Figure S5F represents cells that died during the dissociation step of the organoids for FACS analysis. To address this point, we performed live & dead staining to exclude dead cells and provide clearer data. We refined gating strategy for better clarity in the new S5F panel.

      (11) Figure S6A; the labeling seems incorrect. I would think that red is heterozygous here, and grey mutant. 

      We fixed this mistake, thank you. 

      Reviewer #1 (Significance): 

      The finding that the poorly studied gene FAM53C controls the G1/S transition in cell lines is novel and interesting for the cell cycle field. However, the lack of phenotypes in Famc53-/- mice makes this finding less interesting for a broader audience. Furthermore, the mechanisms are incompletely dissected. The importance of a p53-indepent induction of p21 is not ruled out. And while the direct inhibitory interaction between FAM53C and DYRK1A is convincing (and also reported by others; PMID: 37802655), the authors do not (yet) convincingly show that DYRK1A inhibition can rescue a cell proliferation defect in FAM53C-deficient cells. 

      Altogether, this study can be of interest to basic researchers in the cell cycle field. 

      I am a cell biologist studying cell cycle fate decisions, and adaptation of cancer cells & stem cells to (drug-induced) stress. My technical expertise aligns well with the work presented throughout this paper, although I am not familiar with biolayer interferometry. 

      Reviewer #2 (Evidence, reproducibility and clarity): 

      Summary 

      In this study Hammond et al. investigated the role of Dual-specificity Tyrosine Phosphorylation regulated Kinase 1A (DYRK1) in G1/S transition. By exploiting Dependency Map portal, they identified a previously unexplored protein FAM53C as potential regulator of G1/S transition. Using RNAi, they confirmed that depletion of FAM53C suppressed proliferation of human RPE1 cells and that this phenotype was dependent on the presence protein RB. In addition, they noted increased level of CDKN1A transcript and p21 protein that could explain G1 arrest of FAM53Cdepleted cells but surprisingly, they did not observe activation of other p53 target genes. Proteomic analysis identified DYRK1 as one of the main interactors of FAM53C and the interaction was confirmed in vitro. Further, they showed that purified FAM53C blocked the ability of DYRK1 to phosphorylate cyclin D in vitro although the activity of DYRK1 was likely not inhibited (judging from the modification of FAM53C itself). Instead, it seems more likely that FAM53C competes with cyclin D in this assay. Authors claim that the G1 arrest caused by depletion of FAM53C was rescued by inhibition of DYRK1 but this was true only in cells lacking functional p53. This is quite confusing as DYRK1 inhibition reduced the fraction of G1 cells in p53 wild type cells as well as in p53 knock-outs, suggesting that FAM53C may not be required for regulation of DYRK1 function. Instead of focusing on the impact of FAM53C on cell cycle progression, authors moved towards investigating its potential (and perhaps more complex) roles in differentiation of IPSCs into cortical organoids and in mice. They observed a lower level of proliferating cells in the organoids but if that reflects an increased activity of DYRK1 or if it is just an off target effect of the genetic manipulation remains unclear. Even less clear is the phenotype in FAM53C knock-out mice. Authors did not observe any significant changes in survival nor in organ development but they noted some behavioral differences. Weather and how these are connected to the rate of cellular proliferation was not explored. In the summary, the study identified previously unknown role of FAM53C in proliferation but failed to explain the mechanism and its physiological relevance at the level of tissues and organism. Although some of the data might be of interest, in current form the data is too preliminary to justify publication.

      Major points 

      (1) Whole study is based on one siRNA to Fam53C and its specificity was not validated. Level of the knock down was shown only in the first figure and not in the other experiments. The observed phenotypes in the cell cycle progression may be affected by variable knock-down efficiency and/or potential off target effects. 

      We thank the Reviewer for raising this important point. First, we need to clarify that our experiments were performed with a pool of siRNAs (not one siRNA). Second, commercial antibodies against FAM53C are not of the best quality and it has been challenging to detect FAM53C using these antibodies in our hands – the results are often variable. In addition, to better address the Reviewer’s point and control for the phenotypes we have observed, we performed two additional series of experiments: first, we have confirmed G1 arrest in RPE-1 cells with individual siRNAs, providing more confidence for the specificity of this arrest (Fig. S1B); second, we have new data indicating that other cell lines arrest in G1 upon FAM53C knock-down (Fig. S1E,F and Fig. 4F).

      (2) Experiments focusing on the cell cycle progression were done in a single cell line RPE1 that showed a strong sensitivity to FAM53C depletion. In contrast, phenotypes in IPSCs and in mice were only mild suggesting that there might be large differences across various cell types in the expression and function of FAM53C. Therefore, it is important to reproduce the observations in other cell types. 

      As mentioned above, we have new data indicating that other cell lines arrest in G1 upon FAM53C knock-down (three cancer cell lines) (Fig. S1E,F and Fig. 4F).

      (3) Authors state that FAM53C is a direct inhibitor of DYRK1A kinase activity (Line 203), however this model is not supported by the data in Fig 4A. FAM53C seems to be a good substrate of DYRK1 even at high concentrations when phosphorylations of cyclin D is reduced. It rather suggests that DYRK1 is not inhibited by FAM53C but perhaps FAM53C competes with cyclin D. Further, authors should address if the phosphorylation of cyclin D is responsible for the observed cell cycle phenotype. Is this Cyclin D-Thr286 phosphorylation, or are there other sites involved? 

      We revised the text of the manuscript to include the possibility that FAM53C could act as a competitive substrate and/or an inhibitor.

      We removed most of the Cyclin D phosphorylation/stability data from the revised manuscript. As the Reviewers pointed out, some of these data were statistically significant but the biological effects were small. As discussed above in our response to Reviewer #1, the analysis of Cyclin D phosphorylation and stability are complicated by the upregulation of p21 upon FAM53C knockdown, in particular because p21 can be part of Cyclin D complexes, which may affect its protein levels in cells (as was nicely showed in a previous study from the lab of Tobias Meyer – Chen et al., Mol Cell, 2013). Instead of focusing on Cyclin D levels and stability, we refocused the manuscript on RB and p53 downstream of FAM53C loss.

      We note, however, that we used specific Thr286 phospho-antibodies, which have been used extensively in the field. Our data in Figure 1 with palbociclib place FAM53C upstream of Cyclin D/CDK4,6. We performed Cyclin D overexpression experiments but RPE-1 cells did not tolerate high expression of Cyclin D1 (T286A mutant) and we have not been able to conduct more ‘genetic’ studies. 

      (4) At many places, information on statistical tests is missing and SDs are not shown in the plots. For instance, what statistics was used in Fig 4C? Impact of FAM53C on cyclin D phosphorylation does not seem to be significant. In the same experiment, does DYRK1 inhibitor prevent modification of cyclin D? 

      As discussed above, we removed some of these data and re-focused the manuscript on p53-p21 as a second pathway activated by loss of FAM53C.

      (5) Validation of SM13797 compound in terms of specificity to DYRK1 was not performed. 

      This is an important point. We had cited an abstract from the company (Biosplice) but we agree that providing data is critical. We have now revised the manuscript with a new analysis of the compound’s specificity using kinase assays. These data are shown in Fig. S3F-H.

      (6) A fraction of cells in G1 is a very easy readout but it does not measure progression through the G1 phase. Extension of the S phase or G2 delay would indirectly also result in reduction of the G1 fraction. Instead, authors could measure the dynamics of entry to S phase in cells released from a G1 block or from mitotic shake off. 

      The Reviewer made a good point. As discussed in our response to Reviewer #1, with p53-null RPE-1 cells, we found that cell numbers do not increase in these conditions where we had observed a cell cycle re-entry (Fig. 4E), which was accompanied by apoptotic cell death (Fig. S4I). Thus, cells re-enter the cell cycle but die as they progress through S-phase and G2/M. We note that inhibition of DYRK1A has been shown to decrease expression of G2/M regulators (PMID: 38839871), which may contribute to the inability of cells treated to DYRK1Ai to divide.

      Because our data in RPE-1 cells showed that p21 knock-down was not sufficient to allow the FAM53C knock-down cells to re-enter the cell cycle, we did not further analyze p21 in HCT-116 cells. These data indicate that G1 entry by flow cytometry will not always translate into proliferation.

      Other points:

      (7) Fig. 2C, 2D, 2E graphs should begin with 0 

      We remade these graphs.

      (8) Fig. 5D shows that the difference in p21 levels is not significant in FAM53C-KO cells but difference is mentioned in the text. 

      We replaced the panel by the correct panel; we apologize for this error.

      (9) Fig. 6D comparison of datasets of extremely different sizes does not seem to be appropriate

      We agree and revised the text. We hope that the Reviewer will agree with us that it is worth showing these data, which are clearly preliminary but provide evidence of a possible role for FAM53C in the brain.

      (10) Could there be alternative splicing in mice generating a partially functional protein without exon 4? Did authors confirm that the animal model does not express FAM53C? 

      We performed RNA sequencing of mouse embryonic fibroblasts derived from control and mutant mice. We clearly identified fewer reads in exon 4 in the knockout cells, and no other obvious change in the transcript (data not shown). However, immunoblot with mouse cells for FAM53C never worked well in our hands. We made sure to add this caveat to the revised manuscript.

      Reviewer #2 (Significance): 

      Main problem of this study is that the advanced experimental models in IPSCs and mice did not confirm the observations in the cell lines and thus the whole manuscript does not hold together. Although I acknowledge the effort the authors invested in these experiments, the data do not contribute to the main conclusion of the paper that FAM53C/DYRK1 regulates G1/S transition. 

      Reviewer #3 (Evidence, reproducibility and clarity: 

      This paper identifies FAM53C as a novel regulator of cell cycle progression, particularly at the G1/S transition, by inhibiting DYRK1A. Using data from the Cancer Dependency Map, the authors suggest that FAM53C acts upstream of the Cyclin D-CDK4/6-RB axis by inhibiting DYRK1A.  Specifically, their experiments suggest that FAM53C Knockdown induces G1 arrest in cells, reducing proliferation without triggering apoptosis. DYRK1A Inhibition rescues G1 arrest in P53KO cells, suggesting FAM53C normally suppresses DYRK1A activity. Mass Spectrometry and biochemical assays confirm that FAM53C directly interacts with and inhibits DYRK1A. FAM53C Knockout in Human Cortical Organoids and Mice leads to cell cycle defects, growth impairments, and behavioral changes, reinforcing its biological importance. 

      Strength of the paper: 

      The study introduces a novel cell cycle control signalling module upstream of CDK4/6 in G1/S regulation which could have significant impact. The identification of FAM53C using a depmap correlation analysis is a nice example of the power of this dataset. The experiments are carried out mostly in a convincing manner and support the conclusions of the manuscript. 

      Critique: 

      (1) The experiments rely heavily on siRNA transfections without the appropriate controls. There are so many cases of off-target effects of siRNA in the literature, and specifically for a strong phenotype on S-phase as described here, I would expect to see solid results by additional experiments. This is especially important since the ko mice do not show any significant developmental cell cycle phenotypes. Moreover, FAM53C does not show a strong fitness effect in the depmap dataset, suggesting that it is largely non-essential in most cancer cell lines. For this paper to reach publication in a high-standard journal, I would expect that the authors show a rescue of the S-phase phenotype using an siRNA-resistant cDNA, and show similar S-phase defects using an acute knock out approach with lentiviral gRNA/Cas9 delivery. 

      We thank the Reviewer for this comment. Please refer to the initial response to the three Reviewers, where we discuss our use of single siRNAs and our results in multiple cell lines. Briefly, we can recapitulate the G1 arrest upon FAM53C knock-down using two independent siRNAs in RPE-1 cells. We also observe the same G1 arrest in p53 knockout cells, suggesting it is not due to a non-specific stress response. In addition, the arrest is dependent on RB, which fits with the genetic and biochemical data placing FAM53C upstream of RB, further supporting a specific phenotype. Human cancer cell lines also arrest in G1 upon FAM53C knock-down, not just RPE-1 cells. Finally, we hope the Reviewer will agree with us that compensatory mechanisms are very common in the cell cycle – which may explain the lack of phenotypes in vivo or upon long-term knockout of FAM53C.

      (2) The S-phase phenotype following FAM53C should be demonstrated in a larger variety of TP53WT and mutant cell lines. Given that this paper introduces a new G1/S control element, I think this is important for credibility. Ideally, this should be done with acute gRNA/Cas9 gene deletion using a lentiviral delivery system; but if the siRNA rescue experiments work and validate an on-target effect, siRNA would be an appropriate alternative. 

      We now show data with three cancer cell lines (U2OS, A549, and HCT-116 – Fig. S1E,F and Fig. 4F), in addition to our results in RPE-1 cells and in human cortical organoids. We note that the knock-down experiments are complemented by overexpression data (Fig. 1G-I), by genetic data (our original DepMap screen), and our biochemical data (showing direct binding of FAM53C to DYRK1A).

      (3) The western blot images shown in the MS appear heavily over-processed and saturated (See for example S4B, 4A, B, and E). Perhaps the authors should provide the original un-processed data of the entire gels? 

      For several of our panels (e.g., 4E and S4B, now panels S3J and S3K)), we used a true “immunoassay” (as indicated in the legend – not an immunoblot), which is much more quantitative and avoids error-prone steps in standard immunoblots (“Western blots”). Briefly, this system was developed by ProteinSimple. It uses capillary transfer of proteins and ELISA-like quantification with up to 6 logs of dynamic range (see their web site https://www.proteinsimple.com/wes.html). The “bands” we show are just a representation of the luminescence signals in capillaries. We made sure to further clarify the figure legends in the revised manuscript.

      Data in 4A are also not a western blot but a radiograph.

      For immunoblots, we will provide all the source data with uncropped blots with the final submission.

      (4) A critical experiment for the proposed mechanism is the rescue of the FAM53C S-phase reduction using DYRK1A inhibition shown in Figure 4. The legend here states that the data were extracted from BrdU incorporation assays, but in Figure S4D only the PI histograms are shown, and the S-phase population is not quantified. The authors should show the BrdU scatterplot and quantify the phenotype using the S-phase population in these plots. G1 measurements from PI histograms are not precise enough to allow for conclusions. Also, why are the intensities of the PI peaks so variable in these plots? Compare, for example, the HCT116 upper and lower panels where the siRNA appears to have caused an increase in ploidy. 

      We apologize for the confusion and we fixed these errors, for most of the analyses, we used PI to measure G1 and S-phase entry. We added relevant flow cytometry plots to supplemental figures (Fig. S1G, H, I, as well as Fig. S4E and S4K, and Fig. S5F).

      (5) There's an apparent contradiction in how RB deletion rescues the G1 arrest (Figure 2) while p21 seems to maintain the arrest even when DYRK1A is inhibited. Is p21 not induced when FAM53C is depleted in RB ko cells? This should be measured and discussed. 

      This comment and comments from the two other Reviewers made us reconsider our model. We re-read carefully the Meyer paper and think that DYRK1A activity may be understood when considering levels of both CycD and p21 at the same time in a continuum (as was nicely showed in a previous study from the lab of Tobias Meyer – Chen et al., Mol Cell, 2013). While our genetic and biochemical data support a role for FAM53C in DYRK1A inhibition, it is obvious that the regulation of cell cycle progression by FAM53C is not exclusively due to this inhibition. As discussed above and below, we noted an upregulation of p21 upon FAM53C knock-down, and activation of p53 and its targets likely contributes significantly to the phenotypes observed. We added new experiments to support this more complex model (Figure 4 and Figure S4, with new model in S4L).

      Reviewer #3 (Significance): 

      In conclusion, I believe that this MS could potentially be important for the cell cycle field and also provide a new target pathway that could be relevant for cancer therapy. However, the paper has quite a few gaps and inconsistencies that need to be addressed with further experiments. My main worry is that the acute depletion phenotypes appear so strong, while the gene is nonessential in mice and shows only a minor fitness effect in the depmap screens. More convincing controls are necessary to rule out experimental artefacts that misguide the interpretation of the results.

      We appreciate this comment and hope that the Reviewer will agree it is still important to share our data with the field, even if the phenotypes in mice are modest.

    1. Author response:

      Reviewer #1 (Public review): 

      Summary: 

      Cotton et al. investigated the role of tusB in antibiotic tolerance in Yersinia pseudotuberculosis. They used the IP2226 strain and introduced appropriate mutations and complementation constructs. Assays were performed to measure growth rates, antibiotic tolerance, tRNA modification, gene expression and proteomic profiles. In addition, experiments to measure ribosome pausing and bioinformatic analysis of codon usage in ribosomal proteins provided in-depth mechanistic support for the conclusions. 

      Strengths: 

      The findings are consistent with the authors having uncovered new mechanistic insights into bacterial antibiotic tolerance mediated by reducing ribosomal protein abundance. 

      Weaknesses: 

      Since the WT strain grows faster than the tusB mutant, there is a question of how growth rate, per se, impacts some of the analysis done. The authors should address this issue. In addition, it may not be essential, but would analysis of another slow-growing mutant (in some other antibiotic tolerance pathway if available) serve as a good control in this context? 

      We would like to thank the reviewer for their time spent reviewing our manuscript and for their positive review. We plan to address their comment as to how growth rate impacts the analyses and plan to incorporate another slow-growing mutant in the revised version of the manuscript.

      Reviewer #2 (Public review): 

      Summary: 

      This study addresses a critical clinical challenge-bacterial antibiotic tolerance (a key driver of treatment failure distinct from genetic resistance)-by uncovering a novel regulatory role of the conserved s2U tRNA modification in Yersinia pseudotuberculosis. Its strengths are notable and lay a solid foundation for understanding phenotypic drug tolerance. The study is the first to link s2U tRNA modification loss to antibiotic tolerance, specifically targeting translation/transcription-inhibiting antibiotics (doxycycline, gentamicin, rifampicin). By establishing a causal chain - s2U deficiency → codon-specific ribosome pausing (at AAA/CAA/GAA) → reduced ribosomal protein translation → global translational suppression → tolerance - it expands the functional landscape of tRNA modifications beyond canonical translation fidelity, filling a gap in how RNA epigenetics shapes bacterial stress adaptation. 

      Strengths: 

      This study makes a valuable contribution to understanding tRNA modification-mediated antibiotic tolerance. 

      Weaknesses: 

      There are several limitations that weaken the robustness of the study's mechanistic conclusions. Addressing these gaps would significantly enhance its impact and translational potential. 

      We would like to thank the reviewer for their time spent reviewing our manuscript, and for both their positive comments about the significance and novelty of this work as well as their critiques. We plan to address their specific recommendations in the revised manuscript by focusing on the contribution of specific ribosomal proteins (i.e. the 30S subunit protein, S13) through overexpression, codon replacement, and stability experiments. We also plan to design experiments to assess in vivo relevance and assess possible impacts on other pathways involved in antibiotic tolerance.

      Reviewer #3 (Public review): 

      Summary: 

      In the manuscript of Cotten et al., the authors study the 2-thiolation of tRNA in bacterial antibiotic resistance. The wildtype organism, Yersinia pseudotuberculosis, downregulates 2-thiolation as a response to antibiotics targeting the ribosome. In this manuscript, the authors show that a knockout of tusB causes slower translation. They provide evidence on the mechanisms of the slowing by determining transcription and translation, ribosome profiling and performing codon-usage analysis. They successfully determined that 2 codons are drivers of the translation slowdown, and the data is highly conclusive. Technically, I have nothing to criticize. 

      Strengths: 

      All in all, the study is very well made, and the writing is clear and concise. It covers a wide array of state-of-the-art analyses to unravel the interplay of tRNA modifications in translation. 

      Weaknesses: 

      The only question that remains to be asked is why the slowed translation leads to a better survival of the bacteria under antibiotic stress. In my opinion, the mechanism itself remains unclear. Thus, the statement that "We expect that this reduction in ribosomal proteins is globally reducing the translational capacity of the cell and is responsible for inducing tolerance to ribosome and RNA polymerase-targeting antibiotics" does not truly emphasize the remaining open question of why slowed translation favors survival. Therefore, I would recommend a minor text revision. 

      We would like to thank the reviewer for their time spent reviewing our manuscript and for their positive review of the technical aspects, experimental design, and writing. We will incorporate their suggested text revision into the revised manuscript, and will add to this statement if additional planned experiments shed light on this remaining question.